@article {pmid39701698,
year = {2024},
author = {Bao, YY and Li, MX and Gao, XX and Wei, WJ and Huang, WJ and Lin, LZ and Wang, H and Zheng, NN and Li, HK},
title = {[Astragalus polysaccharides improve adipose tissue aging in naturally aged mice via indole-3-lactic acid].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {49},
number = {22},
pages = {5998-6007},
doi = {10.19540/j.cnki.cjcmm.20240508.401},
pmid = {39701698},
issn = {1001-5302},
mesh = {Animals ; Mice ; *Aging/drug effects ; *Adipose Tissue/drug effects/metabolism ; *Polysaccharides/pharmacology ; *Indoles/pharmacology ; Male ; *Astragalus Plant/chemistry ; 3T3-L1 Cells ; Humans ; Adipocytes/drug effects/metabolism/cytology ; Mice, Inbred C57BL ; Cellular Senescence/drug effects ; Drugs, Chinese Herbal/pharmacology/administration & dosage ; Gastrointestinal Microbiome/drug effects ; },
abstract = {Plant polysaccharides are effective components that widely present in traditional Chinese medicine(TCM), exhibiting rich biological activities. However, as most plant polysaccharides cannot be directly absorbed and utilized by the human digestive system, it is now believed that their mode of action mainly involves interaction with intestinal microbiota, leading to the production of functional small molecules. The efficacy of Astragalus polysaccharide(APS) is extensive, including weight loss, improvement of fatty liver, reduction of blood lipids, and enhancement of insulin sensitivity, which may also be related to the regulation of intestinal microbiota. Adipose tissue senescence is an important characteristic of the physiological aging process in the body, often occurring prior to the aging of other important organs. Its main features include the accumulation of senescent cells and exacerbation of inflammation within the tissue. Therefore, to explore the potential protective effects of APS on aging, the improvement of adipose tissue aging phenotype in naturally aging mice was observed using APS, and combined with metagenomic metabolomics, corresponding microbial metabolic functional molecules were identified. Furthermore, functional tests in cell aging models were conducted. The results showed that APS significantly improved the adipocyte aging characteristics of naturally aging mice: specifically reducing aging-induced adipocyte hypertrophy; decreasing the protein expression of aging markers cyclin-dependent kinase inhibitor p21(P21) and multiple tumor suppressor 1(P16); lowering the tissue inflammation reaction. Metagenomic metabolomic analysis of serum from mice in each group revealed that APS significantly increased the content of indole-3-lactic acid(ILA) in naturally aging mice. Further in vitro studies showed that ILA could improve the aging of 3T3-L1 mouse embryonic fibroblasts induced by bleomycin, reduce the protein expression of the aging marker P21, alleviate inflammation, and enhance the ability of preadipocytes to mature. Therefore, APS had the efficacy of protecting naturally aging mice, and its action may be related to the increase in the intestinal microbiota metabolite ILA. This study suggested that TCM may serve as an important entry point for explaining the mechanism of action of TCM by regulating intestinal microbiota and their functional metabolites.},
}

Animals
Mice
*Aging/drug effects
*Adipose Tissue/drug effects/metabolism
*Polysaccharides/pharmacology
*Indoles/pharmacology
Male
*Astragalus Plant/chemistry
3T3-L1 Cells
Humans
Adipocytes/drug effects/metabolism/cytology
Mice, Inbred C57BL
Cellular Senescence/drug effects
Drugs, Chinese Herbal/pharmacology/administration & dosage
Gastrointestinal Microbiome/drug effects

@article {pmid39696556,
year = {2024},
author = {Amano, Y and Sachdeva, R and Gittins, D and Anantharaman, K and Lei, S and Valentin-Alvarado, LE and Diamond, S and Beppu, H and Iwatsuki, T and Mochizuki, A and Miyakawa, K and Ishii, E and Murakami, H and Jaffe, AL and Castelle, C and Lavy, A and Suzuki, Y and Banfield, JF},
title = {Diverse microbiome functions, limited temporal variation and substantial genomic conservation within sedimentary and granite rock deep underground research laboratories.},
journal = {Environmental microbiome},
volume = {19},
number = {1},
pages = {105},
pmid = {39696556},
issn = {2524-6372},
support = {JPJ007597//The Ministry of Economy, Trade and Industry of Japan/ ; 19K05342//the Japan Society for the Promotion of Science/ ; OCE2049478//National Science Foundation/ ; DE-AC02-05CH11231//the Watershed Function Scientific Focus Area funded by the U.S. Department of Energy/ ; 2230766//NSF "Four Networks for Geologic Hydrogen Storage"/ ; },
abstract = {BACKGROUND: Underground research laboratories (URLs) provide a window on the deep biosphere and enable investigation of potential microbial impacts on nuclear waste, CO2 and H2 stored in the subsurface. We carried out the first multi-year study of groundwater microbiomes sampled from defined intervals between 140 and 400 m below the surface of the Horonobe and Mizunami URLs, Japan.

RESULTS: We reconstructed draft genomes for > 90% of all organisms detected over a four year period. The Horonobe and Mizunami microbiomes are dissimilar, likely because the Mizunami URL is hosted in granitic rock and the Horonobe URL in sedimentary rock. Despite this, hydrogen metabolism, rubisco-based CO2 fixation, reduction of nitrogen compounds and sulfate reduction are well represented functions in microbiomes from both URLs, although methane metabolism is more prevalent at the organic- and CO2-rich Horonobe URL. High fluid flow zones and proximity to subsurface tunnels select for candidate phyla radiation bacteria in the Mizunami URL. We detected near-identical genotypes for approximately one third of all genomically defined organisms at multiple depths within the Horonobe URL. This cannot be explained by inactivity, as in situ growth was detected for some bacteria, albeit at slow rates. Given the current low hydraulic conductivity and groundwater compositional heterogeneity, ongoing inter-site strain dispersal seems unlikely. Alternatively, the Horonobe URL microbiome homogeneity may be explained by higher groundwater mobility during the last glacial period. Genotypically-defined species closely related to those detected in the URLs were identified in three other subsurface environments in the USA. Thus, dispersal rates between widely separated underground sites may be fast enough relative to mutation rates to have precluded substantial divergence in species composition. Species overlaps between subsurface locations on different continents constrain expectations regarding the scale of global subsurface biodiversity.

CONCLUSIONS: Our analyses reveal microbiome stability in the sedimentary rocks and surprising microbial community compositional and genotypic overlap over sites separated by hundreds of meters of rock, potentially explained by dispersal via slow groundwater flow or during a prior hydrological regime. Overall, microbiome and geochemical stability over the study period has important implications for underground storage applications.},
}

@article {pmid39695983,
year = {2024},
author = {Su, L and Guo, J and Shi, W and Tong, W and Li, X and Yang, B and Xiang, Z and Qin, C},
title = {Metagenomic analysis reveals the community composition of the microbiome in different segments of the digestive tract in donkeys and cows: implications for microbiome research.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {530},
pmid = {39695983},
issn = {1471-2180},
support = {2021YFF0702900//National Key Research and Development Program of China/ ; 2023-PT180-01//Non-profit Central Research Institute Fund of Chinese Academy of Medical Sciences/ ; 2021-I2M-1-039, 2021-I2M-1-034//CAMS initiative for Innovative Medicine of China/ ; },
mesh = {Animals ; *Equidae/microbiology ; Cattle/microbiology ; *Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; *Feces/microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Gastrointestinal Tract/microbiology ; Sequence Analysis, DNA/methods ; Metagenome ; Bacteroidetes/genetics/isolation & purification/classification ; },
abstract = {INTRODUCTION: The intestinal microbiota plays a crucial role in health and disease. This study aimed to assess the composition and functional diversity of the intestinal microbiota in donkeys and cows by examining samples collected from different segments of the digestive tract using two distinct techniques: direct swab sampling and faecal sampling.

RESULTS: In this study, we investigated and compared the effects of multiple factors on the composition and function of the intestinal microbial community. Approximately 300 GB of metagenomic sequencing data from 91 samples obtained from various segments of the digestive tract were used, including swabs and faecal samples from monogastric animals (donkeys) and polygastric animals (cows). We assembled 4,004,115 contigs for cows and 2,938,653 contigs for donkeys, with a total of 9,060,744 genes. Our analysis revealed that, compared with faecal samples, swab samples presented a greater abundance of Bacteroidetes, whereas faecal samples presented a greater abundance of Firmicutes. Additionally, we observed significant variations in microbial composition among different digestive tract segments in both animals. Our study identified key bacterial species and pathways via different methods and provided evidence that multiple factors can influence the microbial composition. These findings provide new insights for the accurate characterization of the composition and function of the gut microbiota in microbiome research.

CONCLUSIONS: The results obtained by both sampling methods in the present study revealed that the composition and function of the intestinal microbiota in donkeys and cows exhibit species-specific and region-specific differences. These findings highlight the importance of using standardized sampling protocols to ensure accurate and consistent characterization of the intestinal microbiota in various animal species. The implications and underlying mechanisms of these associations provide multiple perspectives for future microbiome research.},
}

Animals
*Equidae/microbiology
Cattle/microbiology
*Metagenomics/methods
*Gastrointestinal Microbiome/genetics
*Feces/microbiology
*Bacteria/classification/genetics/isolation & purification
*Gastrointestinal Tract/microbiology
Sequence Analysis, DNA/methods
Metagenome
Bacteroidetes/genetics/isolation & purification/classification

@article {pmid39695885,
year = {2024},
author = {Galic, I and Bez, C and Bertani, I and Venturi, V and Stankovic, N},
title = {Herbicide-treated soil as a reservoir of beneficial bacteria: microbiome analysis and PGP bioinoculants in maize.},
journal = {Environmental microbiome},
volume = {19},
number = {1},
pages = {107},
pmid = {39695885},
issn = {2524-6372},
support = {451-03-47/2023-01/ 200042//Ministarstvo Prosvete, Nauke i Tehnološkog Razvoja/ ; 451-03-47/2023-01/ 200042//Ministarstvo Prosvete, Nauke i Tehnološkog Razvoja/ ; Research and Training Grant 1818//FEMS/ ; },
abstract = {BACKGROUND: Herbicides are integral to agricultural weed management but can adversely affect non-target organisms, soil health, and microbiome. We investigated the effects of herbicides on the total soil bacterial community composition using 16S rRNA gene amplicon community profiling. Further, we aimed to identify herbicide-tolerant bacteria with plant growth-promoting (PGP) capabilities as a mitigative strategy for these negative effects, thereby promoting sustainable agricultural practices.

RESULTS: A bacterial community analysis explored the effects of long-term S-metolachlor application on soil bacterial diversity, revealing that the herbicide's impact on microbial communities is less significant than the effects of temporal factors (summer vs. winter) or agricultural practices (continuous maize cultivation vs. maize-winter wheat rotation). Although S-metolachlor did not markedly alter the overall bacteriome structure in our environmental context, the application of enrichment techniques enabled the selection of genera such as Pseudomonas, Serratia, and Brucella, which were rare in metagenome analysis of soil samples. Strain isolation revealed a rich source of herbicide-tolerant PGP bacteria within the culturable microbiome fraction, termed the high herbicide concentration tolerant (HHCT) bacterial culture collection. Within the HHCT collection, we isolated 120 strains that demonstrated significant in vitro PGP and biocontrol potential, and soil quality improvement abilities. The most promising HHCT isolates were combined into three consortia, each exhibiting a comprehensive range of plant-beneficial traits. We evaluated the efficacy and persistence of these multi-strain consortia during 4-week in pot experiments on maize using both agronomic parameters and 16S rRNA gene community analysis assessing early-stage plant development, root colonization, and rhizosphere persistence. Notably, 7 out of 10 inoculated consortia partners successfully established themselves and persisted in the maize root microbiome without significantly altering host root biodiversity. Our results further evidenced that all three consortia positively impacted both seed germination and early-stage plant development, increasing shoot biomass by up to 47%.

CONCLUSIONS: Herbicide-treated soil bacterial community analysis revealed that integrative agricultural practices can suppress the effects of continuous S-metolachlor application on soil microbial diversity and stabilize microbiome fluctuations. The HHCT bacterial collection holds promise as a source of beneficial bacteria that promote plant fitness while maintaining herbicide tolerance.},
}

@article {pmid39589125,
year = {2024},
author = {Zhang, Z and Tong, M and Ding, W and Liu, S and Jong, M-C and Radwan, AA and Cai, Z and Zhou, J},
title = {Changes in the diversity and functionality of viruses that can bleach healthy coral.},
journal = {mSphere},
volume = {9},
number = {12},
pages = {e0081624},
doi = {10.1128/msphere.00816-24},
pmid = {39589125},
issn = {2379-5042},
mesh = {*Anthozoa/virology/microbiology ; Animals ; *Microbiota/genetics ; *Viruses/genetics/classification ; *Metagenomics ; Bacteria/genetics/classification/virology/isolation & purification ; Symbiosis ; Bacteriophages/genetics/physiology/classification/isolation & purification ; },
abstract = {UNLABELLED: Coral microbiomes play a crucial role in maintaining the health and functionality of holobionts. Disruption in the equilibrium of holobionts, including bacteria, fungi, and archaea, can result in the bleaching of coral. However, little is known about the viruses that can infect holobionts in coral, especially bacteriophages. Here, we employed a combination of amplicon and metagenomic analyses on Acropora muricata and Galaxea astreata to investigate the diversity and functionality of viruses in healthy and bleached corals. Analysis showed that the alpha diversity of holobionts (bacteria, eukaryotes, zooxanthellae, and lysogenic and lytic viruses) was higher in bleached corals than that in healthy corals. Meanwhile, bleached corals exhibited a relatively higher abundance of specific viral classes, including Revtraviricetes, Arfiviricetes, Faserviricetes, Caudoviricetes, Herviviricetes, and Tectiliviricetes; moreover, we found that the expression levels of functional genes involved in carbon and sulfur metabolism were enriched. An increase in Vibrio abundance has been reported as a notable factor in coral bleaching; our analysis also revealed an increased abundance of Vibrio in bleached coral. Finally, bleached corals contained a higher abundance of Vibrio phages and encoded more virulence factor genes to increase the competitiveness of Vibrio after coral bleaching. In conclusion, we attempted to understand the causes of coral bleaching from the perspective of phage-bacteria-coral tripartite interaction.

IMPORTANCE: Viruses, especially bacteriophages, outnumber other microorganisms by approximately 10-fold and represent the most abundant members of coral holobionts. Corals represent a model system for the study of symbiosis, the influence of viruses on organisms inhabiting healthy coral reef, the role of rapid horizontal gene transfer, and the expression of auxiliary metabolic genes. However, the least studied component of coral holobiont are viruses. Therefore, there is a critical need to investigate the viral community of viruses, and their functionality, in healthy and bleached coral. Here, we compared the composition and functionality of viruses in healthy and bleached corals and found that viruses may participate in the induction of coral bleaching by enhancing the expression of virulence genes and other auxiliary metabolic functions.},
}

*Anthozoa/virology/microbiology
Animals
*Microbiota/genetics
*Viruses/genetics/classification
*Metagenomics
Bacteria/genetics/classification/virology/isolation & purification
Symbiosis
Bacteriophages/genetics/physiology/classification/isolation & purification

@article {pmid39161223,
year = {2024},
author = {Stokholm, J and Thorsen, J and Schoos, AM and Rasmussen, MA and Brandt, S and Sørensen, SJ and Vahman, N and Chawes, B and Bønnelykke, K},
title = {Infantile colic is associated with development of later constipation and atopic disorders.},
journal = {Allergy},
volume = {79},
number = {12},
pages = {3360-3372},
doi = {10.1111/all.16274},
pmid = {39161223},
issn = {1398-9995},
support = {//Region Hovedstaden/ ; //Strategiske Forskningsråd/ ; //Lundbeck Foundation/ ; //Sundhed og Sygdom, Det Frie Forskningsråd/ ; },
mesh = {Humans ; *Constipation/epidemiology/etiology ; *Colic/epidemiology/etiology ; *Gastrointestinal Microbiome ; Male ; Female ; Infant ; Child, Preschool ; Dermatitis, Atopic/epidemiology/complications ; Child ; Prospective Studies ; Asthma/epidemiology/diagnosis/microbiology/etiology ; Hypersensitivity, Immediate/epidemiology/complications ; Risk Factors ; },
abstract = {BACKGROUND: Infantile colic is a common condition with limited knowledge about later clinical manifestations. We evaluated the role of the early life gut microbiome in infantile colic and later development of atopic and gastrointestinal disorders.

METHODS: Copenhagen Prospective Studies on Asthma in Childhood2010 cohort was followed with 6 years of extensive clinical phenotyping. The 1-month gut microbiome was analyzed by 16S rRNA sequencing. Infantile colic was evaluated at age 3 months by interviews. Clinical endpoints included constipation to age 3 years and prospectively diagnosed asthma and atopic dermatitis in the first 6 years of life, and allergic sensitization from skin prick tests, specific Immunoglobulin E, and component analyses.

RESULTS: Of 695 children, 55 children (7.9%) had infantile colic. Several factors were associated with colic including race, breastfeeding, and pets. The 1-month gut microbiome composition and taxa abundances were not associated with colic, however a sparse Partial Least Squares model including combined abundances of nine species was moderately predictive of colic: median, cross-validated AUC = 0.627, p = .003. Children with infantile colic had an increased risk of developing constipation (aOR, 2.88 [1.51-5.35], p = .001) later in life, but also asthma (aHR, 1.69 [1.02-2.79], p = .040), atopic dermatitis (aHR, 1.84 [1.20-2.81], p = .005) and had a higher number of positive allergic components (adjusted difference, 116% [14%-280%], p = .012) in the first 6 years. These associations were not mediated by gut microbiome differences.

CONCLUSIONS: We link infantile colic with risk of developing constipation and atopic disorders in the first 6 years of life, which was not mediated through an altered gut microbiome at age 1-month. These results suggest infantile colic to involve gastrointestinal and/or atopic mechanisms.},
}

Humans
*Constipation/epidemiology/etiology
*Colic/epidemiology/etiology
*Gastrointestinal Microbiome
Male
Female
Infant
Child, Preschool
Dermatitis, Atopic/epidemiology/complications
Child
Prospective Studies
Asthma/epidemiology/diagnosis/microbiology/etiology
Hypersensitivity, Immediate/epidemiology/complications
Risk Factors

@article {pmid38742484,
year = {2024},
author = {Makri, N and Ring, N and Shaw, DJ and Athinodorou, A and Robinson, V and Paterson, GK and Richardson, J and Gow, D and Nuttall, T},
title = {Cytological evaluation, culture and genomics to evaluate the microbiome in healthy rabbit external ear canals.},
journal = {Veterinary dermatology},
volume = {35},
number = {5},
pages = {479-491},
doi = {10.1111/vde.13256},
pmid = {38742484},
issn = {1365-3164},
support = {//R(D)SVS Hospital for Small Animals/ ; },
mesh = {Animals ; Rabbits/microbiology ; *Ear Canal/microbiology ; *Microbiota ; Female ; Male ; Otoscopy ; Bacteria/genetics/classification/isolation & purification ; Genomics ; Fungi/genetics/classification/isolation & purification ; },
abstract = {BACKGROUND: Lop-eared rabbits may be predisposed to otitis externa (OE) as a consequence of their ear conformation. Although otoscopy, otic cytological evaluation and culture are valuable tools in dogs and cats, published data on rabbits remain lacking.

HYPOTHESIS/OBJECTIVES: This study aimed to assess the utility of otoscopy and cytological results in evaluating healthy rabbit external ear canals (EECs) and to characterise ear cytological and microbiological findings through culture techniques and metagenomic sequencing.

ANIMALS: Sixty-three otitis-free client-owned rabbits.

MATERIALS AND METHODS: All rabbits underwent otoscopy and ear cytological evaluation. In a subset of 12 rabbits, further bacterial and fungal culture, fungal DNA assessment and metagenomic sequencing were performed.

RESULTS: Otic cytological results revealed yeast in 73%, cocci in 42.9% and rods in 28.6% of healthy rabbit EECs. Compared to upright-eared rabbits, lop-eared rabbits had more discharge and more bacteria per oil immersion field. Culture isolated eight different species yet metagenomic sequencing identified 36, belonging to the Bacillota (Firmicutes), Pseudomonadota and Actinomycetota phyla. Staphylococcus were the most commonly observed species with both methods. Ten of 12 rabbits were yeast-positive on cytological evaluation with only three yielding fungal growth identified as Yarrowia (Candida) lipolytica, Eurotium echinulatum and Cystofilobasidium infirmominiatum.

Healthy rabbit EECs lack inflammatory cells yet can host yeast and bacteria, emphasising the need to evaluate cytological results alongside the clinical signs. Lop-ear anatomy may predispose to bacterial overgrowth and OE. Notably, yeasts may be present despite a negative culture.},
}

Animals
Rabbits/microbiology
*Ear Canal/microbiology
*Microbiota
Female
Male
Otoscopy
Bacteria/genetics/classification/isolation & purification
Genomics
Fungi/genetics/classification/isolation & purification

@article {pmid39695297,
year = {2024},
author = {Conteville, LC and Silva, JVD and Andrade, BGN and Coutinho, LL and Palhares, JCP and Regitano, LCA},
title = {Recovery of metagenome-assembled genomes from the rumen and fecal microbiomes of Bos indicus beef cattle.},
journal = {Scientific data},
volume = {11},
number = {1},
pages = {1385},
pmid = {39695297},
issn = {2052-4463},
mesh = {Animals ; Cattle/microbiology ; *Feces/microbiology ; *Metagenome ; *Rumen/microbiology ; *Phylogeny ; Gastrointestinal Microbiome ; Brazil ; Male ; Archaea/genetics/classification ; Bacteria/genetics/classification ; Microbiota ; },
abstract = {Nelore is a Bos indicus beef breed that is well-adapted to tropical environments and constitutes most of the world's largest commercial cattle herd: the Brazilian bovine herd. Despite its significance, microbial genome recovery from ruminant microbiomes has largely excluded representatives from Brazilian Nelore cattle. To address this gap, this study presents a comprehensive dataset of microbial genomes recovered from the rumen and feces of 52 Brazilian Nelore bulls. A total of 1,526 non-redundant metagenome-assembled genomes (MAGs) were recovered from their gastrointestinal tract, with 497 ruminal and 486 fecal classified as high-quality. Phylogenetic analysis revealed that the bacterial MAGs fall into 12 phyla, with Firmicutes and Bacteroidota being the most predominant, while all archaeal MAGs belong to the genus Methanobrevibacter. The exploration of these microbial genomes will provide valuable insights into the metabolic potential and functional roles of individual microorganisms within host-microbiome interactions, contributing to a better understanding of the microbiome's roles in bovine performance.},
}

Animals
Cattle/microbiology
*Feces/microbiology
*Metagenome
*Rumen/microbiology
*Phylogeny
Gastrointestinal Microbiome
Brazil
Male
Archaea/genetics/classification
Bacteria/genetics/classification
Microbiota

@article {pmid39695203,
year = {2024},
author = {Jeon, J and Park, Y and Lee, DH and Kim, JH and Jin, YK and Hong, JK and Lee, YM},
title = {Microbial profiling of the East Siberian Sea sediments using 16S rRNA gene and metagenome sequencing.},
journal = {Scientific data},
volume = {11},
number = {1},
pages = {1350},
pmid = {39695203},
issn = {2052-4463},
mesh = {*Geologic Sediments/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Metagenome ; *Archaea/genetics/classification ; *Bacteria/genetics/classification ; Arctic Regions ; Microbiota ; Oceans and Seas ; Siberia ; },
abstract = {The Arctic Ocean is experiencing significant global warming, leading to reduced sea-ice cover, submarine permafrost thawing, and increased river discharge. The East Siberian Sea (ESS) undergoes more significant terrestrial inflow from coastal erosion and river runoff than other Arctic seas. Despite extensive research on environmental changes, microbial communities and their functions in the ESS, which are closely related to environmental conditions, remain largely unexplored. Here, we investigated microbial communities in ESS surface sediments spanning latitudes from 73°N to 77°N using 16S rRNA amplicon sequencing, and reconstructed 211 metagenome-assembled genomes (MAGs) using shotgun metagenome sequencing. Taxonomic analysis identified 209 bacterial MAGs, with the predominant phyla Pseudomonadota (n = 82), Actinobacteriota (n = 38), Desulfobacterota (n = 23), along with 2 archaeal MAGs of Thermoproteota. Notably, 86% of the MAGs (n = 183) could not be classified into known species, indicating the potential presence of novel and unidentified microorganisms in the ESS. This dataset provides invaluable information on the microbial diversity and ecological functions in the rapidly changing ESS.},
}

*Geologic Sediments/microbiology
*RNA, Ribosomal, 16S/genetics
*Metagenome
*Archaea/genetics/classification
*Bacteria/genetics/classification
Arctic Regions
Microbiota
Oceans and Seas
Siberia

@article {pmid39693444,
year = {2024},
author = {Ruff, SE and de Angelis, IH and Mullis, M and Payet, JP and Magnabosco, C and Lloyd, KG and Sheik, CS and Steen, AD and Shipunova, A and Morozov, A and Reese, BK and Bradley, JA and Lemonnier, C and Schrenk, MO and Joye, SB and Huber, JA and Probst, AJ and Morrison, HG and Sogin, ML and Ladau, J and Colwell, F},
title = {A global comparison of surface and subsurface microbiomes reveals large-scale biodiversity gradients, and a marine-terrestrial divide.},
journal = {Science advances},
volume = {10},
number = {51},
pages = {eadq0645},
doi = {10.1126/sciadv.adq0645},
pmid = {39693444},
issn = {2375-2548},
mesh = {*Microbiota/genetics ; *Biodiversity ; *Archaea/genetics/classification ; *Phylogeny ; *Bacteria/genetics/classification ; Metagenome ; Seawater/microbiology ; Ecosystem ; },
abstract = {Subsurface environments are among Earth's largest habitats for microbial life. Yet, until recently, we lacked adequate data to accurately differentiate between globally distributed marine and terrestrial surface and subsurface microbiomes. Here, we analyzed 478 archaeal and 964 bacterial metabarcoding datasets and 147 metagenomes from diverse and widely distributed environments. Microbial diversity is similar in marine and terrestrial microbiomes at local to global scales. However, community composition greatly differs between sea and land, corroborating a phylogenetic divide that mirrors patterns in plant and animal diversity. In contrast, community composition overlaps between surface to subsurface environments supporting a diversity continuum rather than a discrete subsurface biosphere. Differences in microbial life thus seem greater between land and sea than between surface and subsurface. Diversity of terrestrial microbiomes decreases with depth, while marine subsurface diversity and phylogenetic distance to cultured isolates rivals or exceeds that of surface environments. We identify distinct microbial community compositions but similar microbial diversity for Earth's subsurface and surface environments.},
}

*Microbiota/genetics
*Biodiversity
*Archaea/genetics/classification
*Phylogeny
*Bacteria/genetics/classification
Metagenome
Seawater/microbiology
Ecosystem

@article {pmid39637857,
year = {2024},
author = {Vaher, K and Cabez, MB and Parga, PL and Binkowska, J and van Beveren, GJ and Odendaal, ML and Sullivan, G and Stoye, DQ and Corrigan, A and Quigley, AJ and Thrippleton, MJ and Bastin, ME and Bogaert, D and Boardman, JP},
title = {The neonatal gut microbiota: A role in the encephalopathy of prematurity.},
journal = {Cell reports. Medicine},
volume = {5},
number = {12},
pages = {101845},
doi = {10.1016/j.xcrm.2024.101845},
pmid = {39637857},
issn = {2666-3791},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics/physiology ; Infant, Newborn ; Female ; Male ; *Infant, Premature ; Feces/microbiology ; Brain/pathology/microbiology ; Brain Diseases/microbiology/pathology ; Gestational Age ; Magnetic Resonance Imaging/methods ; Premature Birth/microbiology ; },
abstract = {Preterm birth correlates with brain dysmaturation and neurocognitive impairment. The gut microbiome associates with behavioral outcomes in typical development, but its relationship with neurodevelopment in preterm infants is unknown. We characterize fecal microbiome in a cohort of 147 neonates enriched for very preterm birth using 16S-based and shotgun metagenomic sequencing. Delivery mode strongly correlates with the preterm microbiome shortly after birth. Low birth gestational age, infant sex assigned at birth, and antibiotics associate with microbiome composition at neonatal intensive care unit discharge. We integrate these data with term-equivalent structural and diffusion brain MRI. Bacterial community composition associates with MRI features of encephalopathy of prematurity. Particularly, abundances of Escherichia coli and Klebsiella spp. correlate with microstructural parameters in deep and cortical gray matter. Metagenome functional capacity analyses suggest that these bacteria may interact with brain microstructure via tryptophan and propionate metabolism. This study indicates that the gut microbiome associates with brain development following preterm birth.},
}

Humans
*Gastrointestinal Microbiome/genetics/physiology
Infant, Newborn
Female
Male
*Infant, Premature
Feces/microbiology
Brain/pathology/microbiology
Brain Diseases/microbiology/pathology
Gestational Age
Magnetic Resonance Imaging/methods
Premature Birth/microbiology

@article {pmid39577267,
year = {2025},
author = {Ngo, C and Morrell, JM and Tummaruk, P},
title = {Boar semen microbiome: Insights and potential implications.},
journal = {Animal reproduction science},
volume = {272},
number = {},
pages = {107647},
doi = {10.1016/j.anireprosci.2024.107647},
pmid = {39577267},
issn = {1873-2232},
mesh = {Animals ; *Semen/microbiology ; Swine/microbiology/physiology ; Male ; *Microbiota ; Semen Analysis/veterinary ; Bacteria/classification/isolation & purification/genetics ; },
abstract = {The pioneers of next-generation sequencing technology and bioinformatic analyses initiated a new era in microbiology research by offering profound insights into bacterial microbiome communities. In the pig farming sector, while considerable attention has been devoted to the gut microbiome and the microbiome of the female reproductive tract, research on the microbiome of boar semen remains limited. Nonetheless, published studies have provided valuable insights, serving as important references and sparking ideas for further investigations into the seminal microbiome. Factors such as breed, seasons, feed additives, hygiene management, and antibiotic use are believed to exert a notable influence on the diversity and richness of bacterial genera in the boar seminal microbiome, potentially affecting semen quality. Moreover, current shifts towards sustainability in the swine industry, coupled with global guidelines concerning the prudent use of antibiotics in stored boar semen for artificial insemination, underscore the need for insights into factors influencing seminal bacteria. The objective of this review is to elucidate the current understanding of boar bacterial contents using conventional culture methods, as well as the boar seminal microbiome through metagenomics and bioinformatics. It also aims to review specific microbiome communities, such as those in the reproductive tract and gut, and their connections to semen quality. In addition, strategic enhancements for processing boar semen doses through alternative methods to improve seminal quality are proposed.},
}

Animals
*Semen/microbiology
Swine/microbiology/physiology
Male
*Microbiota
Semen Analysis/veterinary
Bacteria/classification/isolation & purification/genetics

@article {pmid39565113,
year = {2024},
author = {Nowak, VV and Hou, P and Owen, JG},
title = {Microbial communities associated with marine sponges from diverse geographic locations harbor biosynthetic novelty.},
journal = {Applied and environmental microbiology},
volume = {90},
number = {12},
pages = {e0072624},
doi = {10.1128/aem.00726-24},
pmid = {39565113},
issn = {1098-5336},
support = {Doctoral Scholarship//Victoria University of Wellington (WGTN)/ ; Contract 16/172//Manatu Hauora | Health Research Council of New Zealand (HRC)/ ; RDF-VUW1601//Royal Society Te Apārangi (Royal Society of New Zealand)/ ; RTVU1908 and UOAX2010//Ministry for Business Innovation and Employment (MBIE)/ ; },
mesh = {*Porifera/microbiology ; Animals ; New Zealand ; *Bacteria/genetics/classification/metabolism/isolation & purification ; *Metagenome ; *Microbiota ; Mediterranean Sea ; Multigene Family ; Metagenomics ; Phylogeny ; },
abstract = {Marine sponges are a prolific source of biologically active small molecules, many of which originate from sponge-associated bacteria. Identifying the producing bacteria is a key step in developing sustainable routes for the production of these metabolites. To facilitate the required computational analyses, we developed MetaSing, a reproducible singularity-based pipeline for assembly, identification of high-quality metagenome-assembled genomes (MAGs), and analysis of biosynthetic gene clusters (BGCs) from metagenomic short-read data. We applied this pipeline to metagenomic sequencing data from 16 marine sponges collected from New Zealand, Tonga, and the Mediterranean Sea. This analysis yielded 643 MAGs representing 510 species. Of the 2,670 BGCs identified across all samples, 70.8% were linked to a MAG. Comparison of BGCs to those identified from previously sequenced bacteria revealed high biosynthetic novelty in variety of underexplored phyla, including Poribacteria, Acidobacteriota, and Dadabacteria. Alongside the observation that each sample contains unique biosynthetic potential, this holds great promise for natural product discovery and for furthering the understanding of different sponge holobionts.IMPORTANCEDiscovery of new chemical compounds such as natural products is a crucial endeavor to combat the increasing resistance to antibiotics and other drugs. This manuscript demonstrates that microbial communities associated with marine sponges investigated in this work encode the potential to produce novel chemistry. Lesser studied bacterial taxa that are often difficult to cultivate are particularly rich in potential.},
}

*Porifera/microbiology
Animals
New Zealand
*Bacteria/genetics/classification/metabolism/isolation & purification
*Metagenome
*Microbiota
Mediterranean Sea
Multigene Family
Metagenomics
Phylogeny

@article {pmid39515242,
year = {2025},
author = {Wang, Y and Chen, S and Chen, Y and Xu, J and Zhou, J and He, Q and Lin, Z and Xu, KQ and Fan, G},
title = {Structure-activity relationship between crystal plane and pyrite-driven autotrophic denitrification efficacy: Electron transfer and metagenome-based microbial mechanism.},
journal = {Water research},
volume = {268},
number = {Pt B},
pages = {122756},
doi = {10.1016/j.watres.2024.122756},
pmid = {39515242},
issn = {1879-2448},
mesh = {*Denitrification ; Structure-Activity Relationship ; *Sulfides/chemistry/metabolism ; Nitrates/metabolism ; Water Purification ; *Electron Transport/genetics ; *Metagenome/genetics ; Bacteria/enzymology/genetics ; *Iron/chemistry/metabolism ; Electrochemistry ; Oxidation-Reduction ; *Microbiota ; },
abstract = {Pyrite-driven autotrophic denitrification (PAD) has been recognized as a promising treatment technology for nitrate removal. Although the occurrence of PAD has been found in recent years, there is a knowledge gap about effects of crystal plane of pyrite on the performance and mechanism of PAD system. Here, this study investigated the effects of crystal planes ({100},
{111}
and {210})
of single-crystal pyrite on denitrification performance, electron transfer, and microbial mechanism in PAD system. The removal efficiency of nitrate in B-{210}
reached 100%, which was 1.67-fold and 2.86-fold higher than that of B-{100}
and B-{111},
respectively. X-ray photoelectron spectroscopy and electrochemical results indicated that Fe-S bonds of pyrite with {210}
crystal plane were more susceptible to breakage by Fe[3+] oxidation assault, and leaching microbially available Fe[2+] and sulfur intermediates to drive autotrophic denitrification. Metagenomic results suggested that community of functional pyrite-driven denitrifiers varied in response to crystal plane, and abundances of N-S transformation and EET-related microbes and genes in B-{210}
notably up-regulated compared to B-{100}
and B-{111}.
In addition, this work proposed a dual-mode for electron transfer pathway during pyrite oxidation and nitrogen transformation in PAD system. In B-{210},
Fe(II)- and sulfur-driven denitrifiers obtained electron after pyrite oxidation-dissolution, and the enrichment of pyrite-oxidizing bacteria in B-{210}
could enhance the electron transfer from pyrite through electron shuttles. This work highlighted that stronger surface reactivity and electron shuttle effect in B-{210}
enhanced electron transfer, leading to favorable PAD performance in B-{210}.
Overall, this study provides novel insights into the structure-activity relationship between the crystal plane structure of pyrite and denitrification activity in PAD system.},
}

*Denitrification
Structure-Activity Relationship
*Sulfides/chemistry/metabolism
Nitrates/metabolism
Water Purification
*Electron Transport/genetics
*Metagenome/genetics
Bacteria/enzymology/genetics
*Iron/chemistry/metabolism
Electrochemistry
Oxidation-Reduction
*Microbiota

@article {pmid39503478,
year = {2024},
author = {Sun, H and Liu, X and Wang, T and Liu, S and Zhang, R and Guo, X and Yu, Z and Zhao, Y and Shen, P and Zhang, Y},
title = {Rhizosphere microbiomes are closely linked to seagrass species: a comparative study of three coastal seagrasses.},
journal = {Applied and environmental microbiology},
volume = {90},
number = {12},
pages = {e0175424},
doi = {10.1128/aem.01754-24},
pmid = {39503478},
issn = {1098-5336},
support = {U2106208//NSFC-Shandong Joint Fund/ ; 41976147//MOST | National Natural Science Foundation of China (NSFC)/ ; },
mesh = {*Rhizosphere ; *Microbiota ; *Zosteraceae/microbiology ; China ; Bacteria/classification/genetics/isolation & purification/metabolism ; Soil Microbiology ; Alismatales/microbiology ; Metagenome ; },
abstract = {UNLABELLED: Seagrass meadows are important marine ecosystems in coastal areas, offering ecological and economic services to the mankind. However, these ecosystems are facing declines due to climate changes and human activities. Rhizosphere-associated microbiomes play critical roles in the survival and adaptation of seagrasses. While prior studies have explored the general microbial communities and their roles in seagrass meadows, there is a gap in understanding the specific rhizosphere microbiomes of different seagrass species and their interdependent relationships. Our study analyzed the microbial community composition and their metabolism in the rhizosphere of Ruppia sinensis (RS), Zostera japonica (ZJ), and Zostera marina (ZM) obtained from the coastal area of Shandong, China, using high throughput and metagenome sequencing. We found that Rhodobacteraceae, Desulfocapsaceae, and Sulfurovaceae were enriched in RS, ZJ, and ZM samples, respectively, compared with the other two seagrass species, and the bacterial connections were decreased from RS to ZM and ZJ samples. The abundances of nirKS and norBC, mediating denitrification, were higher in RS samples with 2.38% ± 0.59% and 2.14% ± 0.24%, respectively. RS samples also showed a higher level of genes in assimilatory sulfate reduction but lower levels in dissimilatory sulfate reduction and oxidation, with a greater ability to convert sulfide into L-cysteine and acetate. Metagenome-assembled genomes from metagenome of RS rhizosphere had a higher diversity and were assigned to eight phyla. Our study could provide a typical project to analyze the bacterial community structures and metabolic functions in the rhizosphere microbiomes of different seagrasses.

IMPORTANCE: Seagrasses are indispensable in marine ecosystems, offering numerous critical services, with their health significantly influenced by associated rhizosphere microbiomes. Although studies have investigated the microbial communities and their ecological roles in seagrass meadows, the correlations between rhizosphere microbiome and seagrass species from a particular geographic region are limited. Some studies concentrated on the bacterial composition within the rhizosphere of various seagrasses, but the functional aspects of these microbiomes remain unexplored. Our research delves into this void, revealing that Ruppia sinensis, Zostera japonica, and Zostera marina host diverse bacterial community in the composition, connections, functions, and metabolism, such as nitrogen and sulfur metabolism. Our study revealed that seagrass species play an important role in shaping the rhizosphere microbiomes in an equivalent environment, emphasizing the importance of seagrass species in shaping the rhizosphere microbial communities.},
}

*Rhizosphere
*Microbiota
*Zosteraceae/microbiology
China
Bacteria/classification/genetics/isolation & purification/metabolism
Soil Microbiology
Alismatales/microbiology
Metagenome

@article {pmid39215755,
year = {2024},
author = {Cannarozzi, AL and Latiano, A and Massimino, L and Bossa, F and Giuliani, F and Riva, M and Ungaro, F and Guerra, M and Brina, ALD and Biscaglia, G and Tavano, F and Carparelli, S and Fiorino, G and Danese, S and Perri, F and Palmieri, O},
title = {Inflammatory bowel disease genomics, transcriptomics, proteomics and metagenomics meet artificial intelligence.},
journal = {United European gastroenterology journal},
volume = {12},
number = {10},
pages = {1461-1480},
doi = {10.1002/ueg2.12655},
pmid = {39215755},
issn = {2050-6414},
support = {PNRR-MAD-2022-12375729//Italian Next Generation Eu Program/ ; },
mesh = {Humans ; *Artificial Intelligence ; *Proteomics/methods ; *Metagenomics/methods ; *Genomics/methods ; *Inflammatory Bowel Diseases/microbiology/genetics ; Precision Medicine/methods ; Transcriptome ; Crohn Disease/microbiology/genetics/immunology ; Gastrointestinal Microbiome/immunology ; Colitis, Ulcerative/microbiology/genetics/immunology ; },
abstract = {Various extrinsic and intrinsic factors such as drug exposures, antibiotic treatments, smoking, lifestyle, genetics, immune responses, and the gut microbiome characterize ulcerative colitis and Crohn's disease, collectively called inflammatory bowel disease (IBD). All these factors contribute to the complexity and heterogeneity of the disease etiology and pathogenesis leading to major challenges for the scientific community in improving management, medical treatments, genetic risk, and exposome impact. Understanding the interaction(s) among these factors and their effects on the immune system in IBD patients has prompted advances in multi-omics research, the development of new tools as part of system biology, and more recently, artificial intelligence (AI) approaches. These innovative approaches, supported by the availability of big data and large volumes of digital medical datasets, hold promise in better understanding the natural histories, predictors of disease development, severity, complications and treatment outcomes in complex diseases, providing decision support to doctors, and promising to bring us closer to the realization of the "precision medicine" paradigm. This review aims to provide an overview of current IBD omics based on both individual (genomics, transcriptomics, proteomics, metagenomics) and multi-omics levels, highlighting how AI can facilitate the integration of heterogeneous data to summarize our current understanding of the disease and to identify current gaps in knowledge to inform upcoming research in this field.},
}

Humans
*Artificial Intelligence
*Proteomics/methods
*Metagenomics/methods
*Genomics/methods
*Inflammatory Bowel Diseases/microbiology/genetics
Precision Medicine/methods
Transcriptome
Crohn Disease/microbiology/genetics/immunology
Gastrointestinal Microbiome/immunology
Colitis, Ulcerative/microbiology/genetics/immunology

@article {pmid38309691,
year = {2025},
author = {Yuan, Q and Liu, W and Hao, W and Chen, Y and Xiao, Y and Li, H and Shui, M and Wu, DT and Wang, S},
title = {Glycosidic linkages of fungus polysaccharides influence the anti-inflammatory activity in mice.},
journal = {Journal of advanced research},
volume = {67},
number = {},
pages = {161-172},
doi = {10.1016/j.jare.2024.01.037},
pmid = {38309691},
issn = {2090-1224},
mesh = {Animals ; Mice ; *Anti-Inflammatory Agents/pharmacology/chemistry ; *Colitis/drug therapy/metabolism/chemically induced ; *Dextran Sulfate ; *Fungal Polysaccharides/chemistry/pharmacology ; Gastrointestinal Microbiome/drug effects ; Disease Models, Animal ; Glycosides/pharmacology/chemistry ; Male ; Mice, Inbred C57BL ; Basidiomycota/chemistry ; Polysaccharides/chemistry/pharmacology ; Cytokines/metabolism ; },
abstract = {INTRODUCTION: Over decades, the source-function relationships of bioactive polysaccharides have been progressively investigated, however, it is still unclear how a defined structure may conduce to the bioactivities of polysaccharides.

OBJECTIVES: To explore the structure-function relationship of fungus polysaccharides, we employed a dextran sulfate sodium (DSS)-induced colitis mouse model to compare the anti-inflammatory activity of two fungus polysaccharides from Dictyophora indusiata (DIP) and Tremella fuciformis (TFP), which exhibit distinct glycosidic linkages.

METHODS: The structures of DIP and TFP were characterized through molecular weight detection, molecular morphology analysis, methylation analysis, and NMR analysis. Subsequently, we employed a DSS-induced colitis model to assess the anti-inflammatory efficacy of DIP and TFP. The colitis symptoms, histological morphology, intestinal inflammatory cytokines, and the composition and function of gut microbiota before and after polysaccharides treatment in colitis mice were also investigated.

RESULTS: DIP, l,3-β-D-glucan with 1,4-β and 1,6-β-D-Glcp as branched chains, exhibited superior therapeutic effect than that of TFP consisted of a linear 1,3-α-D-mannose backbone with D-xylose and L-fucose in the side chains. Both DIP and TFP relieved DSS-induced colitis in a gut microbiota-dependent manner. Furthermore, metagenomics showed that DIP and TFP could partially reverse the bacterial function in colitis mice. Glycoside Hydrolase 1 (GH1) and GH3 were identified as being involved in hydrolyzing the glucose linkages in DIP, while GH92 and GH29 were predicted to be active in cleaving the α-1,3-linked mannose linkages and the glycosidic bonds of L-fucose residues in TFP.

CONCLUSION: Our findings highlight the pivotal role of glycosidic linkages in anti-inflammatory activities of fungus polysaccharides and would promote the design and discovery of polysaccharides with designated activity to be used as functional foods and/or therapeutics.},
}

Animals
Mice
*Anti-Inflammatory Agents/pharmacology/chemistry
*Colitis/drug therapy/metabolism/chemically induced
*Dextran Sulfate
*Fungal Polysaccharides/chemistry/pharmacology
Gastrointestinal Microbiome/drug effects
Disease Models, Animal
Glycosides/pharmacology/chemistry
Male
Mice, Inbred C57BL
Basidiomycota/chemistry
Polysaccharides/chemistry/pharmacology
Cytokines/metabolism

@article {pmid39684893,
year = {2024},
author = {Parkar, N and Young, W and Olson, T and Hurst, C and Janssen, P and Spencer, NJ and McNabb, WC and Dalziel, JE},
title = {Peripherally Restricted Activation of Opioid Receptors Influences Anxiety-Related Behaviour and Alters Brain Gene Expression in a Sex-Specific Manner.},
journal = {International journal of molecular sciences},
volume = {25},
number = {23},
pages = {},
doi = {10.3390/ijms252313183},
pmid = {39684893},
issn = {1422-0067},
support = {C10X1706//Ministry of Business, Innovation and Employment/ ; },
mesh = {Animals ; Male ; Female ; *Anxiety/metabolism ; Rats ; *Loperamide/pharmacology ; *Brain/metabolism/drug effects ; *Rats, Sprague-Dawley ; *Receptors, Opioid/metabolism/genetics ; Behavior, Animal/drug effects ; Gastrointestinal Microbiome/drug effects ; Hippocampus/metabolism/drug effects ; Enteric Nervous System/metabolism ; Gene Expression Regulation/drug effects ; Sex Factors ; Sex Characteristics ; },
abstract = {Although effects of stress-induced anxiety on the gastrointestinal tract and enteric nervous system (ENS) are well studied, how ENS dysfunction impacts behaviour is not well understood. We investigated whether ENS modulation alters anxiety-related behaviour in rats. We used loperamide, a potent μ-opioid receptor agonist that does not cross the blood-brain barrier, to manipulate ENS function and assess changes in behaviour, gut and brain gene expression, and microbiota profile. Sprague Dawley (male/female) rats were acutely dosed with loperamide (subcutaneous) or control solution, and their behavioural phenotype was examined using open field and elevated plus maze tests. Gene expression in the proximal colon, prefrontal cortex, hippocampus, and amygdala was assessed by RNA-seq and caecal microbiota composition determined by shotgun metagenome sequencing. In female rats, loperamide treatment decreased distance moved and frequency of supported rearing, indicating decreased exploratory behaviour and increased anxiety, which was associated with altered hippocampal gene expression. Loperamide altered proximal colon gene expression and microbiome composition in both male and female rats. Our results demonstrate the importance of the ENS for communication between gut and brain for normo-anxious states in female rats and implicate corticotropin-releasing hormone and gamma-aminobutyric acid gene signalling pathways in the hippocampus. This study also sheds light on sexually dimorphic communication between the gut and the brain. Microbiome and colonic gene expression changes likely reflect localised effects of loperamide related to gut dysmotility. These results suggest possible ENS pharmacological targets to alter gut to brain signalling for modulating mood.},
}

Animals
Male
Female
*Anxiety/metabolism
Rats
*Loperamide/pharmacology
*Brain/metabolism/drug effects
*Rats, Sprague-Dawley
*Receptors, Opioid/metabolism/genetics
Behavior, Animal/drug effects
Gastrointestinal Microbiome/drug effects
Hippocampus/metabolism/drug effects
Enteric Nervous System/metabolism
Gene Expression Regulation/drug effects
Sex Factors
Sex Characteristics

@article {pmid39684853,
year = {2024},
author = {Tynior, W and Kłósek, M and Salatino, S and Cuber, P and Hudy, D and Nałęcz, D and Chan, YT and Gustave, C and Strzelczyk, JK},
title = {Metagenomic Analysis of the Buccal Microbiome by Nanopore Sequencing Reveals Structural Differences in the Microbiome of a Patient with Molar Incisor Hypomineralization (MIH) Compared to a Healthy Child-Case Study.},
journal = {International journal of molecular sciences},
volume = {25},
number = {23},
pages = {},
doi = {10.3390/ijms252313143},
pmid = {39684853},
issn = {1422-0067},
support = {PCN-1-111/N/2/O//Medical University of Silesia/ ; },
mesh = {Humans ; *Microbiota/genetics ; *Metagenomics/methods ; *Nanopore Sequencing/methods ; *Dental Enamel Hypoplasia/microbiology/genetics ; Child ; Mouth Mucosa/microbiology/pathology ; Male ; Female ; Bacteria/genetics/classification/isolation & purification ; Case-Control Studies ; Metagenome ; Incisor/microbiology ; Molar Hypomineralization ; },
abstract = {Molar incisor hypomineralization (MIH) is a qualitative developmental defect that affects the enamel tissue of permanent molars and can also occur in permanent incisors. Enamel affected by MIH has reduced hardness, increased porosity, and a higher organic content than unaffected enamel. These characteristics predispose the enamel to accumulation of bacteria and a higher prevalence of caries lesions. Through a groundbreaking metagenomic analysis of the buccal mucosal sample from a patient with MIH, we explored the intricacies of its microbiome compared to a healthy control using state-of-the-art nanopore long-read sequencing. Out of the 210 bacterial taxa identified in the MIH microbiome, we found Streptococcus and Haemophilus to be the most abundant genera. The bacteria with the highest read counts in the patient with MIH included Streptococcus mitis, Haemophilus parainfluenzae, Streptococcus pneumoniae, Rothia dentocariosa, and Gemella haemolysans. Our results revealed a striking contrast between healthy and MIH affected children, with a higher dominance and number of pathogenic species (S. pneumoniae, H. influenzae, and N. meningitidis) and reduced diversity in the MIH-affected patient. This distinct microbial profile not only sheds light on MIH-affected patients, but paves the way for future research, inspiring deeper understanding and larger scale studies.},
}

Humans
*Microbiota/genetics
*Metagenomics/methods
*Nanopore Sequencing/methods
*Dental Enamel Hypoplasia/microbiology/genetics
Child
Mouth Mucosa/microbiology/pathology
Male
Female
Bacteria/genetics/classification/isolation & purification
Case-Control Studies
Metagenome
Incisor/microbiology
Molar Hypomineralization

@article {pmid39684458,
year = {2024},
author = {Salini, A and Zuliani, L and Gonnelli, PM and Orlando, M and Odoardo, A and Ragno, D and Aulitto, M and Zaccone, C and Fusco, S},
title = {Plastic-Degrading Microbial Consortia from a Wastewater Treatment Plant.},
journal = {International journal of molecular sciences},
volume = {25},
number = {23},
pages = {},
doi = {10.3390/ijms252312747},
pmid = {39684458},
issn = {1422-0067},
support = {CUP B53D23015130001//MUR - Italian Ministry of University and Research in the framework of the Next Generation EU action/ ; },
mesh = {*Microbial Consortia ; *Wastewater/microbiology ; *Biodegradation, Environmental ; Sewage/microbiology ; Plastics/metabolism ; Bacteria/metabolism/classification/genetics/isolation & purification ; Microbiota ; },
abstract = {Plastic waste pollution has become a global crisis, with millions of tons of plastic expected to accumulate in landfills and in natural environments, posing a serious threat to wildlife and human health. As current recycling methods remain inefficient, there is an urgent need for innovative enzymatic solutions to break down plastics and enable a circular economy approach. In this study, we explore the plastic-degrading potential of microorganisms enriched from activated sludge (AS) sourced from a municipal wastewater treatment plant (WWTP)-a known microplastic-contaminated industrial niche. Five microbial consortia (i.e., microbiomes) were enriched under selective pressure using low-carbon conditions and high concentrations of polyester polymers, including post-consumer PET, post-consumer PLA, and virgin PLA. Enrichment was performed for 100 days at 37 °C and 50 °C, followed by microbiomes isolation and metagenomic analysis to identify plastic-active bacteria and their enzymes. The results revealed that PLA polymers, but not post-consumer PET, were effectively degraded by the microbiomes, as confirmed by nuclear magnetic resonance (NMR) and gel permeation chromatography (GPC), showing significant molecular weight reduction compared to the abiotic controls. Microbial community analysis highlighted a distinct enrichment profile driven by the polymer composition and the temperature. At 50 °C, the Bacillales order became the predominant population, whereas at 37 °C, a more diverse community within the Proteobacteria and Actinobacteria phyla were selected. Nonetheless, the enriched microbial communities at both temperatures included phyla with members known for polyester degradation. Moreover, at 50 °C, enrichment of putative PET/PLA hydrolases was also observed. These findings suggest that AS microorganisms are a reservoir of polyester-active enzymes, particularly PLA-depolymerases, and hold promise for advancing biotechnological strategies to mitigate plastic pollution through re- and up-cycling.},
}

*Microbial Consortia
*Wastewater/microbiology
*Biodegradation, Environmental
Sewage/microbiology
Plastics/metabolism
Bacteria/metabolism/classification/genetics/isolation & purification
Microbiota

@article {pmid39684246,
year = {2024},
author = {Domínguez-Pino, M and Mellado, S and Cuesta, CM and Grillo-Risco, R and García-García, F and Pascual, M},
title = {Metagenomics Reveals Sex-Based Differences in Murine Fecal Microbiota Profiles Induced by Chronic Alcohol Consumption.},
journal = {International journal of molecular sciences},
volume = {25},
number = {23},
pages = {},
doi = {10.3390/ijms252312534},
pmid = {39684246},
issn = {1422-0067},
support = {2023-I024//the Spanish Ministry of Health-PNSD/ ; CIAICO/2021/203//GVA/ ; RD21/0009/0005//the Primary Addiction Care Research Network/ ; pro-ject IMPaCT-Data, exp. IMP/00019//FGG and RGR were supported by and partially funded by the Institute of Health Carlos III/ ; PID2023-146865OB-I00 and PID2021-124430OA-I00//MCIN/AEI/10.13039/501100011033/ FEDER/ ; },
mesh = {Animals ; Female ; Male ; *Feces/microbiology ; Mice ; *Gastrointestinal Microbiome/drug effects ; *Toll-Like Receptor 4/genetics/metabolism ; *Metagenomics/methods ; *Mice, Knockout ; *RNA, Ribosomal, 16S/genetics ; *Ethanol/adverse effects ; Alcohol Drinking/adverse effects ; Mice, Inbred C57BL ; Sex Factors ; Dysbiosis/microbiology/chemically induced ; Sex Characteristics ; },
abstract = {Chronic ethanol exposure induces an inflammatory response within the intestinal tract, compromising mucosal and epithelial integrity and leading to dysbiosis of the gut microbiome. However, the specific roles of the gut microbiota in mediating ethanol-induced effects, as well as their interactions with the immune system, remain poorly characterized. This study aimed to evaluate sex-based differences in fecal microbiota profiles induced by chronic alcohol consumption and to assess whether TLR4 is involved in these effects. We analyzed the 16S rRNA gene sequencing of fecal samples from male and female wild-type (WT) and TLR4-knockout (TLR4-KO) mice with and without chronic ethanol exposure over a three-month period. Our findings provide evidence, for the first time, that male mice are more susceptible to the effects of ethanol on the fecal microbiota, since ethanol exposure induced greater alterations in the Gram-negative and -positive bacteria with immunogenic capacity in the WT male mice than in the female mice. We also demonstrate that the absence of immune receptor TLR4 leads to different microbiota in both sexes, showing anti-inflammatory and protective properties for intestinal barrier function and resulting in a phenotype more resistant to ethanol's effects. These findings may open new avenues for understanding the relationship between gut microbiota profiles and inflammation in the digestive system induced by chronic alcohol consumption.},
}

Animals
Female
Male
*Feces/microbiology
Mice
*Gastrointestinal Microbiome/drug effects
*Toll-Like Receptor 4/genetics/metabolism
*Metagenomics/methods
*Mice, Knockout
*RNA, Ribosomal, 16S/genetics
*Ethanol/adverse effects
Alcohol Drinking/adverse effects
Mice, Inbred C57BL
Sex Factors
Dysbiosis/microbiology/chemically induced
Sex Characteristics

@article {pmid39683635,
year = {2024},
author = {Ouédraogo, LO and Deng, L and Ouattara, CA and Compaoré, A and Ouédraogo, M and Argaw, A and Lachat, C and Houpt, ER and Saidi, Q and Haerynck, F and Sonnenburg, J and Azad, MB and Tavernier, SJ and Bastos-Moreira, Y and Toe, LC and Dailey-Chwalibóg, T},
title = {Describing Biological Vulnerability in Small, Vulnerable Newborns in Urban Burkina Faso (DenBalo): Gut Microbiota, Immune System, and Breastmilk Assembly.},
journal = {Nutrients},
volume = {16},
number = {23},
pages = {},
doi = {10.3390/nu16234242},
pmid = {39683635},
issn = {2072-6643},
support = {INV-035474 & INV-036154/GATES/Bill & Melinda Gates Foundation/United States ; },
mesh = {Humans ; Burkina Faso ; Female ; Infant, Newborn ; *Gastrointestinal Microbiome ; *Milk, Human/immunology ; Prospective Studies ; *Vagina/microbiology/immunology ; *Immune System ; Pregnancy ; Breast Feeding ; Infant, Small for Gestational Age ; Adult ; },
abstract = {Background: Small vulnerable newborns (SVNs), including those born preterm, small for gestational age, or with low birth weight, are at higher risk of neonatal mortality and long-term health complications. Early exposure to maternal vaginal microbiota and breastfeeding plays a critical role in the development of the neonatal microbiota and immune system, especially in low-resource settings like Burkina Faso, where neonatal mortality rates remain high. Objectives: The DenBalo study aims to investigate the role of maternal and neonatal factors, such as vaginal and gut microbiota, immune development, and early nutrition, in shaping health outcomes in SVNs and healthy infants. Methods: This prospective cohort observational study will recruit 141 mother-infant pairs (70 SVNs and 71 healthy controls) from four health centers in Bobo-Dioulasso, Burkina Faso. The mother-infant pairs will be followed for six months with anthropometric measurements and biospecimen collections, including blood, breast milk, saliva, stool, vaginal swabs, and placental biopsies. Multi-omics approaches, encompassing metagenomics, metabolomics, proteomics, and immune profiling, will be used to assess vaginal and gut microbiota composition and functionality, immune cell maturation, and cytokine levels at critical developmental stages. Conclusions: This study will generate comprehensive data on how microbiota, metabolomic, and proteomic profiles, along with immune system development, differ between SVNs and healthy infants. These findings will guide targeted interventions to improve neonatal health outcomes and reduce mortality, particularly in vulnerable populations.},
}

Humans
Burkina Faso
Female
Infant, Newborn
*Gastrointestinal Microbiome
*Milk, Human/immunology
Prospective Studies
*Vagina/microbiology/immunology
*Immune System
Pregnancy
Breast Feeding
Infant, Small for Gestational Age
Adult

@article {pmid39682735,
year = {2024},
author = {Hemmati, MA and Monemi, M and Asli, S and Mohammadi, S and Foroozanmehr, B and Haghmorad, D and Oksenych, V and Eslami, M},
title = {Using New Technologies to Analyze Gut Microbiota and Predict Cancer Risk.},
journal = {Cells},
volume = {13},
number = {23},
pages = {},
doi = {10.3390/cells13231987},
pmid = {39682735},
issn = {2073-4409},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Neoplasms/microbiology ; Machine Learning ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics/methods ; },
abstract = {The gut microbiota significantly impacts human health, influencing metabolism, immunological responses, and disease prevention. Dysbiosis, or microbial imbalance, is linked to various diseases, including cancer. It is crucial to preserve a healthy microbiome since pathogenic bacteria, such as Escherichia coli and Fusobacterium nucleatum, can cause inflammation and cancer. These pathways can lead to the formation of tumors. Recent advancements in high-throughput sequencing, metagenomics, and machine learning have revolutionized our understanding of the role of gut microbiota in cancer risk prediction. Early detection is made easier by machine learning algorithms that improve the categorization of cancer kinds based on microbiological data. Additionally, the investigation of the microbiome has been transformed by next-generation sequencing (NGS), which has made it possible to fully profile both cultivable and non-cultivable bacteria and to understand their roles in connection with cancer. Among the uses of NGS are the detection of microbial fingerprints connected to treatment results and the investigation of metabolic pathways implicated in the development of cancer. The combination of NGS with machine learning opens up new possibilities for creating customized medicine by enabling the development of diagnostic tools and treatments that are specific to each patient's microbiome profile, even in the face of obstacles like data complexity. Multi-omics studies reveal microbial interactions, biomarkers for cancer detection, and gut microbiota's impact on cancer progression, underscoring the need for further research on microbiome-based cancer prevention and therapy.},
}

Humans
*Gastrointestinal Microbiome
*Neoplasms/microbiology
Machine Learning
High-Throughput Nucleotide Sequencing/methods
Metagenomics/methods

@article {pmid39681310,
year = {2024},
author = {Tobar, Z and Lee, KY and Gaa, ME and Moore, BP and Li, X and Pitesky, ME},
title = {Evaluation of 16s Long Read Metabarcoding for Characterizing the Microbiome and Salmonella Contamination of Retail Poultry Meat.},
journal = {Journal of food protection},
volume = {},
number = {},
pages = {100434},
doi = {10.1016/j.jfp.2024.100434},
pmid = {39681310},
issn = {1944-9097},
abstract = {The traditional gold standard for detection of Salmonella in meat products is bacterial culture with enrichment. While this method is highly sensitive, it is slow and provides an incomplete assessment of isolate taxonomy in positive samples. This study presents a novel PCR based detection assay which amplifies the 16s-ITS-23s region which is an approximately 2500 base pair region of the larger ribosomal rrn operon. Intra-assay variation was assessed by splitting each biological sample into 3 technical replicates. Limits of detection (LOD) were assessed by utilizing a serial dilution of a pure culture of Salmonella enterica subsp. enterica serovar Heidelberg spiked into either sterile 1× PBS or 1× PBS rinsate of a Salmonella culture-negative chicken meat sample. Results indicate the 16s metabarcoding assay evaluated here could not be reliably used for the detection of Salmonella in adulterated retail meat samples as the LOD observed, 4.70 log colony forming units (CFU)/ml, is above the expected concentration of Salmonella in retail poultry meat samples which previous studies have shown range from under 1 to 2 log CFU/ml. However, due to greater taxonomic resolution afforded by using 16s long reads, the assay allowed alpha diversity assessment of the microbiome of raw poultry meat with the ability to assign taxonomy to the species and strain level for some amplicon sequence variants (ASV). This indicates this process may have value characterizing biodiversity and pathogen contamination of poultry samples in earlier steps of the poultry meat production process where bacterial contamination concentrations are likely to be higher.},
}

@article {pmid39630952,
year = {2024},
author = {Gao, F and Shen, Y and Wu, H and Laue, HE and Lau, FK and Gillet, V and Lai, Y and Shrubsole, MJ and Prada, D and Zhang, W and Liu, Z and Bellenger, JP and Takser, L and Baccarelli, AA},
title = {Associations of Stool Metal Exposures with Childhood Gut Microbiome Multiomics Profiles in a Prospective Birth Cohort Study.},
journal = {Environmental science & technology},
volume = {58},
number = {50},
pages = {22053-22063},
doi = {10.1021/acs.est.4c09642},
pmid = {39630952},
issn = {1520-5851},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Feces/microbiology ; Child ; *Metals ; Prospective Studies ; Female ; Male ; Birth Cohort ; Environmental Exposure ; Multiomics ; },
abstract = {Metal exposures are closely related to childhood developmental health. However, their effects on the childhood gut microbiome, which also impacts health, are largely unexplored using microbiome multiomics including the metagenome and metatranscriptome. This study examined the associations of fecal profiles of metal/element exposures with gut microbiome species and active functional pathways in 8- to 12-year-old children (N = 116) participating in the GESTation and Environment (GESTE) cohort study. We analyzed 19 stool metal and element concentrations (B, Na, Mg, Al, K, Ca, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, As, Mo, Cd, Ba, and Pb). Covariate-adjusted linear regression models identified several significant microbiome associations with continuous stool metal/element concentrations. For instance, Zn was positively associated with Turicibacter sanguinis (coef = 1.354, q-value = 0.039) and negatively associated with Eubacterium eligens (coef = -0.794, q-value = 0.044). Higher concentrations of Cd were associated with lower Eubacterium eligens (coef = -0.774, q-value = 0.045). Additionally, a total of 490 significant functional pathways such as biosynthesis and degradation/utilization/assimilation were identified, corresponding to different functions, including amino acid synthesis and carbohydrate degradation. Our results suggest links among metal exposures, pediatric gut microbiome multiomics, and potential health implications. Future work will further explore their relation to childhood health.},
}

Humans
*Gastrointestinal Microbiome
*Feces/microbiology
Child
*Metals
Prospective Studies
Female
Male
Birth Cohort
Environmental Exposure
Multiomics

@article {pmid39601556,
year = {2024},
author = {Yang, J and Wang, H and Lin, X and Liu, J and Feng, Y and Bai, Y and Liang, H and Hu, T and Wu, Z and Lai, J and Liu, J and Zou, Y and Wei, S and Yan, P},
title = {Gut microbiota dysbiosis induced by alcohol exposure in pubertal and adult mice.},
journal = {mSystems},
volume = {9},
number = {12},
pages = {e0136624},
doi = {10.1128/msystems.01366-24},
pmid = {39601556},
issn = {2379-5077},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Dysbiosis/chemically induced/microbiology ; Mice ; *Ethanol ; Male ; Mice, Inbred C57BL ; Metagenome/drug effects ; Liver/metabolism/drug effects/pathology ; Sexual Maturation/drug effects ; },
abstract = {UNLABELLED: Alcohol intake causes many diseases including neuropsychiatric symptoms, nutritional deficiency, progressive pancreatitis, liver cirrhosis, and ischemic heart disease. The gut microbiota changes significantly after alcohol exposure. Alcohol consumption tends to increase in underage and young people, but the feature of the gut microbiota in puberty remains largely unexplored. In this study, we conducted alcohol-exposed pubertal and adult mice model to investigate the intestinal damage and gut microbiota change. Interestingly, the responses of pubertal mice and adult mice after alcohol exposure were different. We found that alcohol dehydrogenase decreased and aldehyde dehydrogenase increased in the liver of pubertal mice, thus reducing the accumulation of toxic acetaldehyde. Furthermore, alcohol exposure caused less intestinal injury in pubertal mice. Through the analysis of metagenome assembly genome, we obtained many unrecognized bacterial genomes. Limosillactobacillus reuteri (cluster_56) and Lactobacillus intestinalis (cluster_57) were assembled from the samples of pubertal mice, which were involved in the production of indole acetic acid and the transformation of bile acids in response to alcohol exposure. This study provided a new insight to investigate the gut microbiota change and explained the difference of the gut microbiota after alcohol exposure between pubertal mice and adult mice.

IMPORTANCE: This study elucidates the significant impact of alcohol exposure on the gut microbiota and metabolic pathways in mice, highlighting the differential responses between adolescent and adult stages. Alcohol exposure was found to damage the intestinal barrier, alter the microbial composition by decreasing beneficial bacteria like Lactobacillus, and increase harmful bacteria such as Alistipes. The study also discovered unique microbial changes and resilience in pubertal mice. Species-level metagenomic analysis revealed specific microbial taxa and metabolic functions affected by alcohol. Metagenome-assembled genomes (MAGs) found many species that could not be annotated by conventional methods including many members of Lachnospiraceae, greatly expanding our understanding of the gut microbiota composition. These findings underscore the need for further research on alcohol's effects on various organs and the implications of microbial metabolites on disease progression.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Dysbiosis/chemically induced/microbiology
Mice
*Ethanol
Male
Mice, Inbred C57BL
Metagenome/drug effects
Liver/metabolism/drug effects/pathology
Sexual Maturation/drug effects

@article {pmid39601555,
year = {2024},
author = {Gao, Y and Zhang, H and Zhu, D and Guo, L},
title = {Different artificial feeding strategies shape the diverse gut microbial communities and functions with the potential risk of pathogen transmission to captive Asian small-clawed otters (Aonyx cinereus).},
journal = {mSystems},
volume = {9},
number = {12},
pages = {e0095424},
doi = {10.1128/msystems.00954-24},
pmid = {39601555},
issn = {2379-5077},
support = {561119219//Scientific research start-up foundation from Lanzhou University/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; *Otters/microbiology ; *Feces/microbiology ; *Animal Feed/analysis/microbiology ; Animals, Zoo/microbiology ; Diet/veterinary ; Bacteria/genetics/isolation & purification/classification ; Fatty Acids, Volatile/metabolism ; },
abstract = {UNLABELLED: Captive otters raised in zoos are fed different artificial diets, which may shape gut microbiota. The objective is to evaluate the impacts of two different artificial diets on microbial communities and function capabilities and short-chain fatty acid (SCFA) profiles in healthy otters' feces. A total of 16 Asian small-clawed otters in two groups (n = 8) were selected. Group A otters were fed raw loaches supplemented with commercial cat food (LSCF) diet, and group B otters were fed raw crucian diet. The communities and functional capabilities of microbiota in feces were assessed with metagenomic sequencing. Captive otters fed two kinds of diets possessed different gut microbial communities and functional capabilities. Various pathogenic bacteria, like Escherichia coli and Clostridium perfringens, were enriched in the samples from the two groups, respectively. Most of the differential pathways of nutrient metabolism were significantly enriched in group A, and the distributions of carbohydrate enzymes in the two groups significantly differed from each other. Multiple resistance genes markedly accumulated in fecal samples of the group A otters with LSCF diet. Higher concentrations of SCFAs were also observed in group A otters. Two feeding strategies were both likely to facilitate the colonization and expansion of various pathogenic bacteria and the accumulation of resistance genes in the intestines of captive otters, suggesting that risk of pathogen transmission existed in the current feeding process. Commercial cat food could supplement various nutrients and provide a substrate for the production of SCFAs, which might be beneficial for the otters' intestinal fermentation and metabolism.

IMPORTANCE: Captive otters fed with different diets possessed distinct gut microbial communities and functions, with the enrichment of several pathogens and multiple resistance genes in their gut microbiota. The current artificial feeding strategies had the possibility to accelerate the colonization and proliferation of various pathogenic bacteria in the intestines of otters and the spread of resistance genes, increasing the risk of diseases. In addition, supplementation with commercial cat food had benefits for otters' intestinal fermentation and the metabolism of gut microbiota.},
}

Animals
*Gastrointestinal Microbiome
*Otters/microbiology
*Feces/microbiology
*Animal Feed/analysis/microbiology
Animals, Zoo/microbiology
Diet/veterinary
Bacteria/genetics/isolation & purification/classification
Fatty Acids, Volatile/metabolism

@article {pmid39584840,
year = {2024},
author = {Bernardin, JR and Young, EB and Gray, SM and Bittleston, LS},
title = {Bacterial community function increases leaf growth in a pitcher plant experimental system.},
journal = {mSystems},
volume = {9},
number = {12},
pages = {e0129824},
doi = {10.1128/msystems.01298-24},
pmid = {39584840},
issn = {2379-5077},
mesh = {*Plant Leaves/microbiology/growth & development ; *Sarraceniaceae/microbiology ; *Microbiota/physiology ; *Bacteria/genetics ; Metagenomics ; },
abstract = {UNLABELLED: Across diverse ecosystems, bacteria and their hosts engage in complex relationships having negative, neutral, or positive interactions. However, the specific effects of leaf-associated bacterial community functions on plant growth are poorly understood. Although microbes can promote plant growth through various biochemical mechanisms, investigating the community's functional contributions to plant growth remains to be explored. To address this gap, we characterized the relationships between bacterial community function and host plant growth in the purple pitcher plant (Sarracenia purpurea). The main aim of our research was to investigate how different bacterial community functions affect the growth and nutrient content in the plant. Previous research has suggested that microbial communities aid in prey decomposition and subsequent nutrient acquisition in carnivorous plants, including S. purpurea. However, the specific functional roles of bacterial communities in plant growth and nutrient uptake are not well known. In this study, sterile, freshly opened pitchers were inoculated with three functionally distinct, pre-assembled bacterial communities. Bacterial community composition and function were measured over 8 weeks using physiological assays, metagenomics, and metatranscriptomics. Distinct community functions affected plant traits; a bacterial community enriched in decomposition was associated with larger leaves with almost double the biomass of control pitchers. Physiological differences in bacterial communities were supported by metatranscriptomics; for example, the bacterial community with the highest chitinase activity had greater expression of transcripts associated with chitinase enzymes. The relationship between bacterial community function and plant growth observed here indicates potential mechanisms, such as chitinase activity, for host-associated bacterial functions to support pitcher plant growth.

IMPORTANCE: This study addresses a gap in understanding the relationships between bacterial community function and plant growth. We inoculated sterile, freshly opened pitcher plant leaves with three functionally distinct bacterial communities to uncover potential mechanisms through which bacterial functions support plant health and growth. Our findings demonstrate that distinct community functions significantly influence plant traits, with some bacterial communities supporting more plant growth than in control pitchers. These results highlight the ecological roles of microbial communities in plants and thus ecosystems and suggest that nutrient cycling is an important pathway through which microbes support host plant health. This research provides valuable insights into plant-microbe interactions and the effects of diverse microbial community functions.},
}

*Plant Leaves/microbiology/growth & development
*Sarraceniaceae/microbiology
*Microbiota/physiology
*Bacteria/genetics
Metagenomics

@article {pmid39557257,
year = {2024},
author = {Dong, J and Wang, L and Bai, Y and Huang, X and Chen, C and Liu, Y},
title = {Study on the physicochemical properties and immune regulatory mechanism of polysaccharide fraction from Aronia Melanocarpa fruit.},
journal = {International journal of biological macromolecules},
volume = {283},
number = {Pt 2},
pages = {137696},
doi = {10.1016/j.ijbiomac.2024.137696},
pmid = {39557257},
issn = {1879-0003},
mesh = {*Photinia/chemistry ; *Polysaccharides/pharmacology/chemistry ; Animals ; Mice ; *Fruit/chemistry ; *Gastrointestinal Microbiome/drug effects ; Chemical Phenomena ; Molecular Weight ; },
abstract = {Aronia Melanocarpa (Michx.) Elliott fruit has been extensively used in the food and medicinal fields. This study aimed to analyze the physicochemical properties of a polysaccharide fraction (AMP2) isolated from this fruit for the first time and investigated its immune regulatory mechanism. The physicochemical properties of AMP2 were determined using high-performance gel permeation chromatography, PMP derivatization-high performance liquid chromatography, Ultraviolet spectroscopy, and infrared spectroscopy. The metagenomic technology was applied to investigate the regulatory effects and mechanisms of AMP2 on the gut microbiota of immunosuppressed mice. The results showed that molecular weight of AMP2 was 83,444 Da, which was mainly composed of D-arabinose, D-xylose, D-mannose, D-rhamnose and D-glucose, and both β-type and α-type glycosidic bonds contained in its structure. AMP2 changed the composition of gut microbiota by increasing the number of beneficial and probiotic bacteria, thereby regulated the intestinal mucosal immune system of host. AMP2 improved intestinal immune system response and antimicrobial capacity through positive regulation of the NOD-like receptor signaling pathway and neutrophil extracellular trap formation. The results demonstrate the potential of AMP2 in immune regulation, providing a new perspective for its subsequent development and contributing to the development and application of related health foods.},
}

*Photinia/chemistry
*Polysaccharides/pharmacology/chemistry
Animals
Mice
*Fruit/chemistry
*Gastrointestinal Microbiome/drug effects
Chemical Phenomena
Molecular Weight

@article {pmid39557245,
year = {2024},
author = {Qin, X and Huang, W and Li, Q},
title = {Lignocellulose biodegradation to humic substances in cow manure-straw composting: Characterization of dissolved organic matter and microbial community succession.},
journal = {International journal of biological macromolecules},
volume = {283},
number = {Pt 3},
pages = {137758},
doi = {10.1016/j.ijbiomac.2024.137758},
pmid = {39557245},
issn = {1879-0003},
mesh = {*Humic Substances/analysis ; *Lignin/chemistry/metabolism ; *Manure/microbiology/analysis ; Cattle ; Animals ; *Composting/methods ; *Biodegradation, Environmental ; Microbiota ; },
abstract = {Composting, a sustainable practice, facilitates the biodegradation of organic waste, notably lignocellulosic biomass, into value-added humic substances. Despite its potential, the application of electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI FT-ICR MS) to characterize dissolved organic matter (DOM) for assessing the changes in maturity during cow manure-straw composting is underexplored. Furthermore, the link between these changes, microbial community succession, and the biochemical pathways of humus formation is seldom investigated. This study leveraged ESI FT-ICR MS and metagenomic analysis to elucidate the molecular changes in DOM, identified key microbes in humus formation, and traced the humus formation pathway during composting. The results highlighted the crucial role of microorganisms such as Thermobifida, Luteimonas, Ascomycota, and Chloroflexi in accelerating the breakdown and transformation of plant biopolymers. Large molecular nitrogen compounds from cow manure-straw were converted into unsaturated, aromatic oxygen compounds, which resemble humic substances in their chemical properties. The ESI FT-ICR MS data revealed that humus formation occurred through a series of reactions, including protein deamination, lignin delignification, and decarbonylation. This research offered new light on strategies to enhance the stabilization and humification of cow manure-straw composting, contributing to more effective composting processes.},
}

*Humic Substances/analysis
*Lignin/chemistry/metabolism
*Manure/microbiology/analysis
Cattle
Animals
*Composting/methods
*Biodegradation, Environmental
Microbiota

@article {pmid39551294,
year = {2024},
author = {Zhang, G and Du, J and Zhang, C and Zhao, Z and Chen, Y and Liu, M and Chen, J and Fan, G and Ma, L and Li, S and Liu, K},
title = {Identification of a PET hydrolytic enzyme from the human gut microbiome unveils potential plastic biodegradation in human digestive tract.},
journal = {International journal of biological macromolecules},
volume = {283},
number = {Pt 3},
pages = {137732},
doi = {10.1016/j.ijbiomac.2024.137732},
pmid = {39551294},
issn = {1879-0003},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Polyethylene Terephthalates/metabolism/chemistry ; *Biodegradation, Environmental ; Hydrolysis ; Gastrointestinal Tract/microbiology/metabolism ; Metagenome ; Hydrolases/metabolism/genetics ; Plastics/chemistry ; Nanoparticles/chemistry ; },
abstract = {Widespread use of polyethylene terephthalate (PET) plastics and their recycling challenges have led to substantial accumulation of PET wastes in global environments, with inevitable consequences for their entry into the food chains. Recent studies have increasingly documented the ingestion of microplastics by humans through food and beverages. However, the fate of these microplastics within the gastrointestinal tract, particularly the role of the human gut microbiota, remains inadequately understood. To address this knowledge gap, we employed a bioinformatics workflow integrated with functional verification to investigate the PET digestion/degradation capabilities of intestinal microorganisms. This approach identified a novel PET hydrolase-HGMP01 from the human gut metagenome, which exhibits the capacity to hydrolyze PET nanoparticles. Moreover, comprehensive exploration for HGMP01 homologues in the human gut metagenome and metatranscriptome unveil their distribution in diverse intestinal microorganisms. This study provides biochemical evidence for an unforeseen role of human gut microbiome in plastic digestion, thus holding substantial implications for human health.},
}

Humans
*Gastrointestinal Microbiome
*Polyethylene Terephthalates/metabolism/chemistry
*Biodegradation, Environmental
Hydrolysis
Gastrointestinal Tract/microbiology/metabolism
Metagenome
Hydrolases/metabolism/genetics
Plastics/chemistry
Nanoparticles/chemistry

@article {pmid39508593,
year = {2024},
author = {Tran, TH and F Escapa, I and Roberts, AQ and Gao, W and Obawemimo, AC and Segre, JA and Kong, HH and Conlan, S and Kelly, MS and Lemon, KP},
title = {Metabolic capabilities are highly conserved among human nasal-associated Corynebacterium species in pangenomic analyses.},
journal = {mSystems},
volume = {9},
number = {12},
pages = {e0113224},
doi = {10.1128/msystems.01132-24},
pmid = {39508593},
issn = {2379-5077},
support = {R01 GM117174/GM/NIGMS NIH HHS/United States ; R35 GM141806/GM/NIGMS NIH HHS/United States ; R35 GM141806, R01 GM117174//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; K23 AI135090/AI/NIAID NIH HHS/United States ; //HHS | NIH | National Human Genome Research Institute (NHGRI)/ ; //HHS | NIH | National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS)/ ; FPILOT45//Forsyth Institute/ ; },
mesh = {*Corynebacterium/genetics/metabolism ; Humans ; *Genome, Bacterial ; *Phylogeny ; Microbiota/genetics ; Genomics ; United States ; Nose/microbiology ; Botswana ; },
abstract = {UNLABELLED: Corynebacterium species are globally ubiquitous in human nasal microbiota across the lifespan. Moreover, nasal microbiota profiles typified by higher relative abundances of Corynebacterium are often positively associated with health. Among the most common human nasal Corynebacterium species are C. propinquum, C. pseudodiphtheriticum, C. accolens, and C. tuberculostearicum. To gain insight into the functions of these four species, we identified genomic, phylogenomic, and pangenomic properties and estimated the metabolic capabilities of 87 distinct human nasal Corynebacterium strain genomes: 31 from Botswana and 56 from the United States. C. pseudodiphtheriticum had geographically distinct clades consistent with localized strain circulation, whereas some strains from the other species had wide geographic distribution spanning Africa and North America. All species had similar genomic and pangenomic structures. Gene clusters assigned to all COG metabolic categories were overrepresented in the persistent versus accessory genome of each species indicating limited strain-level variability in metabolic capacity. Based on prevalence data, at least two Corynebacterium species likely coexist in the nasal microbiota of 82% of adults. So, it was surprising that core metabolic capabilities were highly conserved among the four species indicating limited species-level metabolic variation. Strikingly, strains in the U.S. clade of C. pseudodiphtheriticum lacked genes for assimilatory sulfate reduction present in most of the strains in the Botswana clade and in the other studied species, indicating a recent, geographically related loss of assimilatory sulfate reduction. Overall, the minimal species and strain variability in metabolic capacity implies coexisting strains might have limited ability to occupy distinct metabolic niches.

IMPORTANCE: Pangenomic analysis with estimation of functional capabilities facilitates our understanding of the full biologic diversity of bacterial species. We performed systematic genomic, phylogenomic, and pangenomic analyses with qualitative estimation of the metabolic capabilities of four common human nasal Corynebacterium species, along with focused experimental validations, generating a foundational resource. The prevalence of each species in human nasal microbiota is consistent with the common coexistence of at least two species. We identified a notably high level of metabolic conservation within and among species indicating limited options for species to occupy distinct metabolic niches, highlighting the importance of investigating interactions among nasal Corynebacterium species. Comparing strains from two continents, C. pseudodiphtheriticum had restricted geographic strain distribution characterized by an evolutionarily recent loss of assimilatory sulfate reduction in U.S. strains. Our findings contribute to understanding the functions of Corynebacterium within human nasal microbiota and to evaluating their potential for future use as biotherapeutics.},
}

*Corynebacterium/genetics/metabolism
Humans
*Genome, Bacterial
*Phylogeny
Microbiota/genetics
Genomics
United States
Nose/microbiology
Botswana

@article {pmid39316987,
year = {2024},
author = {Yang, H and Liu, Y and Cao, G and Liu, J and Xiao, S and Xiao, P and Tao, Y and Gao, H},
title = {Effects of lycopene on the growth performance, meat quality, cecal metagenome, and hepatic untargeted metabolome in heat stressed broilers.},
journal = {Poultry science},
volume = {103},
number = {12},
pages = {104299},
pmid = {39316987},
issn = {1525-3171},
mesh = {Animals ; *Chickens/physiology/growth & development ; *Animal Feed/analysis ; *Diet/veterinary ; *Meat/analysis ; *Liver/drug effects/metabolism ; *Lycopene/pharmacology/administration & dosage ; *Cecum/microbiology/drug effects/metabolism ; *Dietary Supplements/analysis ; *Metabolome/drug effects ; Male ; Metagenome ; Random Allocation ; Gastrointestinal Microbiome/drug effects ; Heat-Shock Response/drug effects ; },
abstract = {The occurrence of heat stress in poultry houses is inevitable and leads to oxidative stress in the birds. Lycopene, a natural hydrocarbon carotenoid, possesses potent antioxidant properties. This study aimed to investigate the impact of lycopene on growth performance, meat quality, cecal microflora, and liver metabolome in broilers subjected to heat stress. A total of 480 yellow feather broilers were randomly allocated into 4 treatment groups: birds fed standard diet (Con), birds fed standard diet and supplemented with lycopene (Lyc), birds fed standard diet and subjected to heat stress (Hs), and birds fed with lycopene and subjected to heat stress (Hs-Lyc). As compared with the normal temperature groups, Hs decreased the average daily gain (ADG) of birds during d 1 to 28, lowered the pH value either in breast meat or thigh meat, increased the L* value of breast meat, and decreased the a* value of thigh meat. In comparison with non-Lyc feeding birds, Lyc supplement elevated the ADG during d 1 to 56, increased the pH of breast meat, decrease the L* and b* values of thigh meat, simultaneously increase the a* value of thigh meat. The L* of breast meat and pH of thigh meat exhibited significant differences under Hs-Lyc treatment. Lyc-treated birds exhibited higher elasticity, gumminess, and resilience in breast meat than those in non-Lyc feeding birds. The cecal metagenome analysis indicated that Hs-Lyc treatment increased the abundance of Phocaeicola salanitronis and Prevotella sp.CAG:1058, Bacteroides sp.An269, and Bacteroides sp.An19 at the species level compared with other treatments. The hepatic untargeted metabolome analysis showed that administration of Lyc upregulated 20 metabolites and downregulated 60 metabolites compared to the Con birds. Futhermore, the Hs-Lyc treatment upregulated 34 metabolites and downregulated 45 metabolites compared to the Hs birds. The correlation between the metagenome and metabolome showed that Lyc supplementation induced significant alterations in the citrate cycle, metabolism of butanoate, glycolysis/gluconeogenesis, glyoxylate and dicarboxylate, alanine, aspartate, and glutamate compared with standard supplement. In contrast, Hs-Lyc treatment induced alterations in the citrate cycle, metabolism of pyruvate, glyoxylate, and dicarboxylate, glycolysis/gluconeogenesis, arginine, proline, alanine, aspartate, and glutamate compared with the standard supplement of heat-challenged broilers. In summary, dietary Lyc supplementation promoted the growth performance, changed the meat quality, modulated the cecal metagenome and hepatic metabolome in heat-stressed broilers.},
}

Animals
*Chickens/physiology/growth & development
*Animal Feed/analysis
*Diet/veterinary
*Meat/analysis
*Liver/drug effects/metabolism
*Lycopene/pharmacology/administration & dosage
*Cecum/microbiology/drug effects/metabolism
*Dietary Supplements/analysis
*Metabolome/drug effects
Male
Metagenome
Random Allocation
Gastrointestinal Microbiome/drug effects
Heat-Shock Response/drug effects

@article {pmid39679737,
year = {2024},
author = {Zhao, H and Wang, T},
title = {Debiased high-dimensional regression calibration for errors-in-variables log-contrast models.},
journal = {Biometrics},
volume = {80},
number = {4},
pages = {},
doi = {10.1093/biomtc/ujae153},
pmid = {39679737},
issn = {1541-0420},
mesh = {Humans ; Calibration ; *Models, Statistical ; Gastrointestinal Microbiome ; Computer Simulation ; Regression Analysis ; Bias ; Linear Models ; Biometry/methods ; Data Interpretation, Statistical ; Metagenomics/methods/statistics & numerical data ; },
abstract = {Motivated by the challenges in analyzing gut microbiome and metagenomic data, this work aims to tackle the issue of measurement errors in high-dimensional regression models that involve compositional covariates. This paper marks a pioneering effort in conducting statistical inference on high-dimensional compositional data affected by mismeasured or contaminated data. We introduce a calibration approach tailored for the linear log-contrast model. Under relatively lenient conditions regarding the sparsity level of the parameter, we have established the asymptotic normality of the estimator for inference. Numerical experiments and an application in microbiome study have demonstrated the efficacy of our high-dimensional calibration strategy in minimizing bias and achieving the expected coverage rates for confidence intervals. Moreover, the potential application of our proposed methodology extends well beyond compositional data, suggesting its adaptability for a wide range of research contexts.},
}

Humans
Calibration
*Models, Statistical
Gastrointestinal Microbiome
Computer Simulation
Regression Analysis
Bias
Linear Models
Biometry/methods
Data Interpretation, Statistical
Metagenomics/methods/statistics & numerical data

@article {pmid39679619,
year = {2024},
author = {Steinbach, E and Belda, E and Alili, R and Adriouch, S and Dauriat, CJG and Donatelli, G and Dumont, JL and Pacini, F and Tuszynski, T and Pelloux, V and Jacques, F and Creusot, L and Coles, E and Taillandier, P and Vazquez Gomez, M and Masi, D and Mateo, V and André, S and Kordahi, M and Rouault, C and Zucker, JD and Sokol, H and Genser, L and Chassaing, B and Le Roy, T and Clément, K},
title = {Comparative analysis of the duodenojejunal microbiome with the oral and fecal microbiomes reveals its stronger association with obesity and nutrition.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2405547},
doi = {10.1080/19490976.2024.2405547},
pmid = {39679619},
issn = {1949-0984},
mesh = {Humans ; *Obesity/microbiology ; *Feces/microbiology ; Female ; Male ; Middle Aged ; *Gastrointestinal Microbiome ; Adult ; *Duodenum/microbiology ; *Bacteria/classification/isolation & purification/genetics/metabolism ; Jejunum/microbiology ; Mouth/microbiology ; Nutritional Status ; },
abstract = {The intestinal microbiota is increasingly recognized as a crucial player in the development and maintenance of various chronic conditions, including obesity and associated metabolic diseases. While most research focuses on the fecal microbiota due to its easier accessibility, the small intestine, as a major site for nutrient sensing and absorption, warrants further investigation to determine its microbiota composition and functions. Here, we conducted a clinical research project in 30 age- and sex-matched participants with (n = 15) and without (n = 15) obesity. Duodenojejunal fluid was obtained by aspiration during endoscopy. Phenotyping included clinical variables related to metabolic status, lifestyle, and psychosocial factors using validated questionnaires. We performed metagenomic analyses of the oral, duodenojejunal, and fecal microbiome, alongside metabolomic data from duodenojejunal fluid and feces, integrating these data with clinical and lifestyle information. Our results highlight significant associations between duodenojejunal microbiota composition and usual dietary intake, as well as clinical phenotypes, with larger effect sizes than the associations between these variables and fecal microbiota. Notably, we found that the duodenojejunal microbiota of patients with obesity exhibited higher diversity and showed distinct differences in the abundance of several duodenojejunal microbiota species compared with individuals without obesity. Our findings support the relevance of studying the role of the small intestinal microbiota in the pathogenesis of nutrition-related diseases.},
}

Humans
*Obesity/microbiology
*Feces/microbiology
Female
Male
Middle Aged
*Gastrointestinal Microbiome
Adult
*Duodenum/microbiology
*Bacteria/classification/isolation & purification/genetics/metabolism
Jejunum/microbiology
Mouth/microbiology
Nutritional Status

@article {pmid39679617,
year = {2024},
author = {McAdams, ZL and Gustafson, KL and Russell, AL and Self, R and Petry, AL and Lever, TE and Ericsson, AC},
title = {Supplier-origin gut microbiomes affect host body weight and select autism-related behaviors.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2385524},
doi = {10.1080/19490976.2024.2385524},
pmid = {39679617},
issn = {1949-0984},
mesh = {*Gastrointestinal Microbiome ; Animals ; Mice ; Male ; *Autism Spectrum Disorder/microbiology ; *Body Weight ; Female ; *Behavior, Animal ; Disease Models, Animal ; Humans ; Brain-Gut Axis/physiology ; Bacteria/classification/isolation & purification/genetics ; Autistic Disorder/microbiology/psychology ; },
abstract = {Autism spectrum disorders (ASD) are complex human neurodiversities increasing in prevalence within the human population. In search of therapeutics to improve quality-of-life for ASD patients, the gut microbiome (GM) has become a promising target as a growing body of work supports roles for the complex community of microorganisms in influencing host behavior via the gut-brain-axis. However, whether naturally-occurring microbial diversity within the host GM affects these behaviors is often overlooked. Here, we applied a model of population-level differences in the GM to a classic ASD model - the BTBR T[+] Itpr3[tf]/J mouse - to assess how complex GMs affect host behavior. Leveraging the naturally occurring differences between supplier-origin GMs, our data demonstrate that differing, complex GMs selectively effect host ASD-related behavior - especially neonatal ultrasonic communication - and reveal a male-specific effect on behavior not typically observed in this strain. We then identified that the body weight of BTBR mice is influenced by the postnatal GM which was potentially mediated by microbiome-dependent effects on energy harvest in the gut. These data provide insight into how variability within the GM affects host behavior and growth, thereby emphasizing the need to incorporate microbial diversity within the host GM as an experimental factor in biomedical research.},
}

*Gastrointestinal Microbiome
Animals
Mice
Male
*Autism Spectrum Disorder/microbiology
*Body Weight
Female
*Behavior, Animal
Disease Models, Animal
Humans
Brain-Gut Axis/physiology
Bacteria/classification/isolation & purification/genetics
Autistic Disorder/microbiology/psychology

@article {pmid39679616,
year = {2024},
author = {Seki, D and Kirkegaard, R and Osvatic, J and Hausmann, B and Séneca, J and Pjevac, P and Berger, A and J Hall, L and Wisgrill, L and Berry, D},
title = {Gut microbiota genome features associated with brain injury in extremely premature infants.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2410479},
doi = {10.1080/19490976.2024.2410479},
pmid = {39679616},
issn = {1949-0984},
mesh = {*Gastrointestinal Microbiome ; Humans ; Infant, Newborn ; *Infant, Extremely Premature ; *Brain Injuries/microbiology/genetics ; *Feces/microbiology ; Female ; Male ; Bacteria/genetics/classification/isolation & purification/metabolism ; Genome, Bacterial ; Cohort Studies ; },
abstract = {Severe brain damage is common among premature infants, and the gut microbiota has been implicated in its pathology. Although the order of colonizing bacteria is well described, the mechanisms underlying aberrant assembly of the gut microbiota remain elusive. Here, we employed long-read nanopore sequencing to assess abundances of microbial species and their functional genomic potential in stool samples from a cohort of 30 extremely premature infants. We identify several key microbial traits significantly associated with severe brain damage, such as the genomic potential for nitrate respiration and iron scavenging. Members of the Enterobacteriaceae were prevalent across the cohort and displayed a versatile metabolic potential, including pathogenic and nonpathogenic traits. Predominance of Enterobacter hormaechei and Klebsiella pneumoniae were associated with an overall loss of genomic functional redundancy as well as poor neurophysiological outcome. These findings reveal microbial traits that may be involved in exacerbating brain injury in extremely premature infants and provide suitable targets for therapeutic interventions.},
}

*Gastrointestinal Microbiome
Humans
Infant, Newborn
*Infant, Extremely Premature
*Brain Injuries/microbiology/genetics
*Feces/microbiology
Female
Male
Bacteria/genetics/classification/isolation & purification/metabolism
Genome, Bacterial
Cohort Studies

@article {pmid39678952,
year = {2024},
author = {Sinha, T and Talukdar, NC},
title = {Phylum Level Diversity of Plant Interior Bacteria in Seeds, Supernatant and Pellet Phases of Seed Suspension of Mustard Plant.},
journal = {Indian journal of microbiology},
volume = {64},
number = {4},
pages = {1587-1597},
pmid = {39678952},
issn = {0046-8991},
abstract = {Our previous study explored the bacterial endophytic diversity in a certain quantity of mustard seeds using culture dependent method by development of new isolation strategies. No bacterial colony was initially observed in supernatant obtained after centrifugation of mustard seed suspension. This was later overcome by usage of surfactant whereas pellet part showed presence of bacterial colonies on media. In our present study, presence of bacteria was examined in supernatant and whether the diversity was similar to that of pellet and seeds by culture independent approach. In addition, growth of bacterial colonies on media is explained using GC-MS. In this study, Proteobacteria was the dominant bacterial phyla followed by Firmicutes in pellet, supernatant and seed. This indicated that bacteria were present in supernatant but may not be viable when plated on media. This is either due to antimicrobial compounds or oil-imposed difficulty during their isolation which might have hindered their survival. GC-MS study revealed the presence of compounds with antimicrobial property as suggested by previous literature. Our research conducts fundamental investigations to address the primary objective of understanding the bacterial diversity in mustard seed, pellet, and supernatant. Further research using workflows of metagenomics and metabolomics approaches can enrich our understanding ofthe diversity of microorganisms in seeds.},
}

@article {pmid39676101,
year = {2024},
author = {Wang, C and Zhang, C and He, S and Wang, Q and Gao, H},
title = {The microbiome alterations of supragingival plaque among adolescents using clear aligners: a metagenomic sequencing analysis.},
journal = {Progress in orthodontics},
volume = {25},
number = {1},
pages = {48},
pmid = {39676101},
issn = {2196-1042},
support = {PY2023038//Science research cultivation program of stomatological hospital, Southern medical university/ ; PY2023043//Science research cultivation program of stomatological hospital, Southern medical university/ ; B2023274//Guangdong Medical Research Fund/ ; B2022013//Guangdong Medical Research Fund/ ; },
mesh = {Humans ; Adolescent ; *Dental Plaque/microbiology ; Male ; *Microbiota ; Female ; *Biofilms ; Child ; *Capnocytophaga ; Neisseria ; Metagenomics/methods ; Virulence Factors/genetics ; },
abstract = {BACKGROUND: White spot lesions (WSLs) may develop in adolescents undergoing clear aligner (CA) therapy with poor oral hygiene. The specific effects of CAs on the microbial composition and functional characteristics of supragingival plaques remain unclear. The present study investigated the shift in the supragingival microbial community induced by CAs in adolescents through metagenomic technology.

METHODS: Fifteen adolescents (12-15 years old) with Invisalign appliances were recruited. Supragingival plaque specimens were obtained twice, before treatment (T1) and three months after treatment (T2). All the bacterial plaque specimens were analyzed for microbial communities and functions using metagenomic analyses.

RESULTS: A total of 2,840,242,722 reads disclosed 180 phyla, 3,975 genera, and 16,497 microbiome species. During the first three months, the microbial community was relatively stable. The genus level revealed a higher relative abundance of Capnocytophaga, Neisseria, and Arachnia in the T2 period. Furthermore, the functional analysis suggested that the relative abundances of folate biosynthesis, biotin metabolism and biofilm formation-vibrio cholerae were increased in the T2 period compared to the T1 period. Finally, virulence factor analysis demonstrated that the relative abundance of genes associated with type IV pili (VF0082) and polar flagella (VF0473) was higher in the T2 period than in the T1 period.

CONCLUSION: In adolescents undergoing CA therapy with poor plaque control, caries progresses quickly within three months and noticeable WSLs develop on the tooth surface. Although the microbial community remained relatively steady and CA therapy did not cause significant changes in the overall functional gene composition in the first three months, virulence factors, including type IV pili and flagella, were more abundant and actively contributed to microorganism adhesion and biofilm formation.},
}

Humans
Adolescent
*Dental Plaque/microbiology
Male
*Microbiota
Female
*Biofilms
Child
*Capnocytophaga
Neisseria
Metagenomics/methods
Virulence Factors/genetics

@article {pmid39434565,
year = {2025},
author = {Blattner, LA and Lapellegerie, P and Courtney-Mustaphi, C and Heiri, O},
title = {Sediment Core DNA-Metabarcoding and Chitinous Remain Identification: Integrating Complementary Methods to Characterise Chironomidae Biodiversity in Lake Sediment Archives.},
journal = {Molecular ecology resources},
volume = {25},
number = {1},
pages = {e14035},
pmid = {39434565},
issn = {1755-0998},
mesh = {Animals ; *Chironomidae/genetics/classification ; *Lakes ; *DNA Barcoding, Taxonomic/methods ; *Geologic Sediments/chemistry ; *Biodiversity ; Switzerland ; Larva/genetics/classification ; DNA/genetics/chemistry ; Chitin ; Metagenomics/methods ; },
abstract = {Chironomidae, so-called non-biting midges, are considered key bioindicators of aquatic ecosystem variability. Data derived from morphologically identifying their chitinous remains in sediments document chironomid larvae assemblages, which are studied to reconstruct ecosystem changes over time. Recent developments in sedimentary DNA (sedDNA) research have demonstrated that molecular techniques are suitable for determining past and present occurrences of organisms. Nevertheless, sedDNA records documenting alterations in chironomid assemblages remain largely unexplored. To close this gap, we examined the applicability of sedDNA metabarcoding to identify Chironomidae assemblages in lake sediments by sampling and processing three 21-35 cm long sediment cores from Lake Sempach in Switzerland. With a focus on developing analytical approaches, we compared an invertebrate-universal (FWH) and a newly designed Chironomidae-specific metabarcoding primer set (CH) to assess their performance in detecting Chironomidae DNA. We isolated and identified chitinous larval remains and compared the morphotype assemblages with the data derived from sedDNA metabarcoding. Results showed a good overall agreement of the morphotype assemblage-specific clustering among the chitinous remains and the metabarcoding datasets. Both methods indicated higher chironomid assemblage similarity between the two littoral cores in contrast to the deep lake core. Moreover, we observed a pronounced primer bias effect resulting in more Chironomidae detections with the CH primer combination compared to the FWH combination. Overall, we conclude that sedDNA metabarcoding can supplement traditional remain identifications and potentially provide independent reconstructions of past chironomid assemblage changes. Furthermore, it has the potential of more efficient workflows, better sample standardisation and species-level resolution datasets.},
}

Animals
*Chironomidae/genetics/classification
*Lakes
*DNA Barcoding, Taxonomic/methods
*Geologic Sediments/chemistry
*Biodiversity
Switzerland
Larva/genetics/classification
DNA/genetics/chemistry
Chitin
Metagenomics/methods

@article {pmid39418776,
year = {2024},
author = {Xie, Q and Sun, J and Sun, M and Wang, Q and Wang, M},
title = {Perturbed microbial ecology in neuromyelitis optica spectrum disorder: Evidence from the gut microbiome and fecal metabolome.},
journal = {Multiple sclerosis and related disorders},
volume = {92},
number = {},
pages = {105936},
doi = {10.1016/j.msard.2024.105936},
pmid = {39418776},
issn = {2211-0356},
mesh = {*Neuromyelitis Optica/microbiology/immunology ; Humans ; *Gastrointestinal Microbiome/physiology ; *Feces/microbiology ; Animals ; Female ; Adult ; *Fecal Microbiota Transplantation ; Mice ; Male ; Metabolome/physiology ; Middle Aged ; },
abstract = {BACKGROUND: Neuromyelitis optica spectrum disorder (NMOSD) is a central nervous system inflammatory demyelinating immune-mediated ailment, which is influenced by genetic, epigenetic, and environmental elements. The escalating incidence of NMOSD in recent years implies alterations in environmental risk factors. Recent research has established a correlation between gut microbiomes and the development of NMOSD.

METHODS: Metagenomic shotgun sequencing and gas chromatography-mass spectrometry (GC-MS) were employed to assess alterations of the structure and function in the fecal microbiome, as well as levels of short-chain fatty acids (SCFAs) in fecal and blood samples, among individuals with neuromyelitis optica spectrum disorder (NMOSD) during the acute phase (n = 25), the remission phase (n = 11), and a group of healthy controls (HCs) (n = 24). We further explored the correlation between gut microbiota and the pathogenesis of NMOSD through fecal microbiota transplantation (FMT). The gut microbiome from human donors diagnosed with NMOSD or HCs was transplanted into germ-free mice, followed by an analysis of the alterations in the structure and functionality of the transplanted mice's gut microbiome. Additionally, the impact of microbiome transfer on the immunity and spinal cord of germ-free mice was assessed through various techniques, including ELISA, flow cytometry, western blot, histopathology, and transcriptome sequencing.

RESULTS: (1) At the taxonomic levels of genus and species, there were significant differences in the α-diversity of the microbiome between HCs and NMOSD patients in the acute phase, with NMOSD patients having higher species diversity. (2) In the acute phase, the gut microbiota of NMOSD patients was characterized by Ruminococcaceae_unclassified, Campylobacter, Parabacteroides, Lactobacillus, Akkermansia, Streptococcus oralis, Clostridium leptum, Clostridium asparagiforme, Firmicutes bacterium CAG 238, and Lactobacillus fermentum. (3) The relative abundances of Coprobacter, Turicimonas, Gemmiger, Enterobacter, Roseburia sp.CAG 471, Veillonella tobetsuensis, Proteobacteria bacterium CAG 139, Ruminococcus bicirculans, Lactococcus lactis, Flavonifractor plautii, and Streptococcus cristatus were notably lower in patients experiencing remission compared to NMOSD patients in the acute phase, On the other hand, the relative abundances of Flavonifractor (P = 0.049) and Clostridium aldenense (P = 0.049) were significantly higher. Following medication, the gut microbiome distribution in NMOSD patients during remission closely resembled that of healthy controls (HCs). (4) Compared with HCs, acetate levels in the feces of patients with NMOSD in the acute phase were significantly lower. (5) In addition, we transplanted feces from NMOSD patients into germ-free mice and revealed a significant increase in the levels of IL-6, IL-17A, and IL-23 in the blood of mice belonging to the NMOSD fecal transplantation (NFMT) group. Additionally, the IL-10 level exhibited a significant reduction. Moreover, the proportion of Th17 cells displayed a significant increase, while the proportion of Treg cells exhibited a significant decrease in the spleens of NFMT mice.

CONCLUSION: Patients in the acute phase of neuromyelitis optica spectrum disorder (NMOSD) exhibited imbalances in their gut microbiota and a deficiency in short-chain fatty acids (SCFAs). Following drug treatment, the composition of intestinal microbes in NMOSD patients during the remission phase closely resembled that of the healthy control population. The FMT experiment provided evidence of the significant association between intestinal flora and the pathogenesis of NMOSD. Consequently, investigating gut microbiota and identifying novel microbial markers hold promise for the diagnosis and treatment of NMOSD patients.},
}

*Neuromyelitis Optica/microbiology/immunology
Humans
*Gastrointestinal Microbiome/physiology
*Feces/microbiology
Animals
Female
Adult
*Fecal Microbiota Transplantation
Mice
Male
Metabolome/physiology
Middle Aged

@article {pmid39010331,
year = {2025},
author = {Aydin, Ö and Wahlström, A and de Jonge, PA and Meijnikman, AS and Sjöland, W and Olsson, L and Henricsson, M and de Goffau, MC and Oonk, S and Bruin, SC and Acherman, YIZ and Marschall, HU and Gerdes, VEA and Nieuwdorp, M and Bäckhed, F and Groen, AK},
title = {An integrated analysis of bile acid metabolism in humans with severe obesity.},
journal = {Hepatology (Baltimore, Md.)},
volume = {81},
number = {1},
pages = {19-31},
doi = {10.1097/HEP.0000000000000938},
pmid = {39010331},
issn = {1527-3350},
mesh = {Humans ; *Bile Acids and Salts/metabolism ; Male ; Female ; *Gastrointestinal Microbiome/physiology ; Adult ; Middle Aged ; *Feces/microbiology/chemistry ; *Obesity, Morbid/metabolism/microbiology ; Fibroblast Growth Factors/metabolism ; },
abstract = {BACKGROUND AND AIMS: Bile acids (BA) are vital regulators of metabolism. BAs are AQ6 secreted in the small intestine, reabsorbed, and transported back to the liver, where they can modulate metabolic functions. There is a paucity of data regarding the portal BA composition in humans. This study aimed to address this knowledge gap by investigating portal BA composition and the relation with peripheral and fecal BA dynamics in conjunction with the gut microbiome.

APPROACH AND RESULTS: Thirty-three individuals from the BARIA cohort were included. Portal plasma, peripheral plasma, and feces were collected. BA and C4 levels were measured employing mass spectrometry. FGF19 was measured using ELISA. Gut microbiota composition was determined through metagenomics analysis on stool samples. Considerable diversity in the portal BA composition was observed. The majority (n = 26) of individuals had a 9-fold higher portal than peripheral BA concentration. In contrast, 8 individuals showed lower portal BA concentration compared with peripheral and had higher levels of unconjugated and secondary BA in this compartment, suggesting more distal origin. The altered portal BA profile was associated with altered gut microbiota composition. In particular, taxa within Bacteroides were reduced in abundance in the feces of these individuals.

CONCLUSIONS: Characterization of the portal BA composition in relation to peripheral and fecal BA increased insight into the dynamics of BA metabolism in individuals with obesity. Peripheral BA composition was much more diverse due to microbial metabolism. About 24% of the portal samples was surprisingly low in total BA; the underlying mechanism requires further exploration.},
}

Humans
*Bile Acids and Salts/metabolism
Male
Female
*Gastrointestinal Microbiome/physiology
Adult
Middle Aged
*Feces/microbiology/chemistry
*Obesity, Morbid/metabolism/microbiology
Fibroblast Growth Factors/metabolism

@article {pmid39674265,
year = {2024},
author = {Ravishankar, S and Perez, V and Davidson, R and Roca-Rada, X and Lan, D and Souilmi, Y and Llamas, B},
title = {Filtering out the noise: metagenomic classifiers optimize ancient DNA mapping.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {1},
pages = {},
doi = {10.1093/bib/bbae646},
pmid = {39674265},
issn = {1477-4054},
support = {CE170100015//Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage/ ; GA204260//NHMRC SYNERGY/ ; //Australian Government Research Training Program Scholarship/ ; //Portuguese National Funds/ ; },
mesh = {*DNA, Ancient/analysis ; *Metagenomics/methods ; *Sequence Analysis, DNA/methods ; Humans ; High-Throughput Nucleotide Sequencing/methods ; Metagenome ; Workflow ; DNA Contamination ; },
abstract = {Contamination with exogenous DNA presents a significant challenge in ancient DNA (aDNA) studies of single organisms. Failure to address contamination from microbes, reagents, and present-day sources can impact the interpretation of results. Although field and laboratory protocols exist to limit contamination, there is still a need to accurately distinguish between endogenous and exogenous data computationally. Here, we propose a workflow to reduce exogenous contamination based on a metagenomic classifier. Unlike previous methods that relied exclusively on DNA sequencing reads mapping specificity to a single reference genome to remove contaminating reads, our approach uses Kraken2-based filtering before mapping to the reference genome. Using both simulated and empirical shotgun aDNA data, we show that this workflow presents a simple and efficient method that can be used in a wide range of computational environments-including personal machines. We propose strategies to build specific databases used to profile sequencing data that take into consideration available computational resources and prior knowledge about the target taxa and likely contaminants. Our workflow significantly reduces the overall computational resources required during the mapping process and reduces the total runtime by up to ~94%. The most significant impacts are observed in low endogenous samples. Importantly, contaminants that would map to the reference are filtered out using our strategy, reducing false positive alignments. We also show that our method results in a negligible loss of endogenous data with no measurable impact on downstream population genetics analyses.},
}

*DNA, Ancient/analysis
*Metagenomics/methods
*Sequence Analysis, DNA/methods
Humans
High-Throughput Nucleotide Sequencing/methods
Metagenome
Workflow
DNA Contamination

@article {pmid39669269,
year = {2024},
author = {Lee, KH and Kim, YO and Dho, SH and Yong, JJH and Oh, HS and Lee, JH and Yang, SJ and Cha, I and Chun, J and Lee, EH and Jeong, SJ and Woo, W and Choi, JP and Han, SH and Choi, GB and Huh, JR and Kim, LK and Song, YG},
title = {Altered gut microbiome in convalescent patients with coronavirus disease 2019.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1455295},
pmid = {39669269},
issn = {2235-2988},
mesh = {Humans ; *COVID-19/microbiology ; *Gastrointestinal Microbiome ; Male ; Female ; *Feces/microbiology/virology ; Middle Aged ; Prospective Studies ; *SARS-CoV-2/isolation & purification ; Longitudinal Studies ; *RNA, Ribosomal, 16S/genetics ; Adult ; Severity of Illness Index ; Convalescence ; Bacteria/classification/isolation & purification/genetics ; Aged ; },
abstract = {INTRODUCTION: Coronavirus disease 2019 (COVID-19) alters the gut microbiome. This study aimed to assess the association between the disease severity of COVID-19 and changes in stool microbes through a seven-month follow-up of stool collection.

METHODS: We conducted a multicentre, prospective longitudinal study of 58 COVID-19 patients and 116 uninfected controls. Differences in the gut microbiota were analysed using 16S ribosomal RNA sequencing. The first stool samples were collected at an early convalescent phase of COVID-19, and the second sample was collected at least seven months after COVID-19 infection.

RESULTS AND DISCUSSION: At the order level, Eubacteriales and Bifidobacteriales decreased, while Bacteroidales and Burkholderiales increased in the COVID-19 group compared to the controls. Alpha diversity also decreased in COVID-19 patients compared to controls, with imperfect recovery of the gut microbiome after seven months. The compositional change in the gut microbiome between the early and late convalescent phases was largest in the moderate and severe groups. The severity of COVID-19 was the most influential clinical variable for microbiome composition (Sum of Sqs = 0.686, P = 0.006), and its effect persisted even after partialling out other effects such as antibiotic use and age. Thus, our study indicates a possible interaction between respiratory viral infection and the composition of the gut microbiota community, warranting future mechanistic and prospective longitudinal studies. Additionally, we were able to detect microbiome changes in patients who were re-infected with SARS-CoV-2. Notably, the dominant bacteria in the re-infected group were Lachnospiraceae and Faecalimonas umbilicata, compared to the one-time infected group.},
}

Humans
*COVID-19/microbiology
*Gastrointestinal Microbiome
Male
Female
*Feces/microbiology/virology
Middle Aged
Prospective Studies
*SARS-CoV-2/isolation & purification
Longitudinal Studies
*RNA, Ribosomal, 16S/genetics
Adult
Severity of Illness Index
Convalescence
Bacteria/classification/isolation & purification/genetics
Aged

@article {pmid39551110,
year = {2025},
author = {Adenaike, AS and Akpan, U and Oyedun, IO and Adewole, FA and Agbaje, M and Olusanya, OM and Arowosegbe, MO and Ikeobi, CON},
title = {Gut microbial composition differs among FUNAAB Alpha broiler chicken genotypes raised in a tropical environment.},
journal = {Microbial pathogenesis},
volume = {198},
number = {},
pages = {107126},
doi = {10.1016/j.micpath.2024.107126},
pmid = {39551110},
issn = {1096-1208},
mesh = {Animals ; *Chickens/microbiology ; *Gastrointestinal Microbiome/genetics ; *RNA, Ribosomal, 16S/genetics ; *Genotype ; *Tropical Climate ; *Bacteria/classification/genetics/isolation & purification ; Metagenomics/methods ; Feathers/microbiology ; Bacteroidetes/genetics/isolation & purification/classification ; Phylogeny ; Firmicutes/genetics/isolation & purification/classification ; Actinobacteria/genetics/classification/isolation & purification ; Biodiversity ; DNA, Bacterial/genetics ; Gastrointestinal Tract/microbiology ; },
abstract = {The gut microbiota of FUNAAB Alpha chickens plays a crucial role in determining their overall health and performance. Understanding the various types and diversity of microbiota in the gut of different genotypes of chickens is crucial for enhancing their well-being, productivity, and disease resistance. This study employed 16S rRNA and metagenomics analysis to examine the gut bacteria of three genotypes of FUNAAB Alpha broiler chickens, namely Naked neck, Frizzle, and Normal feather. There were three phyla observed in the three genotypes: Bacteroidetes, Actinobacteria, and Firmicutes. Through the utilisation of 16S rRNA sequencing, we successfully identified and categorised the various microbiota present within the gastrointestinal tract. Our study revealed notable variations in the composition and quantity of microbiota across the three genotypes, suggesting that each genotype possesses a distinct collection of gut bacteria. A wide range of microbiological diversity was observed within the community. Interestingly, the Normal feather chicken exhibited a greater number of operational taxonomic units (OTUs) compared to the Naked neck and Frizzle feather chicken. This study presents significant findings regarding the ceacal microbiota of FUNAAB Alpha chickens, emphasising the variations observed among different genotypes. It is crucial to study composition-modification techniques to enhance host health and performance, as well as to control zoonotic pathogens that can contaminate poultry products and threaten consumers' health.},
}

Animals
*Chickens/microbiology
*Gastrointestinal Microbiome/genetics
*RNA, Ribosomal, 16S/genetics
*Genotype
*Tropical Climate
*Bacteria/classification/genetics/isolation & purification
Metagenomics/methods
Feathers/microbiology
Bacteroidetes/genetics/isolation & purification/classification
Phylogeny
Firmicutes/genetics/isolation & purification/classification
Actinobacteria/genetics/classification/isolation & purification
Biodiversity
DNA, Bacterial/genetics
Gastrointestinal Tract/microbiology

@article {pmid39367251,
year = {2024},
author = {Zheng, J and Sun, Q and Zhang, M and Liu, C and Su, Q and Zhang, L and Xu, Z and Lu, W and Ching, J and Tang, W and Cheung, CP and Hamilton, AL and Wilson O'Brien, AL and Wei, SC and Bernstein, CN and Rubin, DT and Chang, EB and Morrison, M and Kamm, MA and Chan, FKL and Zhang, J and Ng, SC},
title = {Noninvasive, microbiome-based diagnosis of inflammatory bowel disease.},
journal = {Nature medicine},
volume = {30},
number = {12},
pages = {3555-3567},
pmid = {39367251},
issn = {1546-170X},
support = {R4030-22//Research Grants Council, University Grants Committee (RGC, UGC)/ ; 14121322//Research Grants Council, University Grants Committee (RGC, UGC)/ ; 2017PG-IBD003//Leona M. and Harry B. Helmsley Charitable Trust (Helmsley Charitable Trust)/ ; 10210816//Food and Health Bureau of the Government of the Hong Kong Special Administrative Region | Health and Medical Research Fund (HMRF)/ ; 82100573//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Humans ; *Feces/microbiology ; *Inflammatory Bowel Diseases/microbiology/diagnosis ; *Crohn Disease/microbiology/diagnosis ; *Gastrointestinal Microbiome/genetics ; *Biomarkers ; *Colitis, Ulcerative/microbiology/diagnosis ; Female ; Male ; Adult ; Leukocyte L1 Antigen Complex/analysis/metabolism ; Bacteria/genetics/isolation & purification ; Metagenomics/methods ; Middle Aged ; Case-Control Studies ; Microbiota/genetics ; },
abstract = {Despite recent progress in our understanding of the association between the gut microbiome and inflammatory bowel disease (IBD), the role of microbiome biomarkers in IBD diagnosis remains underexplored. Here we developed a microbiome-based diagnostic test for IBD. By utilization of metagenomic data from 5,979 fecal samples with and without IBD from different geographies and ethnicities, we identified microbiota alterations in IBD and selected ten and nine bacterial species for construction of diagnostic models for ulcerative colitis and Crohn's disease, respectively. These diagnostic models achieved areas under the curve >0.90 for distinguishing IBD from controls in the discovery cohort, and maintained satisfactory performance in transethnic validation cohorts from eight populations. We further developed a multiplex droplet digital polymerase chain reaction test targeting selected IBD-associated bacterial species, and models based on this test showed numerically higher performance than fecal calprotectin in discriminating ulcerative colitis and Crohn's disease from controls. Here we discovered universal IBD-associated bacteria and show the potential applicability of a multibacteria biomarker panel as a noninvasive tool for IBD diagnosis.},
}

Humans
*Feces/microbiology
*Inflammatory Bowel Diseases/microbiology/diagnosis
*Crohn Disease/microbiology/diagnosis
*Gastrointestinal Microbiome/genetics
*Biomarkers
*Colitis, Ulcerative/microbiology/diagnosis
Female
Male
Adult
Leukocyte L1 Antigen Complex/analysis/metabolism
Bacteria/genetics/isolation & purification
Metagenomics/methods
Middle Aged
Case-Control Studies
Microbiota/genetics

@article {pmid39591974,
year = {2024},
author = {Peng, Y and Zhu, J and Wang, S and Liu, Y and Liu, X and DeLeon, O and Zhu, W and Xu, Z and Zhang, X and Zhao, S and Liang, S and Li, H and Ho, B and Ching, JY and Cheung, CP and Leung, TF and Tam, WH and Leung, TY and Chang, EB and Chan, FKL and Zhang, L and Ng, SC and Tun, HM},
title = {A metagenome-assembled genome inventory for children reveals early-life gut bacteriome and virome dynamics.},
journal = {Cell host & microbe},
volume = {32},
number = {12},
pages = {2212-2230.e8},
doi = {10.1016/j.chom.2024.10.017},
pmid = {39591974},
issn = {1934-6069},
mesh = {*Gastrointestinal Microbiome/genetics ; Infant ; Humans ; *Virome/genetics ; *Metagenome/genetics ; Child, Preschool ; Infant, Newborn ; Child ; Bacteriophages/genetics/isolation & purification ; Bacteria/genetics/virology/classification ; Genome, Viral/genetics ; Feces/microbiology/virology ; Metagenomics/methods ; Female ; Bifidobacterium/genetics/isolation & purification/classification ; Phylogeny ; Male ; Genome, Bacterial ; },
abstract = {Existing microbiota databases are biased toward adult samples, hampering accurate profiling of the infant gut microbiome. Here, we generated a metagenome-assembled genome inventory for children (MAGIC) from a large collection of bulk and viral-like particle-enriched metagenomes from 0 to 7 years of age, encompassing 3,299 prokaryotic and 139,624 viral species-level genomes, 8.5% and 63.9% of which are unique to MAGIC. MAGIC improves early-life microbiome profiling, with the greatest improvement in read mapping observed in Africans. We then identified 54 candidate keystone species, including several Bifidobacterium spp. and four phages, forming guilds that fluctuated in abundance with time. Their abundances were reduced in preterm infants and were associated with childhood allergies. By analyzing the B. longum pangenome, we found evidence of phage-mediated evolution and quorum sensing-related ecological adaptation. Together, the MAGIC database recovers genomes that enable characterization of the dynamics of early-life microbiomes, identification of candidate keystone species, and strain-level study of target species.},
}

*Gastrointestinal Microbiome/genetics
Infant
Humans
*Virome/genetics
*Metagenome/genetics
Child, Preschool
Infant, Newborn
Child
Bacteriophages/genetics/isolation & purification
Bacteria/genetics/virology/classification
Genome, Viral/genetics
Feces/microbiology/virology
Metagenomics/methods
Female
Bifidobacterium/genetics/isolation & purification/classification
Phylogeny
Male
Genome, Bacterial

@article {pmid39568064,
year = {2024},
author = {Sauma-Sánchez, T and Alcorta, J and Tamayo-Leiva, J and Díez, B and Bezuidenhout, H and Cowan, DA and Ramond, JB},
title = {Functional redundancy buffers the effect of poly-extreme environmental conditions on southern African dryland soil microbial communities.},
journal = {FEMS microbiology ecology},
volume = {100},
number = {12},
pages = {},
doi = {10.1093/femsec/fiae157},
pmid = {39568064},
issn = {1574-6941},
support = {FBIS160422162807//National Research Foundation/ ; 1210912//Fondo Nacional de Desarrollo Científico y Tecnológico/ ; },
mesh = {*Soil Microbiology ; *Bacteria/genetics/classification ; *Archaea/genetics/classification ; *Microbiota ; *Salinity ; *Fungi/genetics/classification ; Climate Change ; Desert Climate ; Soil/chemistry ; Extreme Environments ; Africa, Southern ; Biodiversity ; },
abstract = {Drylands' poly-extreme conditions limit edaphic microbial diversity and functionality. Furthermore, climate change exacerbates soil desiccation and salinity in most drylands. To better understand the potential effects of these changes on dryland microbial communities, we evaluated their taxonomic and functional diversities in two Southern African dryland soils with contrasting aridity and salinity. Fungal community structure was significantly influenced by aridity and salinity, while Bacteria and Archaea only by salinity. Deterministic homogeneous selection was significantly more important for bacterial and archaeal communities' assembly in hyperarid and saline soils when compared to those from arid soils. This suggests that niche partitioning drives bacterial and archaeal communities' assembly under the most extreme conditions. Conversely, stochastic dispersal limitations drove the assembly of fungal communities. Hyperarid and saline soil communities exhibited similar potential functional capacities, demonstrating a disconnect between microbial structure and function. Structure variations could be functionally compensated by different taxa with similar functions, as implied by the high levels of functional redundancy. Consequently, while environmental selective pressures shape the dryland microbial community assembly and structures, they do not influence their potential functionality. This suggests that they are functionally stable and that they could be functional even under harsher conditions, such as those expected with climate change.},
}

*Soil Microbiology
*Bacteria/genetics/classification
*Archaea/genetics/classification
*Microbiota
*Salinity
*Fungi/genetics/classification
Climate Change
Desert Climate
Soil/chemistry
Extreme Environments
Africa, Southern
Biodiversity

@article {pmid39542187,
year = {2025},
author = {Gurumayum, N and Devi, MB and Khound, P and Bhattacharya, A and Sarma, H and Khan, MR and Devi, R},
title = {Bioactive fraction of Musa balbisiana seed mitigates D-galactose-induced brain aging via SIRT1/PGC-1α/FoxO3a activation and intestinal barrier dysfunction by modulating gut microbiota and core metabolites.},
journal = {Free radical biology & medicine},
volume = {226},
number = {},
pages = {43-55},
doi = {10.1016/j.freeradbiomed.2024.11.016},
pmid = {39542187},
issn = {1873-4596},
mesh = {Animals ; *Galactose/adverse effects/toxicity ; *Gastrointestinal Microbiome/drug effects ; Rats ; *Seeds/chemistry ; *Sirtuin 1/metabolism/genetics ; *Plant Extracts/pharmacology ; *Aging/drug effects ; *Oxidative Stress/drug effects ; *Brain/metabolism/drug effects/pathology ; *Forkhead Box Protein O3/metabolism/genetics ; *Musa/chemistry ; *Peroxisome Proliferator-Activated Receptor Gamma Coactivator 1-alpha/metabolism/genetics ; Male ; Rats, Sprague-Dawley ; Glycation End Products, Advanced/metabolism ; Antioxidants/pharmacology/metabolism ; },
abstract = {Aging is an inevitable biological process, and emerging research has highlighted the potential of dietary and pharmacological interventions to decelerate the trajectory of age-related diseases and prolong the health span. This study evaluates the protective effects of Musa balbisiana seed on healthy aging using D-galactose-induced accelerated aging rats. The results suggested that the bioactive ethyl acetate fraction of Musa balbisiana seed extract (BF) exhibited protective effects against aging-induced oxidative stress by reducing oxidative DNA damage, advanced glycation end-product formation, and malondialdehyde levels while restoring antioxidant and glyoxalase enzyme activities. BF also ameliorated neurodegeneration by decreasing acetylcholinesterase enzyme activity and amyloid beta plaque formation. Histopathological analysis demonstrated the protective effects of BF against brain aging, liver disruption, renal damage, and intestinal barrier dysfunction. BF further restored intestinal permeability by upregulating the tight junctions (zonula occludens 1 and 2, claudin 1,2,3 and 4, and occludin) and mucin (mucin 2 and mucin 5ac) gene expression while downregulating the expression of inflammatory cytokines (IL-1β, IL-6, and TNF-α). BF significantly induced the phosphorylation of FoxO3a proteins and upregulated the gene expression of SIRT1, PGC-1α, and TFAM in the hippocampus. Next-generation sequencing (NGS) of 16s rRNA amplicons of fecal metagenomics DNA and metabolites profiling showed that BF intervention restructured the gut microbiota and altered core metabolites related to cholesterol metabolism. Overall, our findings demonstrated the multifaceted protective effects of Musa balbisiana seed against D-galactose-induced aging.},
}

Animals
*Galactose/adverse effects/toxicity
*Gastrointestinal Microbiome/drug effects
Rats
*Seeds/chemistry
*Sirtuin 1/metabolism/genetics
*Plant Extracts/pharmacology
*Aging/drug effects
*Oxidative Stress/drug effects
*Brain/metabolism/drug effects/pathology
*Forkhead Box Protein O3/metabolism/genetics
*Musa/chemistry
*Peroxisome Proliferator-Activated Receptor Gamma Coactivator 1-alpha/metabolism/genetics
Male
Rats, Sprague-Dawley
Glycation End Products, Advanced/metabolism
Antioxidants/pharmacology/metabolism

@article {pmid39515198,
year = {2024},
author = {De Jaeghere, EA and Hamerlinck, H and Tuyaerts, S and Lippens, L and Van Nuffel, AMT and Baiden-Amissah, R and Vuylsteke, P and Henry, S and Trinh, XB and van Dam, PA and Aspeslagh, S and De Caluwé, A and Naert, E and Lambrechts, D and Hendrix, A and De Wever, O and Van de Vijver, KK and Amant, F and Vandecasteele, K and Verhasselt, B and Denys, HG},
title = {Associations of the gut microbiome with outcomes in cervical and endometrial cancer patients treated with pembrolizumab: Insights from the phase II PRIMMO trial.},
journal = {Gynecologic oncology},
volume = {191},
number = {},
pages = {275-286},
doi = {10.1016/j.ygyno.2024.10.020},
pmid = {39515198},
issn = {1095-6859},
mesh = {Humans ; Female ; *Antibodies, Monoclonal, Humanized/adverse effects/therapeutic use/administration & dosage ; *Gastrointestinal Microbiome/drug effects ; Middle Aged ; *Uterine Cervical Neoplasms/drug therapy/microbiology/pathology ; *Endometrial Neoplasms/drug therapy/microbiology/pathology ; *Antineoplastic Agents, Immunological/adverse effects/therapeutic use ; Aged ; Adult ; Feces/microbiology ; },
abstract = {BACKGROUND: The phase II PRIMMO trial investigated a pembrolizumab-based regimen in patients with recurrent and/or metastatic cervical (CC) or endometrial (EC) carcinoma who had at least one prior line of systemic therapy. Here, exploratory studies of the gut microbiome (GM) are presented.

METHODS: The microbial composition of 77 longitudinal fecal samples obtained from 35 patients (CC, n = 15; EC, n = 20) was characterized using 16S rRNA gene sequencing. Analyses included assessment of alpha (Shannon index) and beta diversity (weighted UniFrac), unbiased hierarchical clustering, and linear discriminant analysis effect size. Correlative studies with demographics, disease characteristics, safety, efficacy, and immune monitoring data were performed.

RESULTS: Significant enrichment in multiple bacterial taxa was associated with the occurrence or resistance to severe treatment-related adverse events (overall or gastrointestinal toxicity specifically). Consistent differences in GM taxonomic composition before pembrolizumab initiation were observed between patients with favorable efficacy (e.g., enriched with Blautia genus) and those with poor efficacy (e.g., enriched with Enterobacteriaceae family and its higher-level taxa up to the phylum level, as well as Clostridium genus and its Clostridiaceae family). Two naturally occurring GM clusters with distinct bacterial compositions were identified. These clusters showed a more than four-fold differential risk for death (hazard ratio, 4.4 [95 % confidence interval, 1.9 to 10.3], P < 0.001) and were associated with interesting (but non-significant) trends in peripheral immune monitoring data.

CONCLUSION: Although exploratory, this study offers initial insights into the intricate interplay between the GM and clinical outcomes in patients with CC and EC treated with a pembrolizumab-based regimen.

TRIAL REGISTRATION: ClinicalTrials.gov (identifier NCT03192059) and EudraCT Registry (number 2016-001569-97).},
}

Humans
Female
*Antibodies, Monoclonal, Humanized/adverse effects/therapeutic use/administration & dosage
*Gastrointestinal Microbiome/drug effects
Middle Aged
*Uterine Cervical Neoplasms/drug therapy/microbiology/pathology
*Endometrial Neoplasms/drug therapy/microbiology/pathology
*Antineoplastic Agents, Immunological/adverse effects/therapeutic use
Aged
Adult
Feces/microbiology

@article {pmid39477048,
year = {2024},
author = {Vinayagam, S and Sekar, K and Rajendran, D and Meenakshisundaram, K and Panigrahi, A and Arumugam, DK and Bhowmick, IP and Sattu, K},
title = {The genetic composition of Anopheles mosquitoes and the diverse population of gut-microbiota within the Anopheles subpictus and Anopheles vagus mosquitoes in Tamil Nadu, India.},
journal = {Acta tropica},
volume = {260},
number = {},
pages = {107439},
doi = {10.1016/j.actatropica.2024.107439},
pmid = {39477048},
issn = {1873-6254},
mesh = {Animals ; *Anopheles/microbiology/genetics ; India ; *Phylogeny ; *Gastrointestinal Microbiome ; Mosquito Vectors/microbiology/genetics ; Bacteria/classification/genetics/isolation & purification ; Sequence Analysis, DNA ; Female ; DNA, Ribosomal Spacer/genetics ; },
abstract = {In recent days, in tropical and subtropical regions, secondary vectors of Anopheles mosquitoes are becoming more important in transmitting diseases to humans as primary vectors. Various molecular techniques have separated closely related Anopheles subpictus and Anopheles vagus mosquitoes based on their diversity with other mosquito species. Despite their widespread distribution, the An. subpictus and An. vagus mosquitoes, which carry Plasmodium in their salivary glands, were not considered primary malaria vectors in India. An. vagus mosquitoes are zoophilic and physically similar to An. subpictus. We intend to identify An. subpictus and An. vagus mosquito's sister species based on their Interspaced Transcribed Region-2 (ITS2). We isolated the midgut gDNA from each mosquito and used ITS2-PCR and Sanger sequencing to characterize the mosquito species. BioEdit software aligned the sequences, and MEGA7 built a phylogenetic tree from them. According to this study, the information gathered from these mosquito samples fits the An. subpictus species A form and the An. vagus Indian form. Furthermore, gut microbiome plays an important role in providing nutrients, immunity, and food processing, whereas mosquitoes' midgut microbiota changes their hosts and spreads illnesses. So, we used the Illumina sequencer to look at the gut microbiome diversity of An. subpictus and An. vagus mosquitoes using 16S rRNA-based metagenomic sequencing. Both mosquito species had an abundant phylum of Pseudomonadota (Proteobacteria), Bacillota, Bacteroidota, and Actinomycetota in their gut microbiomes. Notably, both mosquito species had the genus Serratia in their gut. In the subpictus midgut, the genus of Haematosprillum bacteria was dominant, whereas in the vagus mosquito, the genus of Salmonella was dominant. Notably, current research has observed the Sodalis spp. Bacterial genus for the first time.},
}

Animals
*Anopheles/microbiology/genetics
India
*Phylogeny
*Gastrointestinal Microbiome
Mosquito Vectors/microbiology/genetics
Bacteria/classification/genetics/isolation & purification
Sequence Analysis, DNA
Female
DNA, Ribosomal Spacer/genetics

@article {pmid39660058,
year = {2024},
author = {Boer, MD and Melkonian, C and Zafeiropoulos, H and Haas, AF and Garza, DR and Dutilh, BE},
title = {Improving genome-scale metabolic models of incomplete genomes with deep learning.},
journal = {iScience},
volume = {27},
number = {12},
pages = {111349},
pmid = {39660058},
issn = {2589-0042},
abstract = {Deciphering microbial metabolism is essential for understanding ecosystem functions. Genome-scale metabolic models (GSMMs) predict metabolic traits from genomic data, but constructing GSMMs for uncultured bacteria is challenging due to incomplete metagenome-assembled genomes, resulting in many gaps. We introduce the deep neural network guided imputation of reactomes (DNNGIOR), which uses AI to improve gap-filling by learning from the presence and absence of metabolic reactions across diverse bacterial genomes. Key factors for prediction accuracy are: (1) reaction frequency across all bacteria and (2) phylogenetic distance of the query to the training genomes. DNNGIOR predictions achieve an average F1 score of 0.85 for reactions present in over 30% of training genomes. DNNGIOR guided gap-filling was 14 times more accurate for draft reconstructions and 2-9 times for curated models than unweighted gap-filling.},
}

@article {pmid39591453,
year = {2024},
author = {Wang, L and Liu, Y and Ni, H and Zuo, W and Shi, H and Liao, W and Liu, H and Chen, J and Bai, Y and Yue, H and Huang, A and Friedman, J and Si, T and Liu, Y and Chen, M and Dai, L},
title = {Systematic characterization of plant-associated bacteria that can degrade indole-3-acetic acid.},
journal = {PLoS biology},
volume = {22},
number = {11},
pages = {e3002921},
pmid = {39591453},
issn = {1545-7885},
mesh = {*Indoleacetic Acids/metabolism ; *Oryza/microbiology/metabolism ; *Arabidopsis/microbiology/metabolism ; *Plant Roots/microbiology/metabolism ; *Bacteria/metabolism/genetics ; Plant Growth Regulators/metabolism ; Rhizosphere ; Soil Microbiology ; Phylogeny ; Operon/genetics ; Microbiota/physiology ; Seedlings/microbiology/metabolism ; },
abstract = {Plant-associated microbiota affect pant growth and development by regulating plant hormones homeostasis. Indole-3-acetic acid (IAA), a well-known plant hormone, can be produced by various plant-associated bacteria. However, the prevalence of bacteria with the capacity to degrade IAA in the rhizosphere has not been systematically studied. In this study, we analyzed the IAA degradation capabilities of bacterial isolates from the roots of Arabidopsis and rice. Using genomics analysis and in vitro assays, we found that 21 out of 183 taxonomically diverse bacterial isolates possess the ability to degrade IAA. Through comparative genomics and transcriptomic assays, we identified iac-like or iad-like operon in the genomes of these IAA degraders. Additionally, the putative regulator of the operon was found to be highly conserved among these strains through protein structure similarity analysis. Some of the IAA degraders could utilize IAA as their carbon and energy source. In planta, most of the IAA degrading strains mitigated Arabidopsis and rice seedling root growth inhibition (RGI) triggered by exogenous IAA. Moreover, RGI caused by complex synthetic bacterial community can be alleviated by introducing IAA degraders. Importantly, we observed increased colonization preference of IAA degraders from soil to root according to the frequency of the biomarker genes in metagenome-assembled genomes (MAGs) collected from different habitats, suggesting that there is a close association between IAA degraders and IAA producers. In summary, our findings further the understanding of the functional diversity and potential biological roles of plant-associated bacteria in host plant root morphogenesis.},
}

*Indoleacetic Acids/metabolism
*Oryza/microbiology/metabolism
*Arabidopsis/microbiology/metabolism
*Plant Roots/microbiology/metabolism
*Bacteria/metabolism/genetics
Plant Growth Regulators/metabolism
Rhizosphere
Soil Microbiology
Phylogeny
Operon/genetics
Microbiota/physiology
Seedlings/microbiology/metabolism

@article {pmid39513726,
year = {2024},
author = {Zou, L and Zhang, Z and Chen, J and Guo, R and Tong, X and Ju, Y and Lu, H and Yang, H and Wang, J and Zong, Y and Xu, X and Jin, X and Xiao, L and Jia, H and Zhang, T and Liu, X},
title = {Unraveling the impact of host genetics and factors on the urinary microbiome in a young population.},
journal = {mBio},
volume = {15},
number = {12},
pages = {e0277324},
doi = {10.1128/mbio.02773-24},
pmid = {39513726},
issn = {2150-7511},
mesh = {Humans ; Female ; *Microbiota/genetics ; Male ; Adult ; *Bacteria/genetics/classification/isolation & purification ; Young Adult ; Metagenomics ; China ; Host Microbial Interactions/genetics ; Urinary Tract/microbiology ; Whole Genome Sequencing ; Urine/microbiology ; Cohort Studies ; Adolescent ; },
abstract = {UNLABELLED: The significance of the urinary microbiome in maintaining health and contributing to disease development is increasingly recognized. However, a comprehensive understanding of this microbiome and its influencing factors remains elusive. Utilizing whole metagenomic and whole-genome sequencing, along with detailed metadata, we characterized the urinary microbiome and its influencing factors in a cohort of 1,579 Chinese individuals. Our findings unveil the distinctiveness of the urinary microbiome from other four body sites, delineating five unique urotypes dominated by Gardnerella vaginalis, Sphingobium fluviale, Lactobacillus iners, Variovorax sp. PDC80, and Acinetobacter junii, respectively. We identified 108 host factors significantly influencing the urinary microbiome, collectively explaining 12.92% of the variance in microbial composition. Notably, gender-related factors, including sex hormones, emerged as key determinants in defining urotype groups, microbial composition and pathways, with the urinary microbiome exhibiting strong predictive ability for gender (area under the curve [AUC] = 0.843). Furthermore, we discovered 43 genome-wide significant associations between host genetic loci and specific urinary bacteria, Acinetobacter in particular, linked to eight host loci (P < 5 × 10[-8]). These associations were also modulated by gender and sex hormone levels. In summary, our study provides novel insights into the impact of host genetics and other factors on the urinary microbiome, shedding light on its implications for host health and disease.

IMPORTANCE: The urinary microbiome, essential to human health, reveals its unique qualities in our study of 1,579 Chinese individuals. We identified distinctive microbial profiles, or "urotypes," and uncovered strong gender-related influences, particularly from sex hormones, on these microbial communities. Our research highlights significant genetic associations affecting specific urinary bacteria, indicating a deep interaction between our genetics and our microbiome. These insights not only enhance our understanding of the urinary microbiome's role in health and disease but also open new pathways for personalized medical strategies, making our findings crucial for future diagnostic and therapeutic innovations. This work underscores the intricate relationship between our body's biological processes and the microorganisms within, providing valuable knowledge for both scientific and medical communities.},
}

Humans
Female
*Microbiota/genetics
Male
Adult
*Bacteria/genetics/classification/isolation & purification
Young Adult
Metagenomics
China
Host Microbial Interactions/genetics
Urinary Tract/microbiology
Whole Genome Sequencing
Urine/microbiology
Cohort Studies
Adolescent

@article {pmid39319624,
year = {2025},
author = {Shi, Q and Fu, Q and Zhang, J and Hao, G and Liang, C and Duan, F and Ma, J and Zhao, H and Song, W},
title = {Paenibacillus polymyxa J2-4 induces cucumber to enrich rhizospheric Pseudomonas and contributes to Meloidogyne incognita management under field conditions.},
journal = {Pest management science},
volume = {81},
number = {1},
pages = {266-276},
doi = {10.1002/ps.8429},
pmid = {39319624},
issn = {1526-4998},
support = {2023YFD1400400//National Key R&D Program of China/ ; 2022CXGC020710-6//Subproject of Shandong Province Key R&D Plan Project/ ; QNYCX23027//Qingdao Agricultural University Graduate Student Innovation Program/ ; QNYCX24076//Qingdao Agricultural University Graduate Student Innovation Program/ ; },
mesh = {*Tylenchoidea/physiology ; Animals ; *Paenibacillus polymyxa/genetics/physiology ; *Pseudomonas/physiology ; *Rhizosphere ; *Cucumis sativus/microbiology/parasitology ; *Plant Diseases/prevention & control/parasitology/microbiology ; Soil Microbiology ; Pest Control, Biological ; Microbiota ; },
abstract = {BACKGROUND: Root knot nematodes (RKNs) pose a great threat to agricultural production worldwide. The bacterial nematocides have received increasing attention due to their safe and efficient control against RKNs. Here, we investigated the biocontrol efficacy of Paenibacillus polymyxa J2-4 against Meloidogyne incognita in the field and analyzed the rhizosphere microbiome of cucumber under nematode infection after application of the J2-4 strain. Furthermore, a biomarker strain of Pseudomonas spp. was isolated from the J2-4-inoculated rhizosphere soil, and its nematocidal activity and growth-promoting effect on host plants were determined. In addition, chemotaxis assay of P. fluroescens ZJ5 toward root exudates was carried out.

RESULTS: The field experiment demonstrated that P. polymyxa J2-4 could effectively suppressed gall formation in cucumber plants, with the galling index reduced by 67.63% in 2022 and 65.50% in 2023, respectively, compared with controls. Meanwhile, plant height and yield were significantly increased in J2-4 treated plants compared with controls. Metagenomic analysis indicated that J2-4 altered the rhizosphere microbial communities. The relative abundance of Pseudomonas spp. was notably enhanced in the J2-4 group, which was consistent with Linear discriminant analysis Effect Size results that Pseudomonas was determined as one of the biomarkers in the J2-4 group. Furthermore, the ZJ5 strain, one of the biomarker Pseudomonas strains, was isolated from the J2-4-inoculated rhizosphere soil and was identified as Pseudomonas fluorescens. In addition, P. fluorescens ZJ5 exhibited high nematicidal activity in vitro and in vivo, with 99.20% of the mortality rate of M. incognita at 24 h and 69.75% of gall index reduction. The biocontrol efficiency of the synthetic community of ZJ5 plus J2-4 was superior to that of any other single bacteria against M. incognita. Additionally, ZJ5 exhibited great chemotaxis ability toward root exudates inoculated with J2-4.

CONCLUSION: Paenibacillus polymyxa J2-4 has good potential in the biological control against M. incognita under field conditions. Enrichment of the beneficial bacteria Pseudomonas fluorescens ZJ5 in the J2-4-inoculated rhizosphere soil contributes to M. incognita management. © 2024 Society of Chemical Industry.},
}

*Tylenchoidea/physiology
Animals
*Paenibacillus polymyxa/genetics/physiology
*Pseudomonas/physiology
*Rhizosphere
*Cucumis sativus/microbiology/parasitology
*Plant Diseases/prevention & control/parasitology/microbiology
Soil Microbiology
Pest Control, Biological
Microbiota

@article {pmid38839073,
year = {2024},
author = {Davies, JM and Teh, JJ and Ewais, T and Begun, J},
title = {Does Improving Depression Symptoms in Young Adults With Inflammatory Bowel Disease Alter Their Microbiome?.},
journal = {Inflammatory bowel diseases},
volume = {30},
number = {12},
pages = {2428-2439},
pmid = {38839073},
issn = {1536-4844},
mesh = {Humans ; Male ; Female ; Young Adult ; *Depression/microbiology/therapy ; *Feces/microbiology ; Adolescent ; *Inflammatory Bowel Diseases/microbiology/psychology/therapy ; *Gastrointestinal Microbiome ; Adult ; Cross-Sectional Studies ; Cognitive Behavioral Therapy/methods ; Anxiety/microbiology/etiology/therapy ; Longitudinal Studies ; },
abstract = {BACKGROUND: Patients with inflammatory bowel diseases (IBDs) are more likely to have depression and anxiety symptoms compared with healthy individuals and those with other chronic illnesses. Previous studies have shown a link between the microbiome composition and depression symptoms; however, many antidepressant medications have antibacterial activity confounding cross-sectional studies of these populations. Therefore, we aimed to determine whether we could detect longitudinal changes in the microbiome of a subset of patients who participated in a previously published mindfulness-based cognitive therapy (MBCT) study to improve depression symptoms in adolescents and young adults with IBD.

METHODS: Stool samples were collected at baseline and 8 weeks (n = 24 participants, 37 total samples, 13 paired samples). During this time, some participants achieved a 50% reduction in their depression symptoms either through MBCT or treatment as usual with their mental health team (responders). The microbiome composition and function of responders were compared with participants who did not improve their depression scores (nonresponders). Depression scores were determined using the depression, anxiety, and stress score (DASS-21), and metagenomic sequencing of stool samples was performed.

RESULTS: No difference in alpha diversity was found between responders and nonresponders. Beta diversity measures were similarly unchanged. Clinical features including fecal calprotectin, C-reactive protein, and serum IL-6 levels were unchanged.

CONCLUSIONS: In this small longitudinal study, we were not able to detect longitudinal changes in the microbiome associated with improvement in depression scores. Follow-up studies that are sufficiently powered to detect changes in the microbiome are required to confirm our results.},
}

Humans
Male
Female
Young Adult
*Depression/microbiology/therapy
*Feces/microbiology
Adolescent
*Inflammatory Bowel Diseases/microbiology/psychology/therapy
*Gastrointestinal Microbiome
Adult
Cross-Sectional Studies
Cognitive Behavioral Therapy/methods
Anxiety/microbiology/etiology/therapy
Longitudinal Studies

@article {pmid39657789,
year = {2024},
author = {Zdouc, MM and Blin, K and Louwen, NLL and Navarro, J and Loureiro, C and Bader, CD and Bailey, CB and Barra, L and Booth, TJ and Bozhüyük, KAJ and Cediel-Becerra, JDD and Charlop-Powers, Z and Chevrette, MG and Chooi, YH and D'Agostino, PM and de Rond, T and Del Pup, E and Duncan, KR and Gu, W and Hanif, N and Helfrich, EJN and Jenner, M and Katsuyama, Y and Korenskaia, A and Krug, D and Libis, V and Lund, GA and Mantri, S and Morgan, KD and Owen, C and Phan, CS and Philmus, B and Reitz, ZL and Robinson, SL and Singh, KS and Teufel, R and Tong, Y and Tugizimana, F and Ulanova, D and Winter, JM and Aguilar, C and Akiyama, DY and Al-Salihi, SAA and Alanjary, M and Alberti, F and Aleti, G and Alharthi, SA and Rojo, MYA and Arishi, AA and Augustijn, HE and Avalon, NE and Avelar-Rivas, JA and Axt, KK and Barbieri, HB and Barbosa, JCJ and Barboza Segato, LG and Barrett, SE and Baunach, M and Beemelmanns, C and Beqaj, D and Berger, T and Bernaldo-Agüero, J and Bettenbühl, SM and Bielinski, VA and Biermann, F and Borges, RM and Borriss, R and Breitenbach, M and Bretscher, KM and Brigham, MW and Buedenbender, L and Bulcock, BW and Cano-Prieto, C and Capela, J and Carrion, VJ and Carter, RS and Castelo-Branco, R and Castro-Falcón, G and Chagas, FO and Charria-Girón, E and Chaudhri, AA and Chaudhry, V and Choi, H and Choi, Y and Choupannejad, R and Chromy, J and Donahey, MSC and Collemare, J and Connolly, JA and Creamer, KE and Crüsemann, M and Cruz, AA and Cumsille, A and Dallery, JF and Damas-Ramos, LC and Damiani, T and de Kruijff, M and Martín, BD and Sala, GD and Dillen, J and Doering, DT and Dommaraju, SR and Durusu, S and Egbert, S and Ellerhorst, M and Faussurier, B and Fetter, A and Feuermann, M and Fewer, DP and Foldi, J and Frediansyah, A and Garza, EA and Gavriilidou, A and Gentile, A and Gerke, J and Gerstmans, H and Gomez-Escribano, JP and González-Salazar, LA and Grayson, NE and Greco, C and Gomez, JEG and Guerra, S and Flores, SG and Gurevich, A and Gutiérrez-García, K and Hart, L and Haslinger, K and He, B and Hebra, T and Hemmann, JL and Hindra, H and Höing, L and Holland, DC and Holme, JE and Horch, T and Hrab, P and Hu, J and Huynh, TH and Hwang, JY and Iacovelli, R and Iftime, D and Iorio, M and Jayachandran, S and Jeong, E and Jing, J and Jung, JJ and Kakumu, Y and Kalkreuter, E and Kang, KB and Kang, S and Kim, W and Kim, GJ and Kim, H and Kim, HU and Klapper, M and Koetsier, RA and Kollten, C and Kovács, ÁT and Kriukova, Y and Kubach, N and Kunjapur, AM and Kushnareva, AK and Kust, A and Lamber, J and Larralde, M and Larsen, NJ and Launay, AP and Le, NT and Lebeer, S and Lee, BT and Lee, K and Lev, KL and Li, SM and Li, YX and Licona-Cassani, C and Lien, A and Liu, J and Lopez, JAV and Machushynets, NV and Macias, MI and Mahmud, T and Maleckis, M and Martinez-Martinez, AM and Mast, Y and Maximo, MF and McBride, CM and McLellan, RM and Bhatt, KM and Melkonian, C and Merrild, A and Metsä-Ketelä, M and Mitchell, DA and Müller, AV and Nguyen, GS and Nguyen, HT and Niedermeyer, THJ and O'Hare, JH and Ossowicki, A and Ostash, BO and Otani, H and Padva, L and Paliyal, S and Pan, X and Panghal, M and Parade, DS and Park, J and Parra, J and Rubio, MP and Pham, HT and Pidot, SJ and Piel, J and Pourmohsenin, B and Rakhmanov, M and Ramesh, S and Rasmussen, MH and Rego, A and Reher, R and Rice, AJ and Rigolet, A and Romero-Otero, A and Rosas-Becerra, LR and Rosiles, PY and Rutz, A and Ryu, B and Sahadeo, LA and Saldanha, M and Salvi, L and Sánchez-Carvajal, E and Santos-Medellin, C and Sbaraini, N and Schoellhorn, SM and Schumm, C and Sehnal, L and Selem, N and Shah, AD and Shishido, TK and Sieber, S and Silviani, V and Singh, G and Singh, H and Sokolova, N and Sonnenschein, EC and Sosio, M and Sowa, ST and Steffen, K and Stegmann, E and Streiff, AB and Strüder, A and Surup, F and Svenningsen, T and Sweeney, D and Szenei, J and Tagirdzhanov, A and Tan, B and Tarnowski, MJ and Terlouw, BR and Rey, T and Thome, NU and Torres Ortega, LR and Tørring, T and Trindade, M and Truman, AW and Tvilum, M and Udwary, DW and Ulbricht, C and Vader, L and van Wezel, GP and Walmsley, M and Warnasinghe, R and Weddeling, HG and Weir, ANM and Williams, K and Williams, SE and Witte, TE and Rocca, SMW and Yamada, K and Yang, D and Yang, D and Yu, J and Zhou, Z and Ziemert, N and Zimmer, L and Zimmermann, A and Zimmermann, C and van der Hooft, JJJ and Linington, RG and Weber, T and Medema, MH},
title = {MIBiG 4.0: advancing biosynthetic gene cluster curation through global collaboration.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkae1115},
pmid = {39657789},
issn = {1362-4962},
support = {KICH1.LWV04.21.013//NWO/ ; 101000392//Horizon 2020/ ; OSF.23.1.044//NWO Open Science Project 'BiG-CODEC'/ ; 547394769//German Research Foundation/ ; //University of Sydney/ ; NNF22OC0078997//Novo Nodisk Foundation/ ; IM230100154//Australian Research Council Industry Fellowship/ ; //Hans Fischer Society/ ; //UK Government Department for Environment, Food & Rural Affairs (DEFRA) Global Centre on Biodiversity for the Climate/ ; EP/X03142X/1//United Kingdom Research and Innovation/ ; 101072485//Horizon Europe Marie Skłodowska-Curie/ ; //Indonesia Endowment Fund for Education Agency (LPDP)/ ; 106/IV/KS/11/2023//National Research and Innovation Agency/ ; 027/E5/PG.02.00.PL/2024//Ministry of Education/ ; MR/W011247/1//UKRI Future Leaders Fellowship/ ; 101117891-MeDiSyn//ERC Starting/ ; ANR-22-CE44-0011-01 UMISYN//Agence Nationale de la Recherche/ ; BB/X010953/1//Growing Health Institute Strategic Programme/ ; //Department of Biotechnology/ ; //National Agri-Food Biotechnology Institute/ ; 101087181//EU/ ; 212747/SNSF_/Swiss National Science Foundation/Switzerland ; 2021YFA0909500//National Key Research and Development Program of China/ ; 32170080//National Natural Science Foundation of China/ ; //Shanghai Pilot Program for Basic Research - Shanghai Jiao Tong University/ ; 21K06336//KAKENHI/ ; 21/07038-0//São Paulo Research Foundation/ ; VI.Veni.202.130//NWO Talent/ ; MR/V022334/1//UKRI Future Leaders Fellowship/ ; 222676//USDA Evans-Allen Research/ ; F32AT011475/AT/NCCIH NIH HHS/United States ; DGE 21-46756//National Science Foundation Graduate Research Fellowship/ ; //University of Illinois/ ; 802736//European Union Horizon 2020/ ; 735867//Consejo Nacional de Ciencia y Tecnología/ ; //NWO Merian/ ; BB/T007222/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 101066127//European Union/ ; RYC2020-029240-I//Ministerio de Ciencia, Innovación y Universidades/ ; K12 GM068524/GM/NIGMS NIH HHS/United States ; //HZI POF IV Cooperativity and Creativity Project Call/ ; //Alexander von Humboldt-Stiftung/ ; EXC-2124/1-09.029_0//Cluster of Excellence: Controlling Microbes to Fight Infection/ ; NRF-2020R1A6A1A03044512//Korean Government (MSIT)/ ; 2022R1C1C2004118//National Research Foundation of Korea/ ; NE/T010959/1//Signals in the Soil/ ; CZIF2022-007203//Chan Zuckerberg Initiative Foundation/ ; 495740318//German Research Foundation/ ; ANR-24-CE20-7299-01//Agence Nationale de la Recherche/ ; ANR-17-EUR-0007//EUR Saclay Plant Sciences-SPS/ ; 101072485//European Union's Horizon/ ; //European Regional Development Fund/ ; 802736//European Union's Horizon 2020/ ; EP/X03142X/1//United Kingdom Research and Innovation/ ; //Swiss Federal Government/ ; PS00349981//Fulbright/ ; 398967434-TRR 261//Deutsche Forschungsgemeinschaft/ ; DM60066//Italian Ministry of Research/ ; 1229222N//Research Foundation-Flanders (FWO)/ ; R01-GM146224/GM/NIGMS NIH HHS/United States ; NA22NOS4200050//NERRS/ ; BB/V005723/2//BBSRC/ ; 1347411//CONAHCYT/ ; T32GM136583/NH/NIH HHS/United States ; 101130799//European Union's Horizon/ ; CFB 2.0//Novo Nordisk Foundation/ ; //Basic Science Research Program/ ; NRF-RS-2024-00352229//Ministry of Science and ICT/ ; NRF 2018R1A5A2023127//Korea Government (MSIT)/ ; //Werner Siemens Foundation/ ; OCENW.XL21.XL21.088//NWO-XL/ ; DNRF137//Danish National Research Foundation/ ; NNF19SA0059360//Novo Nordisk Foundation INTERACT/ ; CBET-2032243//U.S. National Science Foundation/ ; //Delta Stewardship Council Delta Science Program/ ; //European Union's Horizon 2020 Research/ ; 852600//Innovation Program ERC St/ ; 101072485//European Union's Horizon Europe/ ; //Conahcyt Mexico International PhD Studentship/ ; //Strathclyde University Global Research Scholarship/ ; 3141-00013A//Innovation Fund Denmark/ ; K445/2022//Leibniz Association/ ; 23/01956-2//São Paulo Research Foundation/ ; DGE 2241144//NSF GRFP/ ; 024.004.014//MiCRop Consortium/ ; CF22-1239//Carlsberg Foundation/ ; 102022750//SINTEF/ ; 102029187//SEP AGREE/ ; 102024676-14//POS BIOINFO 2024/ ; 101106349//Marie Sklodowska-Curie/ ; 57/0009//Ministry of Education and Science of Ukraine/ ; //National Research Fund of Ukraine/ ; DE-AC02-05CH11231//U.S. Department of Energy/ ; //German Academic Scholarship Foundation/ ; OCENW.GROOT.2019.063//NWO-XL/ ; //Department of Biotechnology/ ; //University Grants Commission/ ; PROYEXCEL_00012//Spanish "Junta de Andalucía"/ ; GNT2021638//National Health and Medical Research Council/ ; DP230102668//Australian Research Council Discovery Project/ ; 101000794//SECRETed EU Project Horizon 2020/ ; 865738/ERC_/European Research Council/International ; T32-GM136629//Chemical-Biology Interface Training/ ; DGE 21-46756//National Science Foundation Graduate Research Fellowship/ ; 101055020-COMMUNITY//ERC Advanced/ ; 757173//Consejo Nacional de Ciencia y Tecnología/ ; //Horizon Europe Marie Skłodowska-Curie Actions Postdoctoral Fellowship/ ; 101099528//European Innovation Council/ ; 10062709//UK Innovation Funding Agency (UKRI)/ ; //Swedish Pharmaceutical Society PostDoc/ ; 205320_219638/SNSF_/Swiss National Science Foundation/Switzerland ; //Saarland University/ ; BB/X01097X/1//BBSRC Institute Strategic Program/ ; AUFF-E-2022-9-42//AUFF/ ; 101055020-COMMUNITY//ERC Advanced/ ; NNF22OC0079021//Novo Nordisk Foundation Postdoctoral Fellowship/ ; //Natural Science and Research Council of Canada/ ; TTU 09.826//German Center for Infection Research/ ; 10.55776/P 34036//Austrian Science Fund/ ; //Natural Sciences and Engineering Research Council of Canada Discovery/ ; DNRF137//Danish National Research Foundation CeMiSt/ ; },
abstract = {Specialized or secondary metabolites are small molecules of biological origin, often showing potent biological activities with applications in agriculture, engineering and medicine. Usually, the biosynthesis of these natural products is governed by sets of co-regulated and physically clustered genes known as biosynthetic gene clusters (BGCs). To share information about BGCs in a standardized and machine-readable way, the Minimum Information about a Biosynthetic Gene cluster (MIBiG) data standard and repository was initiated in 2015. Since its conception, MIBiG has been regularly updated to expand data coverage and remain up to date with innovations in natural product research. Here, we describe MIBiG version 4.0, an extensive update to the data repository and the underlying data standard. In a massive community annotation effort, 267 contributors performed 8304 edits, creating 557 new entries and modifying 590 existing entries, resulting in a new total of 3059 curated entries in MIBiG. Particular attention was paid to ensuring high data quality, with automated data validation using a newly developed custom submission portal prototype, paired with a novel peer-reviewing model. MIBiG 4.0 also takes steps towards a rolling release model and a broader involvement of the scientific community. MIBiG 4.0 is accessible online at https://mibig.secondarymetabolites.org/.},
}

@article {pmid39654977,
year = {2024},
author = {Wu, J and Wang, D and He, WJ and Li, JY and Mo, X and Li, YJ},
title = {Allergen-specific sublingual immunotherapy altered gut microbiota in patients with allergic rhinitis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1454333},
pmid = {39654977},
issn = {2235-2988},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Sublingual Immunotherapy/methods ; *Rhinitis, Allergic/therapy/microbiology/immunology ; Male ; Female ; Adult ; *Feces/microbiology ; Allergens/immunology ; Young Adult ; Animals ; Middle Aged ; Antigens, Dermatophagoides/immunology ; Dermatophagoides farinae/immunology ; Treatment Outcome ; Adolescent ; Metagenomics/methods ; },
abstract = {INTRODUCTION: Allergen-specific immunotherapy (AIT) induces long-term immune tolerance to allergens and is effective for treating allergic rhinitis (AR). However, the impact of sublingual immunotherapy (SLIT) on gut microbiota from AR patients and its correlation with treatment efficacy remains unclear.

METHODS: In the present study, we enrolled 24 AR patients sensitized to Dermatophagoides farinae (Der-f) and 6 healthy donors (HD). All AR patients received SLIT treatment using standardized Der-f drops. Stool samples were collected from AR patients before treatment, and 1- and 3-months post-treatment, as well as from HD, for metagenomic sequencing analysis.

RESULTS: AR patients had significantly lower richness and diversity in gut microbiota compared to HD, with notable alterations in composition and function. Besides, three months post-SLIT treatment, significant changes in gut microbiota composition at the genus and species levels were observed in AR patients. Streptococcus parasanguinis_B and Streptococcus parasanguinis, which were significantly lower in AR patients compared to HD, increased notably after three months of treatment. LEfSe analysis identified these species as markers distinguishing HD from AR patients and AR patients pre- from post-SLIT treatment. Furthermore, changes in the relative abundance of S. parasanguinis_B were negatively correlated with changes in VAS scores but positively correlated with changes in RCAT scores, suggesting a positive correlation with effective SLIT treatment.

DISCUSSION: SLIT treatment significantly alters the gut microbiota of AR patients, with S. parasanguinis_B potentially linked to its effectiveness. This study offers insights into SLIT mechanisms and suggests that specific strains may serve as biomarkers for predicting SLIT efficacy and as modulators for improving SLIT efficacy.},
}

Humans
*Gastrointestinal Microbiome
*Sublingual Immunotherapy/methods
*Rhinitis, Allergic/therapy/microbiology/immunology
Male
Female
Adult
*Feces/microbiology
Allergens/immunology
Young Adult
Animals
Middle Aged
Antigens, Dermatophagoides/immunology
Dermatophagoides farinae/immunology
Treatment Outcome
Adolescent
Metagenomics/methods

@article {pmid39654975,
year = {2024},
author = {Jarmukhanov, Z and Mukhanbetzhanov, N and Vinogradova, E and Kozhakhmetov, S and Kushugulova, A},
title = {Gut metagenomic features of frailty.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1486579},
pmid = {39654975},
issn = {2235-2988},
mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; *Frailty/microbiology/metabolism ; Male ; Female ; Aged ; Middle Aged ; *Feces/microbiology ; *Metagenomics/methods ; Kazakhstan ; Adult ; Metagenome ; Bacteria/classification/genetics/isolation & purification/metabolism ; Aged, 80 and over ; Metabolic Networks and Pathways/genetics ; },
abstract = {This study investigates the relationship between frailty severity and gut microbiome characteristics in adults in Kazakhstan. We analyzed 158 participants across four frailty severity (mild to very severe) using metagenomic sequencing of stool samples. Frailty was significantly correlated with age, weight, and functional measures like walking speed and grip strength. Microbial diversity decreased significantly with increasing frailty. Beta diversity analysis revealed distinct clustering patterns based at phylum level. Taxonomically, we observed a significant inverse correlation between Firmicutes abundance and frailty. Classes like Clostridia and Erysipelotrichia decreased with frailty, while Bacteroidia and Actinobacteria increased. At the family level, Oscillospiraceae showed a positive correlation with frailty. Functionally, we identified significant correlations between frailty measures and specific metabolic pathways. The frailty index negatively correlated with pathways involved in cobalamin, arginine and molybdenum cofactor biosynthesis and positively correlated with folate biosynthesis. Physical performance measures strongly correlated with pathways related to nucleotide biosynthesis, and one-carbon metabolism. We propose these identified features may constitute a "frailty-associated metabolic signature" in the gut microbiome. This signature suggests multiple interconnected mechanisms through which the microbiome may influence frailty development, including modulation of inflammation, alterations in energy metabolism, and potential impacts on muscle function through microbial metabolites.},
}

*Gastrointestinal Microbiome/genetics
Humans
*Frailty/microbiology/metabolism
Male
Female
Aged
Middle Aged
*Feces/microbiology
*Metagenomics/methods
Kazakhstan
Adult
Metagenome
Bacteria/classification/genetics/isolation & purification/metabolism
Aged, 80 and over
Metabolic Networks and Pathways/genetics

@article {pmid39577368,
year = {2025},
author = {Yang, L and Yao, B and Zhang, S and Yang, Y and Wang, G and Pan, H and Zeng, X and Qiao, S},
title = {Division mechanism of labor in Diqing Tibetan Pigs gut microbiota for dietary fiber efficiently utilization.},
journal = {Microbiological research},
volume = {290},
number = {},
pages = {127977},
doi = {10.1016/j.micres.2024.127977},
pmid = {39577368},
issn = {1618-0623},
mesh = {Animals ; *Gastrointestinal Microbiome ; *Dietary Fiber/metabolism ; Swine ; *Animal Feed ; *Feces/microbiology ; Tibet ; Bacteria/classification/genetics/metabolism/isolation & purification ; Metagenomics ; Xylose/metabolism ; Glycoside Hydrolases/metabolism ; Lactobacillus/metabolism/genetics ; },
abstract = {The Diqing Tibetan (TP) pig is an roughage tolerance breed that inhabits an area with the highest altitude distribution in the world and can be maintained on a diet containing 90 % forage material in confined production systems. Our results showed that TP pigs had a strong capability for high-efficiency utilization of arabinose and xylose. Metagenomic analysis revealed that the secretion of carbohydrate esterases was mainly undertaken by fecal strains of Microbacterium, Alistipes, Acinetobacter, and Faecalibacterium, while Microbacterium, Prevotella, Turicibacter, Lactobacillus, Clostridium, and Streptococcus were responsible for most of the secretion of glycoside hydrolases. Then, a brand new species, which was named Microbacterium sp. Qiao 01 was captured and appeared to have the highest fiber utilization ability in vitro, degrading 36.54 % of the neutral detergent fiber in corn stover. Our results provide strong evidence that efficient utilization of dietary fiber by TP pigs is due to the emergence of highly specialized microbial strategies in the gut. Microorganisms showed preferences and a clear division of labor in the degradation process of dietary fiber. This study has great practical significance for improving the utilization efficiency of livestock feed and alleviating the tension of food insecurity.},
}

Animals
*Gastrointestinal Microbiome
*Dietary Fiber/metabolism
Swine
*Animal Feed
*Feces/microbiology
Tibet
Bacteria/classification/genetics/metabolism/isolation & purification
Metagenomics
Xylose/metabolism
Glycoside Hydrolases/metabolism
Lactobacillus/metabolism/genetics

@article {pmid39544117,
year = {2024},
author = {Roslund, MI and Galitskaya, P and Saarenpää, M and Sinkkonen, A},
title = {Cultivar-dependent differences in plant bud microbiome and functional gene pathways in woody plants commonly used in urban green space.},
journal = {Letters in applied microbiology},
volume = {77},
number = {12},
pages = {},
doi = {10.1093/lambio/ovae110},
pmid = {39544117},
issn = {1472-765X},
support = {346 136//Strategic Research Council/ ; },
mesh = {*Microbiota ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation & purification ; Metagenome ; Archaea/genetics/classification ; Plants/microbiology ; Humans ; Phylogeny ; Metagenomics ; },
abstract = {Plant richness and microbiota have been associated with plant health; hardly any studies have investigated how plant taxa differs in microbiota in the context of human health. We investigated the microbial differences in buds of 83 woody plant taxa used in urban green spaces in hemiboreal climate, using 16S rRNA and whole metagenome shotgun sequencing. Bud microbial community was the richest in Cotoneaster Nanshan and C. integerrimus, and Malus domestica cultivars "Sandra" and "Lobo" and poorest in Ribes glandulosum. Metagenomic shotgun sequencing of two M. domestica and four Ribes varieties confirmed differences in taxa in bud microbiota and indicated higher siderophore synthesis in Malus. Microbial richness, including bacteria, archaea, and viruses, and functional richness of gene pathways was higher in Malus compared to Ribes. The 10 most abundant amplicon sequence units, often referred as species, belonged to the phylum Proteobacteria. The differences between plant taxa were evident in classes Alpha- and Gammaproteobacteria, known for potential human health benefits. Since environmental microbiota contributes to human microbiota and immunoregulation, horticultural cultivars hosting rich microbiota may have human health benefits. Further studies are needed to confirm the effectiveness of microbially-oriented plant selection in optimizing human microbiota and planetary health.},
}

*Microbiota
*RNA, Ribosomal, 16S/genetics
*Bacteria/genetics/classification/isolation & purification
Metagenome
Archaea/genetics/classification
Plants/microbiology
Humans
Phylogeny
Metagenomics

@article {pmid39508239,
year = {2024},
author = {Dames, NR and Rocke, E and Pitcher, G and Rybicki, E and Pfaff, M and Moloney, CL},
title = {Ecological roles of nano-picoplankton in stratified waters of an embayment in the southern Benguela.},
journal = {FEMS microbiology letters},
volume = {371},
number = {},
pages = {},
doi = {10.1093/femsle/fnae094},
pmid = {39508239},
issn = {1574-6968},
support = {116142//National Research Foundation/ ; },
mesh = {South Africa ; *Archaea/classification/metabolism/isolation & purification/genetics ; *Bacteria/classification/metabolism/genetics/isolation & purification ; Plankton/classification ; Microbiota ; Seawater/microbiology/chemistry ; Bays/microbiology ; Ecosystem ; Eukaryota/classification/physiology ; },
abstract = {Nano-picoplankton are the dominant primary producers during the postupwelling period in St Helena Bay, South Africa. Their dynamics on short timescales are not well-understood and neither are the community composition, structure, and potential functionality of the surrounding microbiome. Samples were collected over five consecutive days in March 2018 from three depths (1, 25, and 50 m) at a single sampling station in St Helena Bay. There was clear depth-differentiation between the surface and depth in both diversity and function throughout the sampling period for the archaea, bacteria, and eukaryotes. Daily difference in eukaryote diversity, was more pronounced at 1 and 25 m with increased abundances of Syndiniales and Bacillariophyta. Surface waters were dominated by photosynthetic and photoheterotrophic microorganisms, while samples at depth were linked to nitrogen cycling processes, with high abundances of nitrifiers and denitrifiers. Strong depth gradients found in the nutrient transporters for ammonia were good indicators of measured uptake rates. This study showed that nano-picoplankton dynamics were driven by light availability, nutrient concentrations, carbon biomass, and oxygenation. The nano-picoplankton help sustain ecosystem functioning in St Helena Bay through their ecological roles, which emphasizes the need to monitor this size fraction of the plankton.},
}

South Africa
*Archaea/classification/metabolism/isolation & purification/genetics
*Bacteria/classification/metabolism/genetics/isolation & purification
Plankton/classification
Microbiota
Seawater/microbiology/chemistry
Bays/microbiology
Ecosystem
Eukaryota/classification/physiology

@article {pmid39221872,
year = {2025},
author = {Wang, Z and Xu, M and Li, Q and Lu, S and Liu, Z},
title = {Subchronic Chloroform Exposure Causes Intestinal Damage and Induces Gut Microbiota Disruption and Metabolic Dysregulation in Mice.},
journal = {Environmental toxicology},
volume = {40},
number = {1},
pages = {5-18},
doi = {10.1002/tox.24417},
pmid = {39221872},
issn = {1522-7278},
support = {LH2021C095//Natural Science Foundation of Heilongjiang Province of China/ ; 1452TD008//Heilongjiang Provincial Department of Education filing project/ ; 1451TD002//Heilongjiang Provincial Department of Education filing project/ ; },
mesh = {Animals ; *Chloroform/toxicity ; *Gastrointestinal Microbiome/drug effects ; Female ; Mice ; Cecum/microbiology/drug effects ; Intestines/drug effects/microbiology/pathology ; Environmental Pollutants/toxicity ; },
abstract = {Chloroform is a prevalent toxic environmental pollutant in urban settings, posing risks to human health through exposure via various mediums such as air and tap water. The gut microbiota plays a pivotal role in maintaining host health. However, there is a paucity of research elucidating the impact of chloroform exposure on the gut microbiota. In this investigation, 18 SPF Kunming female mice were stratified into three groups (n = 6) and subjected to oral gavage with chloroform doses equivalent to 0, 50, and 150 mg/kg of body weight over 30 days. Our findings demonstrate that subchronic chloroform exposure significantly perturbs hematological parameters in mice and induces histopathological alterations in cecal tissues, consequently engendering marked disparities in the functional composition of cecal microbiota and metabolic equilibrium of cecal contents. Ultimately, our investigation revealed a statistically robust correlation, exhibiting a high degree of significance, between the intestinal microbiome composition and the metabolites that were differentially expressed consequent to chloroform exposure.},
}

Animals
*Chloroform/toxicity
*Gastrointestinal Microbiome/drug effects
Female
Mice
Cecum/microbiology/drug effects
Intestines/drug effects/microbiology/pathology
Environmental Pollutants/toxicity

@article {pmid39084687,
year = {2024},
author = {Jiang, S and Cai, M and Li, D and Chen, X and Chen, X and Huang, Q and Zhong, C and Zheng, X and Zhou, D and Chen, Z and Zhang, L and Ching, JY and Chen, A and Lu, S and Zhang, L and Hu, L and Liao, Y and Li, Y and He, Z and Wu, J and Huo, H and Liang, Y and Li, W and Zou, Y and Luo, W and Ng, SC and Chan, FK and Chen, X and Deng, Y},
title = {Association of breast milk-derived arachidonic acid-induced infant gut dysbiosis with the onset of atopic dermatitis.},
journal = {Gut},
volume = {74},
number = {1},
pages = {45-57},
doi = {10.1136/gutjnl-2024-332407},
pmid = {39084687},
issn = {1468-3288},
mesh = {*Dermatitis, Atopic/microbiology/metabolism/etiology ; Humans ; *Milk, Human/chemistry ; *Dysbiosis/metabolism/microbiology ; *Gastrointestinal Microbiome ; Infant ; Female ; Animals ; *Arachidonic Acid/metabolism ; *Feces/microbiology ; Mice ; Infant, Newborn ; Male ; Breast Feeding ; },
abstract = {OBJECTIVE: The specific breast milk-derived metabolites that mediate host-microbiota interactions and contribute to the onset of atopic dermatitis (AD) remain unknown and require further investigation.

DESIGN: We enrolled 250 mother-infant pairs and collected 978 longitudinal faecal samples from infants from birth to 6 months of age, along with 243 maternal faecal samples for metagenomics. Concurrently, 239 corresponding breast milk samples were analysed for metabolomics. Animal and cellular experiments were conducted to validate the bioinformatics findings.

RESULTS: The clinical findings suggested that a decrease in daily breastfeeding duration was associated with a reduced incidence of AD. This observation inspired us to investigate the effects of breast milk-derived fatty acids. We found that high concentrations of arachidonic acid (AA), but not eicosapentaenoic acid (EPA) or docosahexaenoic acid, induced gut dysbiosis in infants. Further investigation revealed that four specific bacteria degraded mannan into mannose, consequently enhancing the mannan-dependent biosynthesis of O-antigen and lipopolysaccharide. Correlation analysis confirmed that in infants with AD, the abundance of Escherichia coli under high AA concentrations was positively correlated with some microbial pathways (eg, 'GDP-mannose-derived O-antigen and lipopolysaccharide biosynthesis'). These findings are consistent with those of the animal studies. Additionally, AA, but not EPA, disrupted the ratio of CD4/CD8 cells, increased skin lesion area and enhanced the proportion of peripheral Th2 cells. It also promoted IgE secretion and the biosynthesis of prostaglandins and leukotrienes in BALB/c mice fed AA following ovalbumin immunostimulation. Moreover, AA significantly increased IL-4 secretion in HaCaT cells costimulated with TNF-α and INF-γ.

CONCLUSIONS: This study demonstrates that AA is intimately linked to the onset of AD via gut dysbiosis.},
}

*Dermatitis, Atopic/microbiology/metabolism/etiology
Humans
*Milk, Human/chemistry
*Dysbiosis/metabolism/microbiology
*Gastrointestinal Microbiome
Infant
Female
Animals
*Arachidonic Acid/metabolism
*Feces/microbiology
Mice
Infant, Newborn
Male
Breast Feeding

@article {pmid39653697,
year = {2024},
author = {Palladino, G and Nanetti, E and Scicchitano, D and Cinti, N and Foresto, L and Cozzi, A and Gonzalez Vara Rodriguez, A and Interino, N and Fiori, J and Turroni, S and Candela, M and Rampelli, S},
title = {Zonation of the Vitis vinifera microbiome in Vino Nobile di Montepulciano PDO production area.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {1626},
pmid = {39653697},
issn = {2399-3642},
support = {818290//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; },
mesh = {*Vitis/microbiology ; *Microbiota/genetics ; Italy ; *Wine/microbiology ; Soil Microbiology ; Bacteria/genetics/classification/metabolism/isolation & purification ; Fungi/genetics/classification/metabolism ; Rhizosphere ; },
abstract = {The microbial dimension of the terroir is crucial for wine quality, as microbiomes contribute to plant biofertilization, stress tolerance and pathogen suppression. While microbial terroir can act as a biological signature at large scale, data for local contexts is lacking, hindering the characterization of regional microbial diversity in vineyards. Here, we define the microbial terroir of vineyards across the 12 sub-areas (Additional Geographic Units -AGUs) of the "Consorzio del Vino Nobile di Montepulciano DOCG" PDO area (Italy), a world-renowned wine-producing region. Rhizospheres of Vitis vinifera cultivar Sangiovese and soil samples were collected throughout the 2022 viticultural season and analyzed through an integrated metabarcoding/shotgun metagenomic approach, targeting bacteria and fungi. Wine metabolomics was also perfomed, projecting compositional and functional variations of the microbial terroir at the AGUs level into a corresponding variation in the product metabolic profile. Our findings reveal a unique taxonomic configuration of the Vino Nobile di Montepulciano terroir compared to other vineyards, with microbiomes being "AGU-specific" in taxonomic abundances and plant growth-promoting functions, confirming the potential relevance of characterizing and preserving the microbial terroir to safeguard high-quality traditional wines.},
}

*Vitis/microbiology
*Microbiota/genetics
Italy
*Wine/microbiology
Soil Microbiology
Bacteria/genetics/classification/metabolism/isolation & purification
Fungi/genetics/classification/metabolism
Rhizosphere

@article {pmid39653684,
year = {2024},
author = {Chen, Y and Yang, C and Deng, Z and Xiang, T and Tan, J and Xu, J and Sun, D and Luo, F},
title = {Alterations of gut virome with close interaction in the progression of estrogen deficiency-induced osteoporosis.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2437250},
doi = {10.1080/19490976.2024.2437250},
pmid = {39653684},
issn = {1949-0984},
mesh = {*Gastrointestinal Microbiome ; Animals ; Female ; *Virome ; Mice ; *Osteoporosis/virology ; Humans ; *Estrogens/metabolism ; Ovariectomy ; Bacteria/classification/genetics/isolation & purification/metabolism ; Mice, Inbred C57BL ; Disease Models, Animal ; Disease Progression ; },
abstract = {Previous research has established a link between gut microbiota and osteoporosis (OP) advancement. However, there remains a limited understanding of the crucial contribution of the gut virome in the onset and progression of OP. We employed metagenomic shotgun sequencing and gut virome sequencing to process the ovariectomy (OVX)-induced OP murine model, which revealed significant disparities in bacteriome and virome compositions between subjects with OP and healthy controls. One hundred and seventy-four altered viral strains were identified to participate in the multifaceted regulation of bone loss, involving immune modulation, microbial metabolic activity, and intricate host-virus dynamics. Our findings suggested that the gut virome may influence bone metabolism, potentially altering the balance of bone-modulating compounds like short-chain fatty acids. This comprehensive analysis of the gut virome in OP highlighted the diagnostic potential of combined gut viral and bacterial biomarkers for OP.},
}

*Gastrointestinal Microbiome
Animals
Female
*Virome
Mice
*Osteoporosis/virology
Humans
*Estrogens/metabolism
Ovariectomy
Bacteria/classification/genetics/isolation & purification/metabolism
Mice, Inbred C57BL
Disease Models, Animal
Disease Progression

@article {pmid39648978,
year = {2024},
author = {Ribero, MN and Schiaffino, MR and Filloy, J},
title = {Grassland Afforestation Drives Biotic Homogenisation of Soil Microbial Communities at a Regional Scale.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e17617},
doi = {10.1111/mec.17617},
pmid = {39648978},
issn = {1365-294X},
support = {2018//Secretaría de Ciencia y Técnica, Universidad de Buenos Aires/ ; //Neotropical Grassland Conservancy/ ; PICT 2017//Agencia Nacional de Promoción Científica y Tecnológica/ ; //Consejo Nacional de Investigaciones Científicas y Técnicas/ ; },
abstract = {Grassland afforestation poses a threat to biodiversity beyond land-use conversion. Diversity patterns are shaped by temporal dynamics, particularly, time since afforestation can decline beta diversity and lead to biotic homogenisation. Our study examines the effect of grassland afforestation on soil prokaryotic and fungal beta diversity. We evaluate the contributions of colonisation and extinction processes to beta diversity, as well as the replacement of endemic species by ubiquitous ones. Along a 200 km climatic gradient in Argentina's Pampas region, we analysed grasslands and mature eucalypt plantations at different times since afforestation. Soil samples were collected at each site and analysed using 16S (V3-V4) and ITS2 amplicon sequencing to identify prokaryotic and fungal communities, respectively. The analyses revealed biotic homogenisation at the transition from grassland to newly planted stands, evidenced by a decrease in intratreatment beta diversity. Increasing time since afforestation did not exacerbate this decline. However, our findings indicate that there are different responses between prokaryotes and fungi. The homogenisation of prokaryotes in young stands is due to the low heterogeneity in colonising communities. On the other hand, the decline in fungal beta diversity is likely caused by other mechanisms beyond extinction or replacement. The study highlights the impacts of the afforestation process on the beta diversity of soil microbial communities of grasslands, affecting taxonomic groups in different ways. Although microbial diversity may be partially restored in time in eucalypt plantations, it is important to investigate its underlying mechanisms and the ecological implications for microbial diversity and its spatial distribution.},
}

@article {pmid39647426,
year = {2024},
author = {Ge, H and Li, C and Huang, C and Zhao, L and Cong, B and Liu, S},
title = {Bacterial community composition and metabolic characteristics of three representative marine areas in northern China.},
journal = {Marine environmental research},
volume = {204},
number = {},
pages = {106892},
doi = {10.1016/j.marenvres.2024.106892},
pmid = {39647426},
issn = {1879-0291},
abstract = {Bacteria are essential components of ecosystems, participating in nutrient cycling and biogeochemical processes, and playing a crucial role in maintaining the stability of marine ecosystems. However, the biogeographic distribution patterns of bacterial diversity and metabolic functions in the estuarine and coastal areas of northern China remain unclear. Here, we used metagenomic sequencing to investigate the bacterial community composition and metabolic functions in sediments from the adjacent waters of the Yellow River Estuary, the Yellow Sea Cold Water Mass, and the adjacent waters of the Yangtze River Estuary. Among the 9164 species that were found, the most dominant microbial communities are Pseudomonadota, Actinomycetota, Bacteroidota, and Bacillota, but there are significant differences in the species composition in these three typical habitats. Amino acid metabolism and carbohydrate metabolic pathways were highly enriched. Glycoside hydrolases (GHs) predominate in carbon metabolism across all samples. In nitrogen metabolic pathway, genes related to organic degradation and synthesis are more abundant in the Yellow River Estuary than the other two habitats. In sulfur metabolic pathway, genes involved in assimilatory sulfate reduction are significantly enriched. Assimilatory sulfate reduction might be crucial for sulfur metabolism in coastal regions, with a full assimilatory nitrate reduction pathway found in Desulfobacterota. This research offers insights into the compositional diversity, metabolic functions, and biogeographic distribution patterns of bacterial communities in sediments from typical marine areas of northern China.},
}

@article {pmid39603473,
year = {2025},
author = {Li, Y and Tao, C and Li, S and Chen, W and Fu, D and Jafvert, CT and Zhu, T},
title = {Feasibility study of machine learning to explore relationships between antimicrobial resistance and microbial community structure in global wastewater treatment plant sludges.},
journal = {Bioresource technology},
volume = {417},
number = {},
pages = {131878},
doi = {10.1016/j.biortech.2024.131878},
pmid = {39603473},
issn = {1873-2976},
mesh = {*Machine Learning ; *Sewage/microbiology ; *Wastewater/microbiology ; Water Purification/methods ; Feasibility Studies ; Bacteria/drug effects/genetics ; Drug Resistance, Microbial/genetics ; Microbiota/drug effects ; China ; Drug Resistance, Bacterial/genetics ; },
abstract = {Wastewater sludges (WSs) are major reservoirs and emission sources of antibiotic resistance genes (ARGs) in cities. Identifying antimicrobial resistance (AMR) host bacteria in WSs is crucial for understanding AMR formation and mitigating biological and ecological risks. Here 24 sludge data from wastewater treatment plants in Jiangsu Province, China, and 1559 sludge data from genetic databases were analyzed to explore the relationship between 7 AMRs and bacterial distribution. The results of the Procrustes and Spearman correlation analysis were unsatisfactory, with p-value exceeding the threshold of 0.05 and no strong correlation (r > 0.8). In contrast, explainable machine learning (EML) using SHapley Additive exPlanation (SHAP) revealed Pseudomonadota as a major contributor (39.3 %-74.2 %) to sludge AMR. Overall, the application of ML is promising in analyzing AMR-bacteria relationships. Given the different applicable occasions and advantages of various analysis methods, using ML as one of the correlation analysis tools is strongly recommended.},
}

*Machine Learning
*Sewage/microbiology
*Wastewater/microbiology
Water Purification/methods
Feasibility Studies
Bacteria/drug effects/genetics
Drug Resistance, Microbial/genetics
Microbiota/drug effects
China
Drug Resistance, Bacterial/genetics

@article {pmid39577778,
year = {2025},
author = {Chen, Y and Huang, M and Fu, Y and Gao, T and Gan, Z and Meng, F},
title = {Construction of polylactic acid plastisphere microbiota for enhancing nitrate reduction in denitrification biofilters.},
journal = {Bioresource technology},
volume = {417},
number = {},
pages = {131853},
doi = {10.1016/j.biortech.2024.131853},
pmid = {39577778},
issn = {1873-2976},
mesh = {*Denitrification ; *Polyesters/metabolism/chemistry ; *Nitrates/metabolism ; *Biofilms ; *Microbiota ; Bioreactors/microbiology ; Filtration/methods ; Water Purification/methods ; Biodegradation, Environmental ; },
abstract = {Developing methods for reusing biodegradable plastics, like polylactic acid (PLA) straws, is highly needed. Here, PLAs were applied to substitute traditional commercial ceramic media (CCM) in denitrification biofilters. During long-term operation, replacing CCM with PLA significantly enhanced nitrate removal efficiency from 32.68-54.39 % to 41.64-66.26 %. Ammonia nitrogen effluent maintained below 0.5 mg/L in all reactors. PLA plastisphere shaped unique microbial communities, i.e., denitrifying bacteria Bacillus, Pseudomonas and Acidovorax preferred to inhabit or degrade PLA. Compared to CCM biofilms, PLA diminished the importance of stochastic process in biofilm assembly of PLA plastisphere. Metagenomic sequencing suggested that PLA biofilms possessed greater metabolic capabilities of denitrification and glycolysis compared to CCM. Additionally, Bacillus strain P01 isolated from PLA plastisphere demonstrated strong PLA depolymerization. Overall, this study revealed that PLA serves as carbon source and biofilm carrier, offering a promising approach to integrating plastic reuse with wastewater treatment.},
}

*Denitrification
*Polyesters/metabolism/chemistry
*Nitrates/metabolism
*Biofilms
*Microbiota
Bioreactors/microbiology
Filtration/methods
Water Purification/methods
Biodegradation, Environmental

@article {pmid39549663,
year = {2024},
author = {Méndez, A and Maisto, F and Pavlović, J and Rusková, M and Pangallo, D and Sanmartín, P},
title = {Microbiome shifts elicited by ornamental lighting of granite facades identified by MinION sequencing.},
journal = {Journal of photochemistry and photobiology. B, Biology},
volume = {261},
number = {},
pages = {113065},
doi = {10.1016/j.jphotobiol.2024.113065},
pmid = {39549663},
issn = {1873-2682},
mesh = {*Microbiota ; *Silicon Dioxide/chemistry ; *Bacteria/genetics/radiation effects/isolation & purification/classification ; *Fungi/genetics ; Lighting ; Nanopore Sequencing ; Pilot Projects ; Archaea/genetics/radiation effects ; },
abstract = {Night-time outdoor illumination in combination with natural sunlight can influence the visible phototrophic colonizers (mainly algae) growing on stone facades; however, the effects on the microbiome (invisible to the naked eye) are not clear. The presence of stone-dwelling microbes, such as bacteria, diatoms, fungi, viruses and archaea, drives further biological colonization, which may exacerbate the biodeterioration of substrates. Considering the microbiome is therefore important for conservation of the built heritage. The impact of the following types of lighting on the relative abundance and diversity of the microbiome on granite ashlars was evaluated in a year-long outdoor pilot study: no lighting; lighting with a metal halide lamp (a traditional lighting system currently used to illuminate monuments); and lighting with a novel LED lamp (an environmentally sound prototype lamp with a biostatic effect, halting biological colonization by phototrophs, currently under trial). Culturable fractions of microbiome and whole-genome sequencing by metabarcoding with Oxford Nanopore Sequencing (MinION) was conducted for bacteria and fungi in order to complement both community characterization strategies. In addition, the possible biodeteriorative profiles of the isolated strains, relative to calcium carbonate precipitation/solubilisation and iron oxidation/reduction, were investigated by plate assays. Alpha and beta diversity indexes were also determined, along with the abundance of biocide and antibiotic resistance genes. Culture-dependent microbiological analysis failed to properly show changes in community composition, for which metagenomic approaches like MinION are better suited. Thus, MinION analysis identified shifts in the granite microbiome elicited by ornamental lighting. The novel LED lamp with the biostatic effect on phototrophs caused an increase in the diversity of bacteria and fungi. In this case, the microbiome was more similar to that in the unlit samples. In the samples illuminated by the metal halide lamp, dominance of bacteria was favoured and the presence of fungi was negligible.},
}

*Microbiota
*Silicon Dioxide/chemistry
*Bacteria/genetics/radiation effects/isolation & purification/classification
*Fungi/genetics
Lighting
Nanopore Sequencing
Pilot Projects
Archaea/genetics/radiation effects

@article {pmid39643877,
year = {2024},
author = {Cui, Z and Wang, S and Niu, J and Ma, J and Yang, H},
title = {Bifidobacterium species serve as key gut microbiome regulators after intervention in gestational diabetes mellitus.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {520},
pmid = {39643877},
issn = {1471-2180},
support = {22cz020401-4811009//National High Level Hospital Clinical Research/ ; 81830044//National Natural Science Foundation of China/ ; 2021YFC2700700//National Key Research and Development Program of China/ ; },
mesh = {Humans ; *Diabetes, Gestational/microbiology/metabolism/blood ; Pregnancy ; *Gastrointestinal Microbiome/genetics ; Female ; *Bifidobacterium/genetics ; Adult ; *Feces/microbiology ; Fatty Acids, Volatile/metabolism ; Dysbiosis/microbiology ; Genome-Wide Association Study ; Metagenome ; },
abstract = {Gut microbiome dysbiosis is associated with gestational diabetes mellitus (GDM), and its modulation represents a promising approach for enhancing glycemic control. In this study, we aimed to discover specific alterations in the gut microbiome through lifestyle management. We performed metagenome sequencing on fecal samples and measured short-chain fatty acid (SCFA) in plasma samples from 27 well-controlled GDM pregnancies before and after glycemic control. At the same time, 38 normal glucose tolerance (NGT) samples served as controls. Additionally, we employed two-sample Mendelian Randomization (MR) to validate our findings against Genome-Wide Association Study (GWAS) database. Our dynamic analysis revealed Bifidobacterium genus increased in GDM patients after intervention. The MR analysis confirmed that the family of Bifidobacteriaceae (OR 0.929, 95% CI, 0.886-0.975; P = 0.003) was the only negatively associated family with GDM. Further analysis indicated the increased abundance of Bifidobacterium species were negatively correlated with glycemic traits (Spearman rho mean - 0.32 ± 0.34) but positively correlated with plasma SCFA levels (Spearman rho mean 0.24 ± 0.19). Functional analysis revealed that the quorum-sensing pathway had the strongest effect on the ability of Bifidobacterium to promote glucose homeostasis (Spearman rho = -0.34), suggesting its role in regulating intestinal microbiota. Finally, the multivariable MR analysis demonstrated that two pathways, COLANSYN PWY and PWY 7323, responsible for cell surface compound synthesis in gram-negative bacteria, mediated 14.83% (P = 0.017) and 16.64% (P = 0.049) of the protective effects of Bifidobacteriaceae against GDM, respectively. In summary, Bifidobacterium is an effective gut microbiota regulator for GDM-related glucose homeostasis.},
}

Humans
*Diabetes, Gestational/microbiology/metabolism/blood
Pregnancy
*Gastrointestinal Microbiome/genetics
Female
*Bifidobacterium/genetics
Adult
*Feces/microbiology
Fatty Acids, Volatile/metabolism
Dysbiosis/microbiology
Genome-Wide Association Study
Metagenome

@article {pmid39643362,
year = {2024},
author = {Shen, C and Yu, Y and Zhang, X and Zhang, H and Chu, M and Yuan, B and Guo, Y and Li, Y and Zhou, J and Mao, J and Xu, X},
title = {The dynamic of physicochemical properties, volatile compounds and microbial community during the fermentation of Chinese rice wine with diverse cereals.},
journal = {Food research international (Ottawa, Ont.)},
volume = {198},
number = {},
pages = {115319},
doi = {10.1016/j.foodres.2024.115319},
pmid = {39643362},
issn = {1873-7145},
mesh = {*Wine/analysis/microbiology ; *Fermentation ; *Volatile Organic Compounds/analysis ; *Oryza/chemistry ; *Odorants/analysis ; Microbiota ; Edible Grain/chemistry/microbiology ; Gas Chromatography-Mass Spectrometry ; Taste ; Amino Acids/analysis/metabolism ; Esters/analysis/metabolism ; Bacteria/classification/metabolism ; East Asian People ; },
abstract = {This study investigates the impact of liquid state fermentation on the key flavor compounds and microbial community structure in Chinese rice wine brewed from five different raw materials: buckwheat, sorghum, japonica rice, glutinous rice, and black rice. Using HS-SPME-GC-MS and HPLC, the volatile compounds were analyzed across various grain liquefaction methods, detecting 82 volatiles, including esters, alcohols, aldehydes, and acids. The concentration of flavor compounds such as esters, amino acids, phenolic acids, and organic acids varied significantly depending on the raw material used. Based on odor activity values, 31 key compounds were identified, including 15 ethyl esters, like ethyl laurate, responsible for the unique and complex aroma of the rice wines. Bitter amino acids, making up over 50 % of the total amino acids, were predominant. Among the varieties, the buckwheat-fermented wine exhibited the highest ester content (27.39 mg/L), nearly double that of other samples, along with elevated amino acids (1.47 mg/mL) and phenolic acids (904.29 mg/L). Black rice ranked second in amino acid content (0.93 mg/mL), while glutinous rice had the highest organic acid content (239.76 mg/mL). Metagenomic sequencing on the fifth day of fermentation revealed significant differences in microbial community structure among the raw materials. Saccharomyces, Aspergillus, Thermomyces, Epicoccus, and Albertella were dominant fungi, while Weissella, Thermoactinomyces, Bacillus, and Saccharopolyspora were dominant bacteria. Sensory analysis showed that buckwheat-fermented rice wine was distinguished by its honey, floral, creamy, and umami attributes, while balancing alcohol, acidity, bitterness, and Qu aroma. The results demonstrate the significant influence of raw material selection and liquefaction method on both flavor profile and microbial diversity in Chinese rice wine.},
}

*Wine/analysis/microbiology
*Fermentation
*Volatile Organic Compounds/analysis
*Oryza/chemistry
*Odorants/analysis
Microbiota
Edible Grain/chemistry/microbiology
Gas Chromatography-Mass Spectrometry
Taste
Amino Acids/analysis/metabolism
Esters/analysis/metabolism
Bacteria/classification/metabolism
East Asian People

@article {pmid39643360,
year = {2024},
author = {Li, N and Xu, W and Meng, L and Zhao, Y and Zhao, X and Zheng, N and Zhang, Y and Wang, J},
title = {Metagenomics reveals differences in spore-forming bacterial diversity in raw milk in different regions and seasons in China.},
journal = {Food research international (Ottawa, Ont.)},
volume = {198},
number = {},
pages = {115317},
doi = {10.1016/j.foodres.2024.115317},
pmid = {39643360},
issn = {1873-7145},
mesh = {*Seasons ; Animals ; *Milk/microbiology ; China ; *Spores, Bacterial/genetics ; *Metagenomics ; Food Microbiology ; Bacteria/genetics/classification/isolation & purification ; Biodiversity ; },
abstract = {The spore-forming bacteria in the dairy industry are notable for their spores resilience and capacity to survive heating processes, allowing them to germinate and enter the vegetative stage, potentially leading to spoilage of the milk. Additionally, these spores can form biofilms, becoming a persistent source of contamination in processing environments. In this study, we collected a total of 165 raw milk from six different parts in China in spring, summer, autumn, and winter, respectively. Metagenomics sequencing method was used to explore and compare the differences in spore-forming bacterial composition and diversity in raw milk samples. Among these samples, four genera and 207 species of spore-forming bacteria were identified, with the genus Bacillus and the species Paenibacillus darwinianus dominant. Seasonal variations had a greater impact on the composition and abundance of spore-forming bacteria in raw milk than regional differences. Notable, raw milk samples collected during the spring and summer exhibited a higher number of unique spore-forming bacterial species compared to those collected in other seasons. Moreover, different regions and seasons have their own dominant bacteria. Metabolism of cofactors and vitamins, energy metabolism, carbohydrate metabolism, and amino acid metabolism were the main metabolic pathways. Hence, specific strategies need to be adopted to prevent and control spore-forming bacteria in raw milk in different regions and seasons.},
}

*Seasons
Animals
*Milk/microbiology
China
*Spores, Bacterial/genetics
*Metagenomics
Food Microbiology
Bacteria/genetics/classification/isolation & purification
Biodiversity

@article {pmid39643345,
year = {2024},
author = {Jian, C and Sun, M and Ma, T and Wang, W and Lv, B and Wang, J and Su, X and Li, S and Guo, Y},
title = {Revealing the formation mechanisms of key flavor components during the fermentation of bamboo shoots by combining flavoromics and metagenomics.},
journal = {Food research international (Ottawa, Ont.)},
volume = {198},
number = {},
pages = {115361},
doi = {10.1016/j.foodres.2024.115361},
pmid = {39643345},
issn = {1873-7145},
mesh = {*Fermentation ; *Metagenomics ; *Taste ; *Volatile Organic Compounds/analysis/metabolism ; *Odorants/analysis ; *Metabolomics ; Flavoring Agents/metabolism ; Plant Shoots ; Fermented Foods/microbiology ; Bacteria/genetics/classification/metabolism ; Food Microbiology ; Amino Acids/analysis/metabolism ; Microbiota ; },
abstract = {Microbial metabolism plays a critical role in the flavor development of Guangxi fermented bamboo shoots (GFBS). To clarify the role of microorganisms in flavor formation and predict the metabolic pathways of key characteristic flavor compounds, this study employed metabolomics, Odor Activity Value (OAV), and Taste Activity Value (TAV) calculations, integrated with Partial Least Squares Discriminant Analysis (PLS-DA), to investigate changes in GFBS flavors-represented by volatile flavor compounds, organic acids, and free amino acids-across a 30-day fermentation period. Metagenomic datasets were used to identify taxonomic and functional changes in the microbial community. As a result, 26 characteristic flavor compounds (OAV or TAV > 1) were identified in mature GFBS, and 23 differential flavor compounds were identified at different fermentation stages using PLS-DA (VIP > 1.2). The top 10 microbial genera associated with these characteristic flavor compounds were identified, including Acinetobacter, Enterobacter, Raoultella, Enterococcus, Klebsiella, Lactococcus, Leuconostoc, Weissella, Lactiplantibacillus and Limosilactobacillus. Based on these findings, a predictive metabolic network of key flavor compounds in GFBS was constructed, providing a comprehensive understanding of the diverse metabolic roles of microorganisms during fermentation. This work lays a theoretical foundation for the standardized production and quality control of GFBS flavor.},
}

*Fermentation
*Metagenomics
*Taste
*Volatile Organic Compounds/analysis/metabolism
*Odorants/analysis
*Metabolomics
Flavoring Agents/metabolism
Plant Shoots
Fermented Foods/microbiology
Bacteria/genetics/classification/metabolism
Food Microbiology
Amino Acids/analysis/metabolism
Microbiota

@article {pmid39643336,
year = {2024},
author = {Li, T and Cao, W and Li, D and Wei, C and Yan, Y and Zeng, X},
title = {Metagenomic insights into quorum sensing-associated microbial profiling and its correlations with flavor compounds of Maotai-flavor liquor: A case study of stacking fermented grains.},
journal = {Food research international (Ottawa, Ont.)},
volume = {198},
number = {},
pages = {115324},
doi = {10.1016/j.foodres.2024.115324},
pmid = {39643336},
issn = {1873-7145},
mesh = {*Quorum Sensing ; *Fermentation ; *Flavoring Agents/metabolism ; *Metagenomics/methods ; Taste ; Food Microbiology ; Bacteria/genetics/metabolism/classification ; Fungi/genetics/metabolism ; Edible Grain/microbiology ; Alcoholic Beverages/microbiology ; Microbiota ; },
abstract = {Stacking fermentation is typical process of Maotai-flavor Baijiu and microbial composition determine content of flavors. To date, the knowledge on the driving force of microbial composition was as yet unknown. Since quorum sensing molecule (QSM) plays an important role in modifying microbial interactions. Therefore, the objectives of the present study were: (1) to describe the microbial profile associated with QSM in stacking grains using metagenomics; (2) to elucidate how QSM shapes microbial interactions and accordingly regulates flavor synthesis. Results indicated that bacterial QSM including AI-2, DSF, and AHL as well as fungal QSM aromatic alcohols and farnesol were prevalent in the stacking fermented grains. Thereinto, AI-2 might be an important driving force of microbial composition due to its highest abundance. AI-2 in Limosilactobacillus fermentum, Pediococcus pentosaceus, and Weissella cibaria perhaps modified microbial interactions together with fungal QSM in Schizosaccharomyces pombe and Pichia membranifaciens. The role of AI-2 was much higher than that of fungal QSM. Furthermore, QSM indirectly influenced the synthesis of important flavors such as ethyl lactate, phenylethanol, and ethyl phenylacetate through the dynamic of microbial composition. Together, this current study for the first time explored the effects of QSM on microbial composition and flavor synthesis in the Baijiu field.},
}

*Quorum Sensing
*Fermentation
*Flavoring Agents/metabolism
*Metagenomics/methods
Taste
Food Microbiology
Bacteria/genetics/metabolism/classification
Fungi/genetics/metabolism
Edible Grain/microbiology
Alcoholic Beverages/microbiology
Microbiota

@article {pmid39642431,
year = {2024},
author = {Bertini, F and Catania, V and Scirè Calabrisotto, L and Dara, M and Bisanti, L and La Corte, C and Staropoli, M and Piazzese, D and Parisi, MG and Parrinello, D and Cammarata, M},
title = {A multi-comprehensive approach to assess the responses of the Mediterranean mussel Mytilus galloprovincialis (Lamarck, 1919) to a simulation of a diesel-oil mixture spill.},
journal = {Aquatic toxicology (Amsterdam, Netherlands)},
volume = {279},
number = {},
pages = {107188},
doi = {10.1016/j.aquatox.2024.107188},
pmid = {39642431},
issn = {1879-1514},
abstract = {Oil spills are a major cause of pollution impacting marine ecosystems. In this work, the effects of short-term exposure to three different concentrations of a hydrocarbon mixture (HC), that simulated the action of such an event, were investigated on Mytilus galloprovincialis specimens. Physiological effects were measured using a battery of biomarkers consisting of cellular activity (phagocytosis), immune-related enzymes, chaperonins (HSP70 and HSC70), and histomorphological alterations. Different concentrations of HC led to a significant decrease in phagocytosis, especially following high concentrations. Immune-related enzymes evaluated in hemolymph and digestive gland extract showed up-regulation, suggesting the activation of antioxidant, detoxicant, and inflammatory responses. Morphological alterations of digestive gland tubules were observed after exposure to the HC. HSP70 and HSC70 activity was up regulated following the treatments, indicating their involvement in maintaining organism homeostasis. In addition, the diversity and composition of hemolymph and digestive gland microbiota exposed to HC were analyzed by automated ribosomal intergenic spacer analysis (ARISA) and a Next Generation Sequencing (NGS) approach to evaluate the connection with hydrocarbon contamination. Metagenomic analysis revealed significant differences in the hemolymph and digestive gland microbiota composition between mussels exposed and unexposed to HC. Exposure to increasing HC concentrations had a positive effect on microbial diversity with clear adaptative responses, and an increase in the relative abundance of several known degrading bacterial genera, including Alcanivorax, Roseovarius, Pseudomonas, Vibrio, Oleibacter. These results show the utility of a multi-comprehensive approach to evaluating functional adaptation in terms of immunological dysfunctions and microbiota alteration in the sentinel organism M. galloprovincialis.},
}

@article {pmid39608199,
year = {2025},
author = {Bhat, AH and Malik, IM and Tak, H and Ganai, BA and Bharti, P},
title = {Host, parasite, and microbiome interaction: Trichuris ovis and its effect on sheep gut microbiota.},
journal = {Veterinary parasitology},
volume = {333},
number = {},
pages = {110356},
doi = {10.1016/j.vetpar.2024.110356},
pmid = {39608199},
issn = {1873-2550},
mesh = {Animals ; Sheep ; *Sheep Diseases/parasitology/microbiology ; *Gastrointestinal Microbiome ; *Trichuris ; *Host-Parasite Interactions ; *Trichuriasis/veterinary/parasitology/microbiology ; RNA, Ribosomal, 16S/genetics ; Cecum/microbiology/parasitology ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {Sheep that are infected with gastrointestinal helminths experience a significant impact on their health and productivity. Among the helminths, nematodes like Haemonchus contortus, Oesophagostomum spp., Bunostomum trigonocephalum, Nematodirus battus, Trichostrongylus spp. and Teladorsagia circumcincta are particularly pathogenic. Understanding the interactions among parasites, hosts, and their microbiomes is crucial in developing new approaches in the management of parasites. This study examines the bacterial profile of Trichuris ovis, a highly prevalent nematode among Kashmir Merino sheep, and the influence of nematode infection on the caecal microbiome of its host. Sheep were selected based on T. ovis infection status, and samples were collected from infected and non-infected caecum. The 16S rRNA metagenomic analysis revealed distinct microbial communities in T. ovis, infected caecum, and non-infected caecum. Proteobacteria dominated the T. ovis microbiome, while infected caecum was rich in Bacteroidota and Spirochaetota, and non-infected caecum had a higher proportion of Firmicutes and Verrucomicrobiota. At the genus level, T. ovis was predominantly associated with Escherichia/Shigella, while infected caecum had higher proportions of Bacteroides, Prevotella, and Treponema. Non-infected caecum was characterized by WCHB1-41, Prevotella, and Succiniclasticum like genera. Alpha and beta diversity indicated significant differences in microbiome among the groups, with higher diversity observed in infected caecum. The study found T. ovis infection significantly alters the caecal microbiome of sheep, introducing potentially pathogenic bacteria and reducing beneficial ones. These findings underscore the complex relationship between host, parasite, and microbiome, highlighting the need for comprehensive strategies to manage helminth infections and their broader ecological impacts.},
}

Animals
Sheep
*Sheep Diseases/parasitology/microbiology
*Gastrointestinal Microbiome
*Trichuris
*Host-Parasite Interactions
*Trichuriasis/veterinary/parasitology/microbiology
RNA, Ribosomal, 16S/genetics
Cecum/microbiology/parasitology
Bacteria/classification/genetics/isolation & purification

@article {pmid39419193,
year = {2024},
author = {Chen, H and Zeng, M and Batool, SS and Zhao, Y and Yu, Z and Zhou, J and Liu, K and Huang, J},
title = {Metagenomic analysis reveals effects of gut microbiome in response to neoadjuvant chemoradiotherapy in advanced rectal cancer.},
journal = {Genomics},
volume = {116},
number = {6},
pages = {110951},
doi = {10.1016/j.ygeno.2024.110951},
pmid = {39419193},
issn = {1089-8646},
mesh = {Humans ; *Rectal Neoplasms/therapy/microbiology/genetics/metabolism ; *Gastrointestinal Microbiome ; *Neoadjuvant Therapy ; Chemoradiotherapy ; Female ; Male ; Middle Aged ; Metagenomics ; Aged ; Metagenome ; Feces/microbiology ; Bacteria/genetics/classification/metabolism ; },
abstract = {Neoadjuvant chemoradiotherapy can enhance survival rate of patients with advanced rectal cancer, but its effectiveness varies considerably. Previous studies have indicated that gut microbes may serve as biomarkers for predicting treatment efficacy. However, the specific roles of the gut microbiome in patients who have good response to nCRT remains unclear. In this study, shotgun metagenomic sequencing technology was used to analyze the fecal microbiome of patients with varying responses to nCRT. Our findings revealed that beneficial intestinal bacteria and genes from different metabolic pathways (carbohydrate metabolism, amino acid metabolism, and sulfur metabolism) were significantly enriched in patients with good response. Additionally, causal relationship in which microbial-derived GDP-D-rhamnose and butyrate could influence the response to nCRT was clarified. Our results offered new insights into the different response to nCRT, and provided valuable reference points for improving the effectiveness of nCRT in patients with advanced colorectal cancer.},
}

Humans
*Rectal Neoplasms/therapy/microbiology/genetics/metabolism
*Gastrointestinal Microbiome
*Neoadjuvant Therapy
Chemoradiotherapy
Female
Male
Middle Aged
Metagenomics
Aged
Metagenome
Feces/microbiology
Bacteria/genetics/classification/metabolism

@article {pmid39640900,
year = {2024},
author = {Pahirah, N and Narkwichean, A and Taweechotipatr, M and Wannaiampikul, S and Duang-Udom, C and Laosooksathit, W},
title = {Comparison of Gut Microbiomes Between Neonates Born by Cesarean Section and Vaginal Delivery: Prospective Observational Study.},
journal = {BioMed research international},
volume = {2024},
number = {},
pages = {8302361},
pmid = {39640900},
issn = {2314-6141},
mesh = {Humans ; *Cesarean Section ; *Gastrointestinal Microbiome ; Infant, Newborn ; Female ; Prospective Studies ; *Delivery, Obstetric ; Pregnancy ; *RNA, Ribosomal, 16S/genetics ; Male ; Feces/microbiology ; Thailand ; Bifidobacterium ; },
abstract = {Background: Balanced diversity and abundance of gut microbiome play important roles in human health, including neonatal health. Though not established, there is evidence that the delivery route could alter the diversity of neonatal gut microbiomes. Objective: The objective of the study was to investigate the differences in the gut microbiomes of neonates delivered via cesarean section compared to those born by vaginal delivery and to identify the predominant microbial taxa present in each group. Study Design: A prospective observational study of 281 healthy neonates born between February 2021 and April 2023 at Her Royal Highness Maha Chakri Sirindhorn Medical Center, Srinakharinwirot University, Thailand, was performed. The study population was divided into two groups: 139 neonates born via vaginal delivery and 141 neonates born via cesarean section. The microbiota composition of each neonate's fecal sample was identified by using 16S ribosomal ribonucleic acid metagenomic sequencing. Results: Neonates delivered vaginally exhibited a gut microbiome with higher abundance and diversity than those delivered by cesarean delivery. Bifidobacterium was the dominant genus in both groups. Bifidobacterium breve was the dominant species and was significantly higher in cesarean-delivered neonates compared to those delivered vaginally (24.0% and 9.2%, respectively) (p < 0.001). However, the taxonomy of only 89 (64.0%) and 44 (31.43%) fecal samples could be identified from the vaginal and cesarean delivery groups, respectively. Conclusion: Route of delivery is associated with neonatal gut microbiome abundance and diversity. Neonates delivered via vaginal delivery exhibited higher diversity but lower abundance of the dominant species in the gut microbiome. Trial Registration: Thai Clinical Trials Registry identifier: TCTR20221024003.},
}

Humans
*Cesarean Section
*Gastrointestinal Microbiome
Infant, Newborn
Female
Prospective Studies
*Delivery, Obstetric
Pregnancy
*RNA, Ribosomal, 16S/genetics
Male
Feces/microbiology
Thailand
Bifidobacterium

@article {pmid39639355,
year = {2024},
author = {Benga, L and Rehm, A and Gougoula, C and Westhoff, P and Wachtmeister, T and Benten, WPM and Engelhardt, E and Weber, APM and Köhrer, K and Sager, M and Janssen, S},
title = {The host genotype actively shapes its microbiome across generations in laboratory mice.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {256},
pmid = {39639355},
issn = {2049-2618},
mesh = {Animals ; Mice ; Female ; *Genotype ; *Mice, Inbred BALB C ; *Mice, Inbred C57BL ; *Microbiota ; Male ; Maternal Inheritance ; Embryo, Mammalian/microbiology ; Host Microbial Interactions ; Pregnancy ; },
abstract = {BACKGROUND: The microbiome greatly affects health and wellbeing. Evolutionarily, it is doubtful that a host would rely on chance alone to pass on microbial colonization to its offspring. However, the literature currently offers only limited evidence regarding two alternative hypotheses: active microbial shaping by host genetic factors or transmission of a microbial maternal legacy.

RESULTS: To further dissect the influence of host genetics and maternal inheritance, we collected two-cell stage embryos from two representative wild types, C57BL6/J and BALB/c, and transferred a mixture of both genotype embryos into hybrid recipient mice to be inoculated by an identical microbiome at birth.

CONCLUSIONS: Observing the offspring for six generations unequivocally emphasizes the impact of host genetic factors over maternal legacy in constant environments, akin to murine laboratory experiments. Interestingly, maternal legacy solely controlled the microbiome in the first offspring generation. However, current evidence supporting maternal legacy has not extended beyond this initial generation, resolving the aforementioned debate. Video Abstract.},
}

Animals
Mice
Female
*Genotype
*Mice, Inbred BALB C
*Mice, Inbred C57BL
*Microbiota
Male
Maternal Inheritance
Embryo, Mammalian/microbiology
Host Microbial Interactions
Pregnancy

@article {pmid39637856,
year = {2024},
author = {Caty, SN and Alvarez-Buylla, A and Vasek, C and Tapia, EE and Martin, NA and McLaughlin, T and Golde, CL and Weber, PK and Mayali, X and Coloma, LA and Morris, MM and O'Connell, LA},
title = {Alkaloids are associated with increased microbial diversity and metabolic function in poison frogs.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2024.10.069},
pmid = {39637856},
issn = {1879-0445},
abstract = {Shifts in host-associated microbiomes can impact both host and microbes.[1][,][2][,][3][,][4][,][5][,][6] It is of interest to understand how perturbations, like the introduction of exogenous chemicals,[7][,][8][,][9][,][10][,][11][,][12][,][13] impact microbiomes. In poison frogs (family Dendrobatidae), the skin microbiome is exposed to alkaloids that the frogs sequester for defense.[14][,][15][,][16][,][17][,][18][,][19] These alkaloids are antimicrobial[20][,][21][,][22]; however, their effect on the frogs' skin microbiome is unknown. To test this, we characterized microbial communities from field-collected dendrobatid frogs. Then, we conducted a laboratory experiment to monitor the effect of the alkaloid decahydroquinoline (DHQ) on the microbiome of two frog species with contrasting alkaloid loads in nature. In both datasets, we found that alkaloid-exposed microbiomes were more phylogenetically diverse, with an increase in diversity among rare taxa. To better understand the isolate-specific response to alkaloids, we cultured microbial isolates from poison frog skin and found that many isolates exhibited enhanced growth or were not impacted by the addition of DHQ. To further explore the microbial response to alkaloids, we sequenced the metagenomes from high- and low-alkaloid frogs and observed a greater diversity of genes associated with nitrogen and carbon metabolism in high-alkaloid frogs. From these data, we hypothesized that some strains may metabolize the alkaloids. We used stable isotope tracing coupled to nanoSIMS (nanoscale secondary ion mass spectrometry), which supported the idea that some of these isolates are able to metabolize DHQ. Together, these data suggest that poison frog alkaloids open new niches for skin-associated microbes with specific adaptations, such as alkaloid metabolism, that enable survival in this environment.},
}

@article {pmid39378970,
year = {2025},
author = {Zharikova, AA and Andrianova, NV and Silachev, DN and Nebogatikov, VO and Pevzner, IB and Makievskaya, CI and Zorova, LD and Maleev, GV and Baydakova, GV and Chistyakov, DV and Goriainov, SV and Sergeeva, MG and Burakova, IY and Gureev, AP and Popkov, VA and Ustyugov, AA and Plotnikov, EY},
title = {Analysis of the brain transcriptome, microbiome and metabolome in ketogenic diet and experimental stroke.},
journal = {Brain, behavior, and immunity},
volume = {123},
number = {},
pages = {571-585},
doi = {10.1016/j.bbi.2024.10.004},
pmid = {39378970},
issn = {1090-2139},
mesh = {Animals ; *Diet, Ketogenic/methods ; Rats ; *Brain/metabolism ; *Gastrointestinal Microbiome/physiology ; Male ; *Metabolome ; *Transcriptome ; *Stroke/metabolism ; *Infarction, Middle Cerebral Artery/metabolism ; Disease Models, Animal ; Rats, Sprague-Dawley ; },
abstract = {The ketogenic diet (KD) has been shown to be effective in treating various brain pathologies. In this study, we conducted detailed transcriptomic and metabolomic profiling of rat brains after KD and ischemic stroke in order to investigate the effects of KD and its underlying mechanisms. We evaluated the effect of a two-month KD on gene expression in intact brain tissue and after middle cerebral artery occlusion (MCAO). We analyzed the effects of KD on gut microbiome composition and blood metabolic profile as well as investigated the correlation between severity of neurological deficits and KD-induced changes. We found transcriptional reprogramming in the brain after stroke and KD treatment. The KD altered the expression of genes involved in the regulation of glucose and fatty acid metabolism, mitochondrial function, the immune response, Wnt-associated signaling, stem cell development, and neurotransmission, both in intact rats and after MCAO. The KD led to a significant change in the composition of gut microbiome and the levels of amino acids, acylcarnitines, polyunsaturated fatty acids, and oxylipins in the blood. However, the KD slightly worsened the neurological functions after MCAO, so that the therapeutic effect of the diet remained unproven.},
}

Animals
*Diet, Ketogenic/methods
Rats
*Brain/metabolism
*Gastrointestinal Microbiome/physiology
Male
*Metabolome
*Transcriptome
*Stroke/metabolism
*Infarction, Middle Cerebral Artery/metabolism
Disease Models, Animal
Rats, Sprague-Dawley

@article {pmid39368785,
year = {2025},
author = {Malan-Müller, S and Martín-Hernández, D and Caso, JR and Matthijnssens, J and Rodríguez-Urrutia, A and Lowry, CA and Leza, JC},
title = {Metagenomic symphony of the intestinal ecosystem: How the composition affects the mind.},
journal = {Brain, behavior, and immunity},
volume = {123},
number = {},
pages = {510-523},
doi = {10.1016/j.bbi.2024.09.033},
pmid = {39368785},
issn = {1090-2139},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Brain-Gut Axis/physiology ; Neurodegenerative Diseases/microbiology ; Metagenomics/methods ; Mental Disorders/microbiology/metabolism ; Animals ; Probiotics ; Mental Health ; Brain/metabolism/physiology ; Bacteria/metabolism ; Metagenome ; },
abstract = {Mental health disorders and neurodegenerative diseases place a heavy burden on patients and societies, and, although great strides have been made to understand the pathophysiology of these conditions, advancement in drug development is lagging. The importance of gastrointestinal health in maintaining overall health and preventing disease is not a new concept. Hundreds of years ago, healers from various cultures and civilizations recognized the crucial role of the gut in sustaining health. More than a century ago, scientists began exploring the restorative effects of probiotics, marking the early recognition of the importance of gut microbes. The omics era brought more enlightenment and enabled researchers to identify the complexity of the microbial ecosystems we harbour, encompassing bacteria, eukaryotes (including fungi), archaea, viruses, and other microorganisms. The extensive genetic capacity of the microbiota is dynamic and influenced by the environment. The microbiota therefore serves as a significant entity within us, with evolutionarily preserved functions in host metabolism, immunity, development, and behavior. The significant role of the bacterial gut microbiome in mental health and neurodegenerative disorders has been realized and described within the framework of the microbiota-gut-brain axis. However, the bacterial members do not function unaccompanied, but rather in concert, and there is a substantial knowledge gap regarding the involvement of non-bacterial microbiome members in these disorders. In this review, we will explore the current literature that implicates a role for the entire metagenomic ensemble, and how their complex interkingdom relationships could influence CNS functioning in mental health disorders and neurodegenerative diseases.},
}

Humans
*Gastrointestinal Microbiome/physiology
Brain-Gut Axis/physiology
Neurodegenerative Diseases/microbiology
Metagenomics/methods
Mental Disorders/microbiology/metabolism
Animals
Probiotics
Mental Health
Brain/metabolism/physiology
Bacteria/metabolism
Metagenome

@article {pmid39635041,
year = {2024},
author = {Dora, D and Revisnyei, P and Mihucz, A and Kiraly, P and Szklenarik, G and Dulka, E and Galffy, G and Lohinai, Z},
title = {Metabolic pathways from the gut metatranscriptome are associated with COPD and respiratory function in lung cancer patients.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1381170},
pmid = {39635041},
issn = {2235-2988},
mesh = {Humans ; *Pulmonary Disease, Chronic Obstructive/microbiology/metabolism/physiopathology ; *Gastrointestinal Microbiome/genetics ; *Metabolic Networks and Pathways/genetics ; *Lung Neoplasms/microbiology/genetics ; Male ; *Feces/microbiology ; Female ; Aged ; Middle Aged ; Carcinoma, Non-Small-Cell Lung/genetics/microbiology ; Transcriptome ; Metagenomics/methods ; Bacteria/genetics/classification/isolation & purification/metabolism ; Streptococcus/genetics/isolation & purification/metabolism ; },
abstract = {INTRODUCTION: Changes in the human gut microbiome have been linked to various chronic diseases, including chronic obstructive pulmonary disease (COPD). While substantial knowledge is available on the genomic features of fecal communities, little is known about the microbiome's transcriptional activity. Here, we analyzed the metatranscriptomic (MTR) abundance of MetaCyc pathways, SuperPathways, and protein domain families (PFAM) represented by the gut microbiome in a cohort of non-small cell lung cancer (NSCLC) patients with- or without COPD comorbidity.

METHODS: Fecal samples of 40 NSCLC patients with- or without COPD comorbidity were collected at the time of diagnosis. Data was preprocessed using the Metaphlan3/Humann3 pipeline and BioCyc[©] to identify metabolic SuperPathways. LEfSe analysis was conducted on Pathway- and PFAM abundance data to determine COPD- and non-COPD-related clusters.

RESULTS: Key genera Streptococcus, Escherichia, Gemella, and Lactobacillus were significantly more active transcriptionally compared to their metagenomic presence. LEfSe analysis identified 11 MetaCyc pathways that were significantly overrepresented in patients with- and without COPD comorbidity. According to Spearman's rank correlation, Smoking PY showed a significant negative correlation with Glycolysis IV, Purine Ribonucleoside Degradation and Glycogen Biosynthesis I, and a significant positive correlation with Superpathway of Ac-CoA Biosynthesis and Glyoxylate cycle, whereas forced expiratory volume in the first second (FEV1) showed a significant negative correlation with Glycolysis IV and a significant positive correlation with Glycogen Biosynthesis I. Furthermore, COPD patients showed a significantly increased MTR abundance in ~60% of SuperPathways, indicating a universally increased MTR activity in this condition. FEV1 showed a significant correlation with SuperPathways Carbohydrate degradation, Glycan biosynthesis, and Glycolysis. Taxonomic analysis suggested a more prominent MTR activity from multiple Streptococcus species, Enterococcus (E.) faecalis, E. faecium and Escherichia (E.) coli than expected from their metagenomic abundance. Multiple protein domain families (PFAMs) were identified as more associated with COPD, E. faecium, E.coli, and Streptococcus salivarius, contributing the most to these PFAMs.

CONCLUSION: Metatranscriptome analysis identified COPD-related subsets of lung cancer with potential therapeutic relevance.},
}

Humans
*Pulmonary Disease, Chronic Obstructive/microbiology/metabolism/physiopathology
*Gastrointestinal Microbiome/genetics
*Metabolic Networks and Pathways/genetics
*Lung Neoplasms/microbiology/genetics
Male
*Feces/microbiology
Female
Aged
Middle Aged
Carcinoma, Non-Small-Cell Lung/genetics/microbiology
Transcriptome
Metagenomics/methods
Bacteria/genetics/classification/isolation & purification/metabolism
Streptococcus/genetics/isolation & purification/metabolism

@article {pmid39632378,
year = {2024},
author = {Li, Y and Hu, W and Lin, B and Ma, T and Zhang, Z and Hu, W and Zhou, R and Kwok, LY and Sun, Z and Zhu, C and Zhang, H},
title = {Omic characterizing and targeting gut dysbiosis in children with autism spectrum disorder: symptom alleviation through combined probiotic and medium-carbohydrate diet intervention - a pilot study.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2434675},
doi = {10.1080/19490976.2024.2434675},
pmid = {39632378},
issn = {1949-0984},
mesh = {Humans ; *Autism Spectrum Disorder/diet therapy/microbiology ; Pilot Projects ; *Probiotics/administration & dosage ; *Gastrointestinal Microbiome ; *Dysbiosis/microbiology/diet therapy/therapy ; Male ; Child ; Female ; *Feces/microbiology/chemistry ; Child, Preschool ; Bacteria/classification/isolation & purification/genetics/metabolism ; Dietary Carbohydrates/metabolism/administration & dosage ; Bifidobacterium animalis ; },
abstract = {Autism spectrum disorder (ASD) currently lacks effective diagnostic and therapeutic approaches. Disruptions in the gut ecosystem have been observed in individuals with ASD, suggesting that targeting gut microbiota through probiotic and dietary supplementation may serve as a potential treatment strategy. This two-phase study aimed to characterize the fecal metagenome of children with ASD and investigate the beneficial effects of a combined probiotic and medium-carbohydrate intervention in ASD. Fecal metagenomes of children with ASD were compared to those of typically developing children, revealing intestinal dysbiosis in ASD, characterized by reduced levels of Prevotella sp. Dialister invisus, and Bacteroides sp. along with increased predicted abundances of inosine, glutamate, xanthine, and methylxanthine. The gut bacteriome and phageome exhibited high cooperativity. In a 3-month pilot study, Bifidobacterium animalis subsp. lactis Probio-M8 (Probio-M8) was administered alongside a medium-carbohydrate diet to Chinese children with ASD. The primary endpoint was the Childhood Autism Rating Scale (CARS), while the secondary endpoint was the Gastrointestinal Symptom Rating Scale (GSRS). A total of 72 autistic children were initially recruited for the intervention study, but only 53 completed the intervention. Probio-M8, in combination with dietary intervention, significantly improved CARS and GSRS scores, increased fecal levels of Bifidobacterium animalis, Akkermansia muciniphila, Fusicatenibacter saccharivorans, and Sutterella sp. while also reducing Blautia obeum (Benjamini-Hochberg corrected p ≤ 0.05 for all cases). The intervention also modulated fecal metabolites associated with the metabolism of amino acids (lysine), neurotransmitters (glutamate, γ-aminobutyric acid), polyunsaturated fatty acids (arachidonate, myristic acid), and vitamin B3. In conclusion, Probio-M8 combined with medium-carbohydrate diet effectively improved ASD symptoms, with associated changes in the gut microbiome and metabolome, supporting its potential as an adjunctive therapy for ASD.},
}

Humans
*Autism Spectrum Disorder/diet therapy/microbiology
Pilot Projects
*Probiotics/administration & dosage
*Gastrointestinal Microbiome
*Dysbiosis/microbiology/diet therapy/therapy
Male
Child
Female
*Feces/microbiology/chemistry
Child, Preschool
Bacteria/classification/isolation & purification/genetics/metabolism
Dietary Carbohydrates/metabolism/administration & dosage
Bifidobacterium animalis

@article {pmid39631543,
year = {2024},
author = {Qu, M and Zheng, Y and Cheng, Z and Shi, Y and Wang, W and Wu, X and Chen, J},
title = {Mechanism of chlorobenzene removal in biotrickling filter enhanced by non-thermal plasma: Insights from biodiversity and functional gene perspectives.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {131931},
doi = {10.1016/j.biortech.2024.131931},
pmid = {39631543},
issn = {1873-2976},
abstract = {Biotrickling filter (BTF) technology is inefficient in the treatment of Cl-containing volatile organic compounds (VOCs) such as chlorobenzene (CB). This study adopted non-thermal plasma (NTP) as a pretreatment and conducted in-depth analyses, especially in microorganisms, to investigate strengthening mechanism of a NTP to a BTF in the process. The introduction of NTP enhance efficiency of CB removal from 65 % to 90 %, and CO2 generation from 60 % to 85 %. It is found that the protein content of the extracellular polymeric substances increases from 212 × 10[-3] mg·g[-1] filler to 299 × 10[-3] mg·g[-1] filler, thus CB capturing and utilization enhanced. Metagenomic analysis showed that bacteria with CB-degrading properties were enriched in BTF, and CB was involved in cellular metabolism as a carbon source. The presence of active substances from NTP is found to stimulate the ability of BTF treatment. The findings of this study will provide theoretical support for the application of NTP-BTF technology.},
}

@article {pmid39580871,
year = {2025},
author = {Kumar, S and Bhatia, Z and Seshadri, S},
title = {Formulated chitosan microspheres remodelled the altered gut microbiota and liver miRNA in diet-induced Type-2 diabetic rats.},
journal = {Carbohydrate research},
volume = {547},
number = {},
pages = {109301},
doi = {10.1016/j.carres.2024.109301},
pmid = {39580871},
issn = {1873-426X},
mesh = {*Chitosan/pharmacology/chemistry ; Animals ; *Gastrointestinal Microbiome/drug effects ; *MicroRNAs/metabolism ; *Microspheres ; Rats ; Male ; *Diabetes Mellitus, Type 2/drug therapy/metabolism ; *Diabetes Mellitus, Experimental/drug therapy/chemically induced/metabolism ; *Liver/drug effects/pathology/metabolism ; Hypoglycemic Agents/pharmacology/chemistry ; Metformin/pharmacology ; Diet, High-Fat/adverse effects ; },
abstract = {Chitosan was formulated into a microsphere and comprehensively characterized and evaluated for its anti-inflammatory potential and anti-diabetic properties against the high sugar fat diet-induced diabetic animals. The diabetic model was induced through feeding with a high-sugar fat diet. Metformin, a standard antidiabetic drug, and CMS (chitosan microspheres) were administered orally for 90 days as reversal strategies. Upon completion of the study, the following parameters, such as serum biochemistry, cytokine analysis, tissue histology, liver miRNA sequencing, and Shotgun metagenomics studies from stool samples, were performed. SEM images of the microsphere indicated a smooth morphology, while FTIR and DSC respectively, confirmed the presence of functional groups of chitosan and the thermal stability of the formulation. Following HSFD induction, all the parameters analyzed were altered compared to the control group. In both reversal groups, serum biochemical parameters were restored, which was at par with the control. A significant increase in the anti-inflammatory cytokine IL-10, and a remarkable reduction in TNF-α and MCP-1 inflammatory cytokines were observed in both reversal groups. Tissue histology indicated improvements in low-grade inflammation, induced in the diabetic group. miR-203 was upregulated in the CMS-treated group, while miR-103 was downregulated. The study further delved into the impact on gut microbiota and KEGG. Major phyla i.e., Bacteroidetes, Cyanobacteria, Firmicutes, Proteobacteria, and Verrucomicrobia showed restoration, while upregulation of DNA polymerase zeta in T2D showed reversal after the treatment. The formulation showed reversal at par with metformin and also confirms its anti-diabetic and anti-inflammatory activities of CMS, with microfloral and miR regulatory functions.},
}

*Chitosan/pharmacology/chemistry
Animals
*Gastrointestinal Microbiome/drug effects
*MicroRNAs/metabolism
*Microspheres
Rats
Male
*Diabetes Mellitus, Type 2/drug therapy/metabolism
*Diabetes Mellitus, Experimental/drug therapy/chemically induced/metabolism
*Liver/drug effects/pathology/metabolism
Hypoglycemic Agents/pharmacology/chemistry
Metformin/pharmacology
Diet, High-Fat/adverse effects

@article {pmid39571000,
year = {2024},
author = {Zapién-Campos, R and Bansept, F and Traulsen, A},
title = {Stochastic models allow improved inference of microbiome interactions from time series data.},
journal = {PLoS biology},
volume = {22},
number = {11},
pages = {e3002913},
doi = {10.1371/journal.pbio.3002913},
pmid = {39571000},
issn = {1545-7885},
mesh = {*Stochastic Processes ; *Microbiota ; Models, Biological ; Metagenome ; Humans ; Microbial Interactions/physiology ; Algorithms ; },
abstract = {How can we figure out how the different microbes interact within microbiomes? To combine theoretical models and experimental data, we often fit a deterministic model for the mean dynamics of a system to averaged data. However, in the averaging procedure a lot of information from the data is lost-and a deterministic model may be a poor representation of a stochastic reality. Here, we develop an inference method for microbiomes based on the idea that both the experiment and the model are stochastic. Starting from a stochastic model, we derive dynamical equations not only for the average, but also for higher statistical moments of the microbial abundances. We use these equations to infer distributions of the interaction parameters that best describe the biological experimental data-improving identifiability and precision. The inferred distributions allow us to make predictions but also to distinguish between fairly certain parameters and those for which the available experimental data does not give sufficient information. Compared to related approaches, we derive expressions that also work for the relative abundance of microbes, enabling us to use conventional metagenome data, and account for cases where not a single host, but only replicate hosts, can be tracked over time.},
}

*Stochastic Processes
*Microbiota
Models, Biological
Metagenome
Humans
Microbial Interactions/physiology
Algorithms

@article {pmid39271424,
year = {2024},
author = {Bokulich, NA and Robeson, MS},
title = {Bioinformatics challenges for profiling the microbiome in cancer: pitfalls and opportunities.},
journal = {Trends in microbiology},
volume = {32},
number = {12},
pages = {1163-1166},
doi = {10.1016/j.tim.2024.08.011},
pmid = {39271424},
issn = {1878-4380},
mesh = {Humans ; *Neoplasms/microbiology ; *Microbiota ; *Computational Biology/methods ; *Metagenomics/methods ; *Machine Learning ; Sequence Analysis, DNA/methods ; },
abstract = {Increasing evidence suggests that the human microbiome plays an important role in cancer risk and treatment. Untargeted 'omics' techniques have accelerated research into microbiome-cancer interactions, supporting the discovery of novel associations and mechanisms. However, these techniques require careful selection and use to avoid biases and other pitfalls. In this essay, we discuss selected challenges involved in the analysis of microbiome data in the context of cancer, including the application of machine learning (ML). We focus on DNA sequencing-based (e.g., metagenomics) methods, but many of the pitfalls and opportunities generalize to other omics technologies as well. We advocate for extended training opportunities, community standards, and best practices for sharing data and code to advance transparency and reproducibility in cancer microbiome research.},
}

Humans
*Neoplasms/microbiology
*Microbiota
*Computational Biology/methods
*Metagenomics/methods
*Machine Learning
Sequence Analysis, DNA/methods

@article {pmid39629792,
year = {2024},
author = {González-García, S and Hamdan-Partida, A and Pérez-Ramos, J and Aguirre-Garrido, JF and Bustos-Hamdan, A and Bustos-Martínez, J},
title = {Comparison of the bacterial microbiome in the pharynx and nasal cavity of persistent, intermittent carriers and non-carriers of Staphylococcus aureus.},
journal = {Journal of medical microbiology},
volume = {73},
number = {12},
pages = {},
doi = {10.1099/jmm.0.001940},
pmid = {39629792},
issn = {1473-5644},
mesh = {Humans ; *Pharynx/microbiology ; *Staphylococcus aureus/isolation & purification/genetics ; *Carrier State/microbiology ; *Nasal Cavity/microbiology ; *Microbiota ; *Staphylococcal Infections/microbiology ; Male ; Female ; Adult ; Young Adult ; RNA, Ribosomal, 16S/genetics ; DNA, Bacterial/genetics ; },
abstract = {Introduction. Staphylococcus aureus is a bacterium that colonizes various human sites. The pharynx has been considered as a site of little clinical relevance and little studied. Recently, it has been reported that S. aureus can colonize more the pharynx than the nose. In addition, S. aureus can persist in these sites for prolonged periods of time.Hypothesis. The composition of the pharyngeal and nasal microbiome will differ between persistent, intermittent carriers and non-carriers of S. aureus.Aim. Determine whether the pharyngeal and nasal microbiome is different between carriers and non-carriers of S. aureus.Methodology. S. aureus carriers were monitored by means of pharyngeal and nasal exudates of apparently healthy adult university students for 3 months. Samples from individuals of the same carrier type were pooled, and DNA was extracted and the 16S rRNA was sequenced. The sequences were analysed in MOTHUR v.1.48.0 software, by analysing the percentages of relative abundance in the STAMP 2.1.3 program, in addition to the predictive analysis of metabolic pathways in PICRUSt2.Results. A greater colonization of S. aureus was found in the pharynx than in the nose. The microbiomes of S. aureus carriers and non-carriers do not show significant differences. The main microbiome difference found was between pharyngeal and nasal microbiomes. No significant differences were found in the abundance of the genus Staphylococcus in pharyngeal and nasal S. aureus carriers and non-carriers. The nasal microbiome was found to have more variation compared to the pharyngeal microbiome, which appears to be more stable between individuals and pools. Predictive analysis of metabolic pathways showed a greater presence of Staphylococcus-associated pathways in the nose than in the pharynx.Conclusion. S. aureus can colonize and persist in the pharynx in equal or greater proportion than in the nose. No statistically significant differences were found in the microbiome of the pharyngeal and nasal carriers and non-carriers of S. aureus, but the pharyngeal and nasal microbiomes are different independent of the type of S. aureus carrier or non-carrier. Therefore, the microbiome apparently does not influence the persistence of S. aureus.},
}

Humans
*Pharynx/microbiology
*Staphylococcus aureus/isolation & purification/genetics
*Carrier State/microbiology
*Nasal Cavity/microbiology
*Microbiota
*Staphylococcal Infections/microbiology
Male
Female
Adult
Young Adult
RNA, Ribosomal, 16S/genetics
DNA, Bacterial/genetics

@article {pmid39629129,
year = {2024},
author = {Zhao, Q and Lu, Y and Duan, J and Du, D and Pu, Q and Li, F},
title = {Gut microbiota depletion and FXR inhibition exacerbates zonal hepatotoxicity of sunitinib.},
journal = {Theranostics},
volume = {14},
number = {18},
pages = {7219-7240},
pmid = {39629129},
issn = {1838-7640},
mesh = {Animals ; *Sunitinib/toxicity ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Chemical and Drug Induced Liver Injury/pathology/etiology ; *Liver/drug effects/pathology ; *Mice, Knockout ; *Receptors, Cytoplasmic and Nuclear/metabolism ; Male ; Hepatocytes/drug effects ; Mice, Inbred C57BL ; Endothelial Cells/drug effects ; Apoptosis/drug effects ; Bacteroidetes/drug effects ; Autophagy/drug effects ; },
abstract = {Rationale: Sunitinib is a small-molecule tyrosine kinase inhibitor associated with the side-effect of liver injury. The impaired cell type in liver and the hepatotoxicity mechanisms is still unclear. Methods: Spatial metabolomics, transmission electron microscopy, immunofluorescence co-staining, and isolation of bile duct cells and liver sinusoidal endothelial cells (LSECs) were used to evaluate the zonated hepatotoxicity of sunitinib. Farnesoid X receptor (FXR) conditional knockout mice, metagenomics analysis, bacteria clearance, bacterial culture, Parabacteroides distasonis and 3-oxolithocholic acid supplementation were used to evaluate the hepatotoxicity mechanisms of sunitinib. Results: Phenotype analysis found that hepatic autophagy, apoptosis, and mitochondrial injury were observed in vivo or in vitro after sunitinib treatment. By using spatial metabolomics and isolation of bile duct cells and LSECs, the zonated drug toxicity was observed around the portal vein. Hepatocytes, bile duct cells, and LSECs were damaged after sunitinib treatment. FXR inhibition and gut microbiota depletion aggravated sunitinib-induced liver injury. For diurnal variation, sunitinib-induced liver injury was enhanced at night compared with that at day, and FXR and gut microbiota participated in circadian rhythmic hepatotoxicity induced by sunitinib. Conclusions: Our data suggested activation of FXR and Parabacteroides distasonis supplementation may be used to improve sunitinib-induced hepatotoxicity.},
}

Animals
*Sunitinib/toxicity
*Gastrointestinal Microbiome/drug effects
Mice
*Chemical and Drug Induced Liver Injury/pathology/etiology
*Liver/drug effects/pathology
*Mice, Knockout
*Receptors, Cytoplasmic and Nuclear/metabolism
Male
Hepatocytes/drug effects
Mice, Inbred C57BL
Endothelial Cells/drug effects
Apoptosis/drug effects
Bacteroidetes/drug effects
Autophagy/drug effects

@article {pmid39628196,
year = {2024},
author = {Li, ZX and Li, JH and Zhang, Q and Lu, JJ and Gao, CH and Jin, DS and Xu, MG},
title = {[Response and Assembly Process of Soil Microbial Communities Under Different Reclamation Measures].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {45},
number = {12},
pages = {7326-7336},
doi = {10.13227/j.hjkx.202312247},
pmid = {39628196},
issn = {0250-3301},
mesh = {*Soil Microbiology ; *Fungi/classification ; *Bacteria/classification/genetics/growth & development/isolation & purification ; Mining ; Nitrogen ; Soil/chemistry ; Phosphorus ; Environmental Restoration and Remediation/methods ; Microbiota ; Ecosystem ; },
abstract = {Reclamation is essential for restoring the ecological function of soil in mining areas. However, the microbiological mechanism of soil ecological function reconstruction under different reclamation measures still needs to be clarified. Clarifying the characteristics of soil bacterial and fungal communities, assembly mechanisms, and their relationship with physicochemical properties under different reclamation measures is crucial for reshaping the ecological stability of soil in mining areas. Metagenomic sequencing technology was combined with the null model and neutral model to analyze the differences in soil microbial diversity, community composition, network structure, and community assembly process between the reclaimed natural recovery area （LH） and the reclamation fertilization area （MM）. The results suggested that： ① Compared with that in the LH treatment, the MM treatment significantly increased the soil nutrient content, and the total nitrogen （TN）, total phosphorus （TP）, available phosphorus （AP）, and available potassium （AK） contents increased by 34.70%, 72.72%, 468.98%, and 45.74%, respectively （P<0.05）. ② The dominant bacterial and fungal communities did not change under the LH and MM treatments； however, the abundance of bacterial communities changed significantly. Compared with that in the LH treatment, the relative abundance of Acidobacteria increased significantly by 5.4% in the MM treatment, while the relative abundance of Candidatus Rokubacteria decreased significantly by 235.72% （P<0.05）. Under different reclamation measures, the indicator microorganisms of bacterial and fungal communities changed. ③ Compared with that in the LH treatment, the MM treatment increased the complexity of bacterial networks, decreased the complexity of fungal networks, and increased the number of soil bacterial nodes and links. The reclamation measures transformed the key bacterial groups from Proteobacteria to Candidatus Rokubacteria and Planctomycetes. The key group of fungi was Ascomycota. 4.） The deterministic process dominated the assembly of bacterial and fungal communities. Homogeneous selection contributed the most to the bacterial community assembly in the LH treatment, and heterogeneous selection contributed the most to the MM treatment. The fungal communities were all dominated by heterogeneous selection. These results provide new insights into the soil microbial community structure and ecological function restoration in coal mining subsidence reclamation areas.},
}

*Soil Microbiology
*Fungi/classification
*Bacteria/classification/genetics/growth & development/isolation & purification
Mining
Nitrogen
Soil/chemistry
Phosphorus
Environmental Restoration and Remediation/methods
Microbiota
Ecosystem