@article {pmid37234538,
year = {2023},
author = {Sarrocco, S and Herrera-Estrella, A and Collinge, DB},
title = {Editorial: Plant disease management in the post-genomic era: from functional genomics to genome editing, Volume II.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1203870},
pmid = {37234538},
issn = {1664-302X},
}

@article {pmid37233257,
year = {2023},
author = {Ahmad, N and Ritz, M and Calchera, A and Otte, J and Schmitt, I and Brueck, T and Mehlmer, N},
title = {Biosynthetic Potential of Hypogymnia Holobionts: Insights into Secondary Metabolite Pathways.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {9},
number = {5},
pages = {},
pmid = {37233257},
issn = {2309-608X},
abstract = {Lichens are symbiotic associations consisting of a photobiont (algae or cyanobacteria) and a mycobiont (fungus). They are known to produce a variety of unique secondary metabolites. To access this biosynthetic potential for biotechnological applications, deeper insights into the biosynthetic pathways and corresponding gene clusters are necessary. Here we provide a comprehensive view of the biosynthetic gene clusters of all organisms comprising a lichen thallus: fungi, green algae, and bacteria. We present two high-quality PacBio metagenomes, in which we identified a total of 460 biosynthetic gene clusters. Lichen mycobionts yielded 73-114 clusters, other lichen associated ascomycetes 8-40, green algae of the genus Trebouxia 14-19, and lichen-associated bacteria 101-105 clusters. The mycobionts contained mainly T1PKSs, followed by NRPSs, and terpenes; Trebouxia reads harbored mainly clusters linked to terpenes, followed by NRPSs and T3PKSs. Other lichen-associated ascomycetes and bacteria contained a mix of diverse biosynthetic gene clusters. In this study, we identified for the first time the biosynthetic gene clusters of entire lichen holobionts. The yet untapped biosynthetic potential of two species of the genus Hypogymnia is made accessible for further research.},
}

@article {pmid37225687,
year = {2023},
author = {Zhao, F and Yang, L and Zhang, T and Zhuang, D and Wu, Q and Yu, J and Tian, C and Zhang, Z},
title = {Gut microbiome signatures of extreme environment adaption in Tibetan pig.},
journal = {NPJ biofilms and microbiomes},
volume = {9},
number = {1},
pages = {27},
pmid = {37225687},
issn = {2055-5008},
mesh = {Swine ; Animals ; *Gastrointestinal Microbiome ; Tibet ; Ultraviolet Rays ; Acclimatization ; Acetic Acid ; Extreme Environments ; Mammals ; },
abstract = {Tibetan pigs (TPs) can adapt to the extreme environments in the Tibetan plateau implicated by their self-genome signals, but little is known about roles of the gut microbiota in the host adaption. Here, we reconstructed 8210 metagenome-assembled genomes from TPs (n = 65) living in high-altitude and low-altitude captive pigs (87 from China-CPs and 200 from Europe-EPs) that were clustered into 1050 species-level genome bins (SGBs) at the threshold of 95% average nucleotide identity. 73.47% of SGBs represented new species. The gut microbial community structure analysis based on 1,048 SGBs showed that TPs was significantly different from low-altitude captive pigs. TP-associated SGBs enabled to digest multiple complex polysaccharides, including cellulose, hemicellulose, chitin and pectin. Especially, we found TPs showed the most common enrichment of phyla Fibrobacterota and Elusimicrobia, which were involved in the productions of short- and medium-chain fatty acids (acetic acid, butanoate and propanoate; octanomic, decanoic and dodecanoic acids), as well as in the biosynthesis of lactate, 20 essential amino acids, multiple B vitamins (B1, B2, B3, B5, B7 and B9) and cofactors. Unexpectedly, Fibrobacterota solely showed powerful metabolic capacity, including the synthesis of acetic acid, alanine, histidine, arginine, tryptophan, serine, threonine, valine, B2, B5, B9, heme and tetrahydrofolate. These metabolites might contribute to host adaptation to high-altitude, such as energy harvesting and resistance against hypoxia and ultraviolet radiation. This study provides insights into understanding the role of gut microbiome played in mammalian high-altitude adaptation and discovers some potential microbes as probiotics for improving animal health.},
}

Swine
Animals
*Gastrointestinal Microbiome
Tibet
Ultraviolet Rays
Acclimatization
Acetic Acid
Extreme Environments
Mammals

@article {pmid37223792,
year = {2023},
author = {Bertola, M and Righetti, L and Gazza, L and Ferrarini, A and Fornasier, F and Cirlini, M and Lolli, V and Galaverna, G and Visioli, G},
title = {Perenniality, more than genotypes, shapes biological and chemical rhizosphere composition of perennial wheat lines.},
journal = {Frontiers in plant science},
volume = {14},
number = {},
pages = {1172857},
pmid = {37223792},
issn = {1664-462X},
abstract = {Perennial grains provide various ecosystem services compared to the annual counterparts thanks to their extensive root system and permanent soil cover. However, little is known about the evolution and diversification of perennial grains rhizosphere and its ecological functions over time. In this study, a suite of -OMICSs - metagenomics, enzymomics, metabolomics and lipidomics - was used to compare the rhizosphere environment of four perennial wheat lines at the first and fourth year of growth in comparison with an annual durum wheat cultivar and the parental species Thinopyrum intermedium. We hypothesized that wheat perenniality has a greater role in shaping the rhizobiome composition, biomass, diversity, and activity than plant genotypes because perenniality affects the quality and quantity of C input - mainly root exudates - hence modulating the plant-microbes crosstalk. In support of this hypothesis, the continuous supply of sugars in the rhizosphere along the years created a favorable environment for microbial growth which is reflected in a higher microbial biomass and enzymatic activity. Moreover, modification in the rhizosphere metabolome and lipidome over the years led to changes in the microbial community composition favoring the coexistence of more diverse microbial taxa, increasing plant tolerance to biotic and abiotic stresses. Despite the dominance of the perenniality effect, our data underlined that the OK72 line rhizobiome distinguished from the others by the increase in abundance of Pseudomonas spp., most of which are known as potential beneficial microorganisms, identifying this line as a suitable candidate for the study and selection of new perennial wheat lines.},
}

@article {pmid37221274,
year = {2023},
author = {Megremis, S and Constantinides, B and Xepapadaki, P and Yap, CF and Sotiropoulos, AG and Bachert, C and Finotto, S and Jartti, T and Tapinos, A and Vuorinen, T and Andreakos, E and Robertson, DL and Papadopoulos, NG},
title = {Respiratory eukaryotic virome expansion and bacteriophage deficiency characterize childhood asthma.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {8319},
pmid = {37221274},
issn = {2045-2322},
mesh = {Child ; Humans ; Child, Preschool ; Eukaryota ; *Bacteriophages ; Virome ; Eukaryotic Cells ; *Asthma ; *Anelloviridae ; Asymptomatic Diseases ; },
abstract = {Asthma development and exacerbation is linked to respiratory virus infections. There is limited information regarding the presence of viruses during non-exacerbation/infection periods. We investigated the nasopharyngeal/nasal virome during a period of asymptomatic state, in a subset of 21 healthy and 35 asthmatic preschool children from the Predicta cohort. Using metagenomics, we described the virome ecology and the cross-species interactions within the microbiome. The virome was dominated by eukaryotic viruses, while prokaryotic viruses (bacteriophages) were independently observed with low abundance. Rhinovirus B species consistently dominated the virome in asthma. Anelloviridae were the most abundant and rich family in both health and asthma. However, their richness and alpha diversity were increased in asthma, along with the co-occurrence of different Anellovirus genera. Bacteriophages were richer and more diverse in healthy individuals. Unsupervised clustering identified three virome profiles that were correlated to asthma severity and control and were independent of treatment, suggesting a link between the respiratory virome and asthma. Finally, we observed different cross-species ecological associations in the healthy versus the asthmatic virus-bacterial interactome, and an expanded interactome of eukaryotic viruses in asthma. Upper respiratory virome "dysbiosis" appears to be a novel feature of pre-school asthma during asymptomatic/non-infectious states and merits further investigation.},
}

Child
Humans
Child, Preschool
Eukaryota
*Bacteriophages
Virome
Eukaryotic Cells
*Asthma
*Anelloviridae
Asymptomatic Diseases

@article {pmid37217592,
year = {2023},
author = {Waldrop, MP and Chabot, CL and Liebner, S and Holm, S and Snyder, MW and Dillon, M and Dudgeon, SR and Douglas, TA and Leewis, MC and Walter Anthony, KM and McFarland, JW and Arp, CD and Bondurant, AC and Taş, N and Mackelprang, R},
title = {Permafrost microbial communities and functional genes are structured by latitudinal and soil geochemical gradients.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
pmid = {37217592},
issn = {1751-7370},
abstract = {Permafrost underlies approximately one quarter of Northern Hemisphere terrestrial surfaces and contains 25-50% of the global soil carbon (C) pool. Permafrost soils and the C stocks within are vulnerable to ongoing and future projected climate warming. The biogeography of microbial communities inhabiting permafrost has not been examined beyond a small number of sites focused on local-scale variation. Permafrost is different from other soils. Perennially frozen conditions in permafrost dictate that microbial communities do not turn over quickly, thus possibly providing strong linkages to past environments. Thus, the factors structuring the composition and function of microbial communities may differ from patterns observed in other terrestrial environments. Here, we analyzed 133 permafrost metagenomes from North America, Europe, and Asia. Permafrost biodiversity and taxonomic distribution varied in relation to pH, latitude and soil depth. The distribution of genes differed by latitude, soil depth, age, and pH. Genes that were the most highly variable across all sites were associated with energy metabolism and C-assimilation. Specifically, methanogenesis, fermentation, nitrate reduction, and replenishment of citric acid cycle intermediates. This suggests that adaptations to energy acquisition and substrate availability are among some of the strongest selective pressures shaping permafrost microbial communities. The spatial variation in metabolic potential has primed communities for specific biogeochemical processes as soils thaw due to climate change, which could cause regional- to global- scale variation in C and nitrogen processing and greenhouse gas emissions.},
}

@article {pmid37215132,
year = {2023},
author = {Zhang, L and Wang, F and Jia, L and Yan, H and Gao, L and Tian, Y and Su, X and Zhang, X and Lv, C and Ma, Z and Xue, Y and Lin, Q and Wang, K},
title = {Edwardsiella piscicida infection reshapes the intestinal microbiome and metabolome of big-belly seahorses: mechanistic insights of synergistic actions of virulence factors.},
journal = {Frontiers in immunology},
volume = {14},
number = {},
pages = {1135588},
pmid = {37215132},
issn = {1664-3224},
mesh = {Animals ; Virulence Factors/metabolism ; *Gastrointestinal Microbiome ; Virulence ; *Smegmamorpha/metabolism ; Fishes/metabolism ; *Enteritis ; Metabolome ; },
abstract = {Uncovering the mechanism underlying the pathogenesis of Edwardsiella piscicida-induced enteritis is essential for global aquaculture. In the present study, we identified E. piscicida as a lethal pathogen of the big-belly seahorse (Hippocampus abdominalis) and revealed its pathogenic pattern and characteristics by updating our established bacterial enteritis model and evaluation system. Conjoint analysis of metagenomic and metabolomic data showed that 15 core virulence factors could mutually coordinate the remodeling of intestinal microorganisms and host metabolism and induce enteritis in the big-belly seahorse. Specifically, the Flagella, Type IV pili, and Lap could significantly increase the activities of the representative functional pathways of both flagella assembly and bacterial chemotaxis in the intestinal microbiota (P < 0.01) to promote pathogen motility, adherence, and invasion. Legiobactin, IraAB, and Hpt could increase ABC transporter activity (P < 0.01) to compete for host nutrition and promote self-replication. Capsule1, HP-NAP, and FarAB could help the pathogen to avoid phagocytosis. Upon entering epithelial cells and phagocytes, Bsa T3SS and Dot/Icm could significantly increase bacterial secretion system activity (P < 0.01) to promote the intracellular survival and replication of the pathogen and the subsequent invasion of the neighboring tissues. Finally, LPS3 could significantly increase lipopolysaccharide biosynthesis (P < 0.01) to release toxins and kill the host. Throughout the pathogenic process, BopD, PhoP, and BfmRS significantly activated the two-component system (P < 0.01) to coordinate with other VFs to promote deep invasion. In addition, the levels of seven key metabolic biomarkers, Taurine, L-Proline, Uridine, L-Glutamate, Glutathione, Xanthosine, and L-Malic acid, significantly decreased (P < 0.01), and they can be used for characterizing E. piscicida infection. Overall, the present study systematically revealed how a combination of virulence factors mediate E. piscicida-induced enteritis in fish for the first time, providing a theoretical reference for preventing and controlling this disease in the aquaculture of seahorses and other fishes.},
}

Animals
Virulence Factors/metabolism
*Gastrointestinal Microbiome
Virulence
*Smegmamorpha/metabolism
Fishes/metabolism
*Enteritis
Metabolome

@article {pmid37116481,
year = {2023},
author = {Manara, S and Selma-Royo, M and Huang, KD and Asnicar, F and Armanini, F and Blanco-Miguez, A and Cumbo, F and Golzato, D and Manghi, P and Pinto, F and Valles-Colomer, M and Amoroso, L and Corrias, MV and Ponzoni, M and Raffaetà, R and Cabrera-Rubio, R and Olcina, M and Pasolli, E and Collado, MC and Segata, N},
title = {Maternal and food microbial sources shape the infant microbiome of a rural Ethiopian population.},
journal = {Current biology : CB},
volume = {33},
number = {10},
pages = {1939-1950.e4},
doi = {10.1016/j.cub.2023.04.011},
pmid = {37116481},
issn = {1879-0445},
mesh = {Female ; Humans ; Infant ; Infant, Newborn ; *Microbiota ; Bacteria ; Milk, Human/microbiology ; Mothers ; *Gastrointestinal Microbiome ; Feces/microbiology ; },
abstract = {The human microbiome seeding starts at birth, when pioneer microbes are acquired mainly from the mother. Mode of delivery, antibiotic prophylaxis, and feeding method have been studied as modulators of mother-to-infant microbiome transmission, but other key influencing factors like modern westernized lifestyles with high hygienization, high-calorie diets, and urban settings, compared with non-westernized lifestyles have not been investigated yet. In this study, we explored the mother-infant sharing of characterized and uncharacterized microbiome members via strain-resolved metagenomics in a cohort of Ethiopian mothers and infants, and we compared them with four other cohorts with different lifestyles. The westernized and non-westernized newborns' microbiomes composition overlapped during the first months of life more than later in life, likely reflecting similar initial breast-milk-based diets. Ethiopian and other non-westernized infants shared a smaller fraction of the microbiome with their mothers than did most westernized populations, despite showing a higher microbiome diversity, and uncharacterized species represented a substantial fraction of those shared in the Ethiopian cohort. Moreover, we identified uncharacterized species belonging to the Selenomonadaceae and Prevotellaceae families specifically present and shared only in the Ethiopian cohort, and we showed that a locally produced fermented food, injera, can contribute to the higher diversity observed in the Ethiopian infants' gut with bacteria that are not part of the human microbiome but are acquired through fermented food consumption. Taken together, these findings highlight the fact that lifestyle can impact the gut microbiome composition not only through differences in diet, drug consumption, and environmental factors but also through its effect on mother-infant strain-sharing patterns.},
}

Female
Humans
Infant
Infant, Newborn
*Microbiota
Bacteria
Milk, Human/microbiology
Mothers
*Gastrointestinal Microbiome
Feces/microbiology

@article {pmid37213492,
year = {2023},
author = {Zhang, X and Liang, Y and Zheng, K and Wang, Z and Dong, Y and Liu, Y and Ren, L and Wang, H and Han, Y and McMinn, A and Sung, YY and Mok, WJ and Wong, LL and He, J and Wang, M},
title = {Characterization and genomic analysis of phage vB_ValR_NF, representing a new viral family prevalent in the Ulva prolifera blooms.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1161265},
pmid = {37213492},
issn = {1664-302X},
abstract = {INTRODUCTION: Vibrio is an important bacterial genus containing many pathogenic species. Although more and more Vibrio phages were isolated, the genome, ecology and evolution of Vibrio phages and their roles in bacteriophage therapy, have not been fully revealed.

METHODS: Novel Vibrio phage vB_ValR_NF infecting Vibrio alginolyticus was isolated from the coastal waters of Qingdao during the Ulva prolifera blooms, Characterization and genomic feature of phage vB_ValR_NF has been analysed using phage isolation, sequencing and metagenome method.

RESULTS AND DISCUSSION: Phage vB_ValR_NF has a siphoviral morphology (icosahedral head 114±1 nm in diameter; a tail length of 231±1 nm), a short latent period (30 minutes) and a large burst size (113 virions per cell), and the thermal/pH stability study showed that phage vB_ValR_NF was highly tolerant to a range of pHs (4-12) and temperatures (-20 - 45 °C), respectively. Host range analysis suggests that phage vB_ValR_NF not only has a high inhibitory ability against the host strain V. alginolyticus, but also can infect 7 other Vibrio strains. In addition, the phage vB_ValR_NF has a double-stranded 44, 507 bp DNA genome, with 43.10 % GC content and 75 open reading frames. Three auxiliary metabolic genes associated with aldehyde dehydrogenase, serine/threonine protein phosphatase and calcineurin-like phosphoesterase were predicted, might help the host V. alginolyticus occupy the survival advantage, thus improving the survival chance of phage vB_ValR_NF under harsh conditions. This point can be supported by the higher abundance of phage vB_ValR_NF during the U. prolifera blooms than in other marine environments. Further phylogenetic and genomic analysis shows that the viral group represented by Vibrio phage vB_ValR_NF is different from other well-defined reference viruses, and can be classified into a new family, named Ruirongviridae. In general, as a new marine phage infecting V. alginolyticus, phage vB_ValR_NF provides basic information for further molecular research on phage-host interactions and evolution, and may unravel a novel insight into changes in the community structure of organisms during the U. prolifera blooms. At the same time, its high tolerance to extreme conditions and excellent bactericidal ability will become important reference factors when evaluating the potential of phage vB_ValR_NF in bacteriophage therapy in the future.},
}

@article {pmid37210515,
year = {2023},
author = {Leleiwi, I and Rodriguez-Ramos, J and Shaffer, M and Sabag-Daigle, A and Kokkinias, K and Flynn, RM and Daly, RA and Kop, LFM and Solden, LM and Ahmer, BMM and Borton, MA and Wrighton, KC},
title = {Exposing new taxonomic variation with inflammation - a murine model-specific genome database for gut microbiome researchers.},
journal = {Microbiome},
volume = {11},
number = {1},
pages = {114},
pmid = {37210515},
issn = {2049-2618},
support = {R01AI143288/NH/NIH HHS/United States ; T32 GM132057/GM/NIGMS NIH HHS/United States ; },
mesh = {Humans ; Animals ; Mice ; *Gastrointestinal Microbiome/genetics ; Disease Models, Animal ; Mice, Inbred CBA ; *Microbiota ; Inflammation ; Bacteroidetes ; },
abstract = {BACKGROUND: The murine CBA/J mouse model widely supports immunology and enteric pathogen research. This model has illuminated Salmonella interactions with the gut microbiome since pathogen proliferation does not require disruptive pretreatment of the native microbiota, nor does it become systemic, thereby representing an analog to gastroenteritis disease progression in humans. Despite the value to broad research communities, microbiota in CBA/J mice are not represented in current murine microbiome genome catalogs.

RESULTS: Here we present the first microbial and viral genomic catalog of the CBA/J murine gut microbiome. Using fecal microbial communities from untreated and Salmonella-infected, highly inflamed mice, we performed genomic reconstruction to determine the impacts on gut microbiome membership and functional potential. From high depth whole community sequencing (~ 42.4 Gbps/sample), we reconstructed 2281 bacterial and 4516 viral draft genomes. Salmonella challenge significantly altered gut membership in CBA/J mice, revealing 30 genera and 98 species that were conditionally rare and unsampled in non-inflamed mice. Additionally, inflamed communities were depleted in microbial genes that modulate host anti-inflammatory pathways and enriched in genes for respiratory energy generation. Our findings suggest decreases in butyrate concentrations during Salmonella infection corresponded to reductions in the relative abundance in members of the Alistipes. Strain-level comparison of CBA/J microbial genomes to prominent murine gut microbiome databases identified newly sampled lineages in this resource, while comparisons to human gut microbiomes extended the host relevance of dominant CBA/J inflammation-resistant strains.

CONCLUSIONS: This CBA/J microbiome database provides the first genomic sampling of relevant, uncultivated microorganisms within the gut from this widely used laboratory model. Using this resource, we curated a functional, strain-resolved view on how Salmonella remodels intact murine gut communities, advancing pathobiome understanding beyond inferences from prior amplicon-based approaches. Salmonella-induced inflammation suppressed Alistipes and other dominant members, while rarer commensals like Lactobacillus and Enterococcus endure. The rare and novel species sampled across this inflammation gradient advance the utility of this microbiome resource to benefit the broad research needs of the CBA/J scientific community, and those using murine models for understanding the impact of inflammation on the gut microbiome more generally. Video Abstract.},
}

Humans
Animals
Mice
*Gastrointestinal Microbiome/genetics
Disease Models, Animal
Mice, Inbred CBA
*Microbiota
Inflammation
Bacteroidetes

@article {pmid37169197,
year = {2023},
author = {Wang, Y and Li, Q},
title = {Competition and interaction between DNRA and denitrification in composting ecosystems: Insights from metagenomic analysis.},
journal = {Bioresource technology},
volume = {381},
number = {},
pages = {129140},
doi = {10.1016/j.biortech.2023.129140},
pmid = {37169197},
issn = {1873-2976},
mesh = {Nitrates ; *Ammonium Compounds ; Denitrification ; *Composting ; *Microbiota ; Nitrogen ; Bacteria/genetics ; Oxidation-Reduction ; },
abstract = {This study investigated denitrification and dissimilatory nitrate reduction to ammonium (DNRA) competition for nitrite in composting of sugarcane pith and cow manure. Metagenomic analysis showed that Actinobacteria was the main DNRA microorganism. During heating phase and thermophilic phase, the abundances of denitrification functional genes (nirK and nirS decreased by 40.22% and 98.60%, respectively) and DNRA functional genes (nirB, nirD increased by 195.24% and 176.61%, and nrfA decreased by 45%, respectively) showed different trends. Interestingly, the abundance of nrfA increased by 250% during cooling and maturity phases. Mantel test revealed that competition between denitrification and DNRA microorganisms for NO2[-]-N limited the succession of their respective communities (P < 0.01). Network analysis showed that unclassified Solirubrobacterales, Altererythrobacter and Microbacterium were the key microorganisms in DNRA microbial communities. The results provided new insights into the key microorganisms and their driving factors affecting DNRA and nitrogen management in the composting ecosystems.},
}

Nitrates
*Ammonium Compounds
Denitrification
*Composting
*Microbiota
Nitrogen
Bacteria/genetics
Oxidation-Reduction

@article {pmid37161271,
year = {2023},
author = {Chen, B and Zhang, Z and Zhang, Q and Xu, N and Lu, T and Wang, T and Hong, W and Fu, Z and Penuelas, J and Gillings, M and Qian, H},
title = {Antimicrobial Peptides in the Global Microbiome: Biosynthetic Genes and Resistance Determinants.},
journal = {Environmental science & technology},
volume = {57},
number = {20},
pages = {7698-7708},
doi = {10.1021/acs.est.3c01664},
pmid = {37161271},
issn = {1520-5851},
mesh = {Humans ; Antimicrobial Cationic Peptides/genetics/pharmacology/chemistry ; Antimicrobial Peptides ; *Anti-Infective Agents ; *Microbiota ; *Gastrointestinal Microbiome ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Antimicrobial peptides are a promising new class of antimicrobials that could address the antibiotic resistance crisis, which poses a major threat to human health. These peptides are present in all kingdoms of life, but especially in microorganisms, having multiple origins in diverse taxa. To date, there has been no global study on the diversity of antimicrobial peptides, the hosts in which these occur, and the potential for resistance to these agents. Here, we investigated the diversity and number of antimicrobial peptides in four main habitats (aquatic, terrestrial, human, and engineered) by analyzing 52,515 metagenome-assembled genomes. The number of antimicrobial peptides was higher in the human gut microbiome than in other habitats, and most hosts of antimicrobial peptides were habitat-specific. The relative abundance of genes that confer resistance to antimicrobial peptides varied between habitats and was generally low, except for the built environment and on human skin. The horizontal transfer of potential resistance genes among these habitats was probably constrained by ecological barriers. We systematically quantified the risk of each resistance determinant to human health and found that nearly half of them pose a threat, especially those that confer resistance to multiple AMPs and polymyxin B. Our results help identify the biosynthetic potential of antimicrobial peptides in the global microbiome, further identifying peptides with a low risk of developing resistance.},
}

Humans
Antimicrobial Cationic Peptides/genetics/pharmacology/chemistry
Antimicrobial Peptides
*Anti-Infective Agents
*Microbiota
*Gastrointestinal Microbiome
Anti-Bacterial Agents/pharmacology

@article {pmid37031344,
year = {2023},
author = {Liao, H and Liu, C and Ai, C and Gao, T and Yang, QE and Yu, Z and Gao, S and Zhou, S and Friman, VP},
title = {Mesophilic and thermophilic viruses are associated with nutrient cycling during hyperthermophilic composting.},
journal = {The ISME journal},
volume = {17},
number = {6},
pages = {916-930},
pmid = {37031344},
issn = {1751-7370},
mesh = {*Composting ; *Viruses/genetics ; Archaea ; Bacteria/genetics ; *Microbiota/genetics ; Nutrients ; },
abstract = {While decomposition of organic matter by bacteria plays a major role in nutrient cycling in terrestrial ecosystems, the significance of viruses remains poorly understood. Here we combined metagenomics and metatranscriptomics with temporal sampling to study the significance of mesophilic and thermophilic bacteria and their viruses on nutrient cycling during industrial-scale hyperthermophilic composting (HTC). Our results show that virus-bacteria density dynamics and activity are tightly coupled, where viruses specific to mesophilic and thermophilic bacteria track their host densities, triggering microbial community succession via top-down control during HTC. Moreover, viruses specific to mesophilic bacteria encoded and expressed several auxiliary metabolic genes (AMGs) linked to carbon cycling, impacting nutrient turnover alongside bacteria. Nutrient turnover correlated positively with virus-host ratio, indicative of a positive relationship between ecosystem functioning, viral abundances, and viral activity. These effects were predominantly driven by DNA viruses as most detected RNA viruses were associated with eukaryotes and not associated with nutrient cycling during the thermophilic phase of composting. Our findings suggest that DNA viruses could drive nutrient cycling during HTC by recycling bacterial biomass through cell lysis and by expressing key AMGs. Viruses could hence potentially be used as indicators of microbial ecosystem functioning to optimize productivity of biotechnological and agricultural systems.},
}

*Composting
*Viruses/genetics
Archaea
Bacteria/genetics
*Microbiota/genetics
Nutrients

@article {pmid37208728,
year = {2023},
author = {Yu, J and Meng, J and Qin, Z and Yu, Y and Liang, Y and Wang, Y and Min, D},
title = {Dysbiosis of gut microbiota inhibits NMNAT2 to promote neurobehavioral deficits and oxidative stress response in the 6-OHDA-lesioned rat model of Parkinson's disease.},
journal = {Journal of neuroinflammation},
volume = {20},
number = {1},
pages = {117},
pmid = {37208728},
issn = {1742-2094},
mesh = {Rats ; Animals ; *Parkinson Disease/metabolism ; Oxidopamine/toxicity ; *Gastrointestinal Microbiome/physiology ; Dysbiosis/therapy/metabolism ; NAD ; Oxidative Stress ; },
abstract = {BACKGROUND: New data are accumulating on gut microbial dysbiosis in Parkinson's disease (PD), while the specific mechanism remains uncharacterized. This study aims to investigate the potential role and pathophysiological mechanism of dysbiosis of gut microbiota in 6-hydroxydopamine (6-OHDA)-induced PD rat models.

METHODS: The shotgun metagenome sequencing data of fecal samples from PD patients and healthy individuals were obtained from the Sequence Read Archive (SRA) database. The diversity, abundance, and functional composition of gut microbiota were further analyzed in these data. After the exploration of the functional pathway-related genes, KEGG and GEO databases were used to obtain PD-related microarray datasets for differential expression analysis. Finally, in vivo experiments were performed to confirm the roles of fecal microbiota transplantation (FMT) and upregulated NMNAT2 in neurobehavioral symptoms and oxidative stress response in 6-OHDA-lesioned rats.

RESULTS: Significant differences were found in the diversity, abundance, and functional composition of gut microbiota between PD patients and healthy individuals. Dysbiosis of gut microbiota could regulate NAD[+] anabolic pathway to affect the occurrence and development of PD. As a NAD[+] anabolic pathway-related gene, NMNAT2 was poorly expressed in the brain tissues of PD patients. More importantly, FMT or overexpression of NMNAT2 alleviated neurobehavioral deficits and reduced oxidative stress in 6-OHDA-lesioned rats.

CONCLUSIONS: Taken together, we demonstrated that dysbiosis of gut microbiota suppressed NMNAT2 expression, thus exacerbating neurobehavioral deficits and oxidative stress response in 6-OHDA-lesioned rats, which could be rescued by FMT or NMNAT2 restoration.},
}

Rats
Animals
*Parkinson Disease/metabolism
Oxidopamine/toxicity
*Gastrointestinal Microbiome/physiology
Dysbiosis/therapy/metabolism
NAD
Oxidative Stress

@article {pmid37208617,
year = {2023},
author = {Liao, F and Qian, J and Yang, R and Gu, W and Li, R and Yang, T and Fu, X and Yuan, B and Zhang, Y},
title = {Metagenomics of gut microbiome for migratory seagulls in Kunming city revealed the potential public risk to human health.},
journal = {BMC genomics},
volume = {24},
number = {1},
pages = {269},
pmid = {37208617},
issn = {1471-2164},
mesh = {Animals ; Humans ; *Gastrointestinal Microbiome/genetics ; Metagenomics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; *Viruses/genetics ; Bacteria/genetics ; DNA ; },
abstract = {BACKGROUND: Seagull as a migratory wild bird has become most popular species in southwest China since 1980s. Previously, we analyzed the gut microbiota and intestinal pathogenic bacteria configuration for this species by using 16S rRNA sequencing and culture methods. To continue in-depth research on the gut microbiome of migratory seagulls, the metagenomics, DNA virome and RNA virome were both investigated for their gut microbial communities of abundance and diversity in this study.

RESULTS: The metagenomics results showed 99.72% of total species was bacteria, followed by viruses, fungi, archaea and eukaryota. In particular, Shigella sonnei, Escherichia albertii, Klebsiella pneumonia, Salmonella enterica and Shigella flexneri were the top distributed taxa at species level. PCoA, NMDS, and statistics indicated some drug resistant genes, such as adeL, evgS, tetA, PmrF, and evgA accumulated as time went by from November to January of the next year, and most of these genes were antibiotic efflux. DNA virome composition demonstrated that Caudovirales was the most abundance virus, followed by Cirlivirales, Geplafuvirales, Petitvirales and Piccovirales. Most of these phages corresponded to Enterobacteriaceae and Campylobacteriaceae bacterial hosts respectively. Caliciviridae, Coronaviridae and Picornaviridae were the top distributed RNA virome at family level of this migratory animal. Phylogenetic analysis indicated the sequences of contigs of Gammacoronavirus and Deltacoronavirus had highly similarity with some coronavirus references.

CONCLUSIONS: In general, the characteristics of gut microbiome of migratory seagulls were closely related to human activities, and multiomics still revealed the potential public risk to human health.},
}

Animals
Humans
*Gastrointestinal Microbiome/genetics
Metagenomics
Phylogeny
RNA, Ribosomal, 16S/genetics
Feces/microbiology
*Viruses/genetics
Bacteria/genetics
DNA

@article {pmid37208450,
year = {2023},
author = {Mo, S and Yan, B and Gao, T and Li, J and Kashif, M and Song, J and Bai, L and Yu, D and Liao, J and Jiang, C},
title = {Sulfur metabolism in subtropical marine mangrove sediments fundamentally differs from other habitats as revealed by SMDB.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {8126},
pmid = {37208450},
issn = {2045-2322},
mesh = {*Microbiota ; Geologic Sediments ; Bacteria ; Archaea/genetics ; Sulfur/metabolism ; Phylogeny ; },
abstract = {Shotgun metagenome sequencing provides the opportunity to recover underexplored rare populations and identify difficult-to-elucidate biochemical pathways. However, information on sulfur genes, including their sequences, is scattered in public databases. Here, we introduce SMDB (https://smdb.gxu.edu.cn/)-a manually curated database of sulfur genes based on an in-depth review of the scientific literature and orthology database. The SMDB contained a total of 175 genes and covered 11 sulfur metabolism processes with 395,737 representative sequences affiliated with 110 phyla and 2340 genera of bacteria/archaea. The SMDB was applied to characterize the sulfur cycle from five habitats and compared the microbial diversity of mangrove sediments with that of other habitats. The structure and composition of microorganism communities and sulfur genes were significantly different among the five habitats. Our results show that microorganism alpha diversity in mangrove sediments was significantly higher than in other habitats. Genes involved in dissimilatory sulfate reduction were abundant in subtropical marine mangroves and deep-sea sediments. The neutral community model results showed that microbial dispersal was higher in the marine mangrove ecosystem than in others habitats. The Flavilitoribacter of sulfur-metabolizing microorganism becomes a reliable biomarker in the five habitats. SMDB will assist researchers to analyze genes of sulfur cycle from the metagenomic efficiently.},
}

*Microbiota
Geologic Sediments
Bacteria
Archaea/genetics
Sulfur/metabolism
Phylogeny

@article {pmid37207186,
year = {2023},
author = {Hao, SR and Zhou, YY and Zhang, X and Jiang, HY},
title = {Gut microbiome profiles may be related to atypical antipsychotic associated overweight in Asian children with psychiatric disorder: a preliminary study.},
journal = {Frontiers in cellular and infection microbiology},
volume = {13},
number = {},
pages = {1124846},
pmid = {37207186},
issn = {2235-2988},
mesh = {Humans ; Child ; Overweight/chemically induced/drug therapy/microbiology ; *Gastrointestinal Microbiome/physiology ; *Antipsychotic Agents/adverse effects ; Cross-Sectional Studies ; *Mental Disorders ; Bacteria/genetics ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; },
abstract = {OBJECTIVE: Atypical antipsychotics (APs) modify the gut microbiome, and weight gain in response to AP could be mediated by the gut microbiome. Thus, the present study aimed to explore the changes in the gut bacterial microbiome in AP-exposed children with obesity.

METHODS: To rule out the confounder of AP indication, the gut bacterial microbiome was compared between healthy controls (Con) and AP-exposed individuals with overweight (APO) or normal weight (APN). Fifty-seven AP-treated outpatients (21 APO and 36 APN) and 25 Con were included in this cross-sectional microbiota study.

RESULTS: AP users, regardless of body mass index, exhibited decreased microbial richness and diversity and a distinct metagenomic composition compared to the Con. Although no differences in the microbiota structure were observed between APO and APN groups, the APO group was characterised by a higher abundance of Megamonas and Lachnospira. Additionally, the differences in the microbial functions were observed between APO and APN groups.

CONCLUSIONS: The gut bacterial microbiota of APO children revealed taxonomic and functional differences compared to Con and APN. Further studies are needed to verify these findings and to explore the temporal and causal relationships between these variables.},
}

Humans
Child
Overweight/chemically induced/drug therapy/microbiology
*Gastrointestinal Microbiome/physiology
*Antipsychotic Agents/adverse effects
Cross-Sectional Studies
*Mental Disorders
Bacteria/genetics
RNA, Ribosomal, 16S/genetics
Feces/microbiology

@article {pmid37202728,
year = {2023},
author = {Xing, W and Qi, B and Chen, R and Ding, W and Zhang, F},
title = {Metagenomic analysis reveals taxonomic and functional diversity of microbial communities on the deteriorated wall paintings of Qinling Tomb in the Southern Tang Dynasty, China.},
journal = {BMC microbiology},
volume = {23},
number = {1},
pages = {140},
pmid = {37202728},
issn = {1471-2180},
mesh = {*Microbiota ; Metagenome ; *Cyanobacteria ; Proteobacteria ; China ; },
abstract = {The microbial colonization on ancient murals attracts more and more attention since the threaten by microorganisms was first reported in Lascaux, Spain. However, the biodeterioration or biodegradation of mural paintings resulted by microorganisms is not clear yet. Especially the biological function of microbial communities in different conditions remained largely unaddressed. The two mausoleums of the Southern Tang Dynasty are the largest group of emperor mausoleums during the Five Dynasties and Ten Kingdoms period in China, which are of great significance to the study of the architecture, imperial mausoleum systems and art in the Tang and Song Dynasties. To make clear the species composition and metabolic functions of different microbial communities (MID and BK), we analyzed the samples from the wall paintings in one of the two mausoleums of the Southern Tang Dynasty with metagenomics method. The result showed totally 55 phyla and 1729 genera were detected in the mural paintings. The two microbial community structure were similar with the dominance of Proteobacteria, Actinobacteria and Cyanobacteria. However, the species abundance presented a significant difference between two communities at genus level --- MID is Lysobacter, Luteimonas are predominant in MID while Sphingomonas and Streptomyces are popular in BK, which is partially attributed to the different substrate materials of murals. As a result, the two communities presented the different metabolic patterns that MID community was mainly participated in the formation of biofilm as well as the degradation of exogenous pollutants while the BK was predominantly related to the photosynthesis process and biosynthesis of secondary metabolites. Taken together, these findings indicated the effect of environmental factor on the taxonomic composition and functional diversity of the microbial populations. The installation of artificial lighting needs to be considered carefully in the future protection of cultural relics.},
}

*Microbiota
Metagenome
*Cyanobacteria
Proteobacteria
China

@article {pmid37202719,
year = {2023},
author = {Wang, XY and Meng, JX and Ren, WX and Ma, H and Liu, G and Liu, R and Geng, HL and Zhao, Q and Zhang, XX and Ni, HB},
title = {Amplicon-based metagenomic association analysis of gut microbiota in relation to egg-laying period and breeds of hens.},
journal = {BMC microbiology},
volume = {23},
number = {1},
pages = {138},
pmid = {37202719},
issn = {1471-2180},
mesh = {Animals ; Female ; *Gastrointestinal Microbiome/genetics ; Chickens/microbiology ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Cyanobacteria/genetics ; },
abstract = {BACKGROUND: The gut microbiota plays an essential role in maintaining gut homeostasis and improving performance, with the composition of microbial communities visibly differing across different laying stages in hens and significantly correlating with egg production. To gain further insights into the association between microbial community characteristics and laying periods in Hy-Line variety brown and Isa brown laying hens, we conducted a 16S rRNA amplicon sequencing survey.

RESULTS: Our result revealed the diversity of bacteria in the early laying period was commonly higher than peak, and in Hy-Line variety brown laying hens were generally higher than Isa brown. Principal coordinate analysis (PCoA) and permutational multivariate analysis of variance (PERMANOVA) revealed that the structure and composition of the gut microbiota of laying hens exhibited significant differences among different groups. Phylum Firmicutes, Bacteroidota, Proteobacteria, and Fusobacteriota were found that dominant in the host's feces. Therein, the abundance of Fusobacteriota was higher in the peak period than in the early period, while the abundance of Cyanobacteria in the early period was higher in two breeds of hens. Furthermore, random forest based on machine learning showed that there were several distinctly abundant genera, which can be used as potential biomarkers to differentiate the different groups of laying periods and breeds. In addition, the prediction of biological function indicated the existing discrepancy in microbial function among the microbiota of four groups.

CONCLUSIONS: Our findings offer new insights into the bacterial diversity and intestinal flora composition of different strains of laying hens during various laying periods, contributing significantly to the improvement of production performance and the prevention of chicken diseases.},
}

Animals
Female
*Gastrointestinal Microbiome/genetics
Chickens/microbiology
RNA, Ribosomal, 16S/genetics
*Microbiota
*Cyanobacteria/genetics

@article {pmid37195657,
year = {2023},
author = {Xue, W and Peng, P and Wen, X and Meng, H and Qin, Y and Deng, T and Guo, S and Chen, T and Li, X and Liang, J and Zhang, F and Xie, Z and Jin, M and Liang, Q and Wei, L},
title = {Metagenomic Sequencing Analysis Identifies Cross-Cohort Gut Microbial Signatures Associated With Age-Related Macular Degeneration.},
journal = {Investigative ophthalmology & visual science},
volume = {64},
number = {5},
pages = {11},
doi = {10.1167/iovs.64.5.11},
pmid = {37195657},
issn = {1552-5783},
mesh = {Humans ; Metagenome ; *Gastrointestinal Microbiome/genetics ; Dysbiosis/microbiology ; Bacteria/genetics/metabolism ; Bacteroidetes ; *Macular Degeneration/genetics ; },
abstract = {PURPOSE: Alterations in the gut microbiota have been associated with age-related macular degeneration (AMD). However, the dysbiosis shared by different ethnicity and geographic groups, which may associate with the disease pathogenesis, remain underexplored. Here, we characterized dysbiosis of the gut microbiota in patients with AMD from Chinese and Swiss cohorts and identified cross-cohort signatures associated with AMD.

METHODS: Shotgun metagenomic sequencing was performed on fecal samples from 30 patients with AMD and 30 healthy subjects. Published datasets with 138 samples from Swiss patients with AMD and healthy subjects were re-analyzed. Comprehensive taxonomic profiling was conducted by matching to the RefSeq genome database, metagenome-assembled genome (MAG) database, and Gut Virome Database (GVD). Functional profiling was performed by reconstruction of the MetaCyc pathways.

RESULTS: The α-diversity of the gut microbiota was decreased in patients with AMD according to taxonomic profiles generated using MAG but not RefSeq database as reference. The Firmicutes/Bacteroidetes ratio was also decreased in patients with AMD. Among AMD-associated bacteria shared between Chinese and Swiss cohorts, Ruminococcus callidus, Lactobacillus gasseri, and Prevotellaceae (f) uSGB 2135 were enriched in patients with AMD, whereas Bacteroidaceae (f) uSGB 1825 was depleted in patients with AMD and was negatively associated with hemorrhage size. Bacteroidaceae was one of the major hosts of phages associated with AMD. Three degradation pathways were reduced in AMD.

CONCLUSIONS: These results demonstrated that dysbiosis of the gut microbiota was associated with AMD. We identified cross-cohort gut microbial signatures involving bacteria, viruses, and metabolic pathways, which potentially serve as promising targets for the prevention or treatment of AMD.},
}

Humans
Metagenome
*Gastrointestinal Microbiome/genetics
Dysbiosis/microbiology
Bacteria/genetics/metabolism
Bacteroidetes
*Macular Degeneration/genetics

@article {pmid37195254,
year = {2023},
author = {Free, T},
title = {Long-read sequencing for the metagenomic analysis of microbiomes.},
journal = {BioTechniques},
volume = {74},
number = {4},
pages = {153-155},
doi = {10.2144/btn-2023-0028},
pmid = {37195254},
issn = {1940-9818},
mesh = {*High-Throughput Nucleotide Sequencing ; *Microbiota/genetics ; Metagenome/genetics ; Sequence Analysis, DNA ; Metagenomics ; },
abstract = {One technology, long-read sequencing, and one research field, microbiome studies, have risen to prominence over the last decade. But how can one be used in the other? What changes are being wrought? And what limitations remain? [Formula: see text].},
}

*High-Throughput Nucleotide Sequencing
*Microbiota/genetics
Metagenome/genetics
Sequence Analysis, DNA
Metagenomics

@article {pmid37054839,
year = {2023},
author = {Chunxiao, D and Ma, F and Wu, W and Li, S and Yang, J and Chen, Z and Lian, S and Qu, Y},
title = {Metagenomic analysis reveals indole signaling effect on microbial community in sequencing batch reactors: Quorum sensing inhibition and antibiotic resistance enrichment.},
journal = {Environmental research},
volume = {229},
number = {},
pages = {115897},
doi = {10.1016/j.envres.2023.115897},
pmid = {37054839},
issn = {1096-0953},
mesh = {*Quorum Sensing/physiology ; Drug Resistance, Microbial ; Lactones/pharmacology ; Anti-Bacterial Agents/pharmacology ; *Microbiota ; Indoles/pharmacology ; },
abstract = {Indole is an essential signal molecule in microbial studies. However, its ecological role in biological wastewater treatments remains enigmatic. This study explores the links between indole and complex microbial communities using sequencing batch reactors exposed to 0, 15, and 150 mg/L indole concentrations. A concentration of 150 mg/L indole enriched indole degrader Burkholderiales, while pathogens, such as Giardia, Plasmodium, and Besnoitia were inhibited at 15 mg/L indole concentration. At the same time, indole reduced the abundance of predicted genes in the "signaling transduction mechanisms" pathway via the Non-supervised Orthologous Groups distributions analysis. Indole significantly decreased the concentration of homoserine lactones, especially C14-HSL. Furthermore, the quorum-sensing signaling acceptors containing LuxR, the dCACHE domain, and RpfC showed negative distributions with indole and indole oxygenase genes. Signaling acceptors' potential origins were mainly Burkholderiales, Actinobacteria, and Xanthomonadales. Meanwhile, concentrated indole (150 mg/L) increased the total abundance of antibiotic resistance genes by 3.52 folds, especially on aminoglycoside, multidrug, tetracycline, and sulfonamide. Based on Spearman's correlation analysis, the homoserine lactone degradation genes which were significantly impacted by indole negatively correlated with the antibiotic resistance gene abundance. This study brings new insights into the effect of indole signaling on in biological wastewater treatment plants.},
}

*Quorum Sensing/physiology
Drug Resistance, Microbial
Lactones/pharmacology
Anti-Bacterial Agents/pharmacology
*Microbiota
Indoles/pharmacology

@article {pmid37004601,
year = {2023},
author = {do Socorro Fôro Ramos, E and Bahia, SL and de Oliveira Ribeiro, G and Villanova, F and de Pádua Milagres, FA and Brustulin, R and Pandey, RP and Deng, X and Delwart, E and da Costa, AC and Leal, É},
title = {Characterization of Phietavirus Henu 2 in the virome of individuals with acute gastroenteritis.},
journal = {Virus genes},
volume = {59},
number = {3},
pages = {464-472},
pmid = {37004601},
issn = {1572-994X},
mesh = {Humans ; *Methicillin-Resistant Staphylococcus aureus ; Virome ; *Bacteriophages ; *Siphoviridae ; *Gastroenteritis ; *Staphylococcal Infections/microbiology ; },
abstract = {There is a growing interest in phages as potential biotechnological tools in human health owing to the antibacterial activity of these viruses. In this study, we characterized a new member (named PhiV_005_BRA/2016) of the recently identified phage species Phietavirus Henu 2. PhiV_005_BRA/2016 was detected through metagenomic analysis of stool samples of individuals with acute gastroenteritis. PhiV_005_BRA/2016 contains double-stranded linear DNA (dsDNA), it has a genome of 43,513 base pairs (bp), with a high identity score (99%) with phage of the genus Phietavirus, species of Phietavirus Henu 2. Life style prediction indicated that PhiV_005_BRA/2016 is a lysogenic phage whose the main host is methicillin-resistant Staphylococcus aureus (MRSA). Indeed, we found PhiV_005_BRA/2016 partially integrated in the genome of distinct MRSA strains. Our findings highlights the importance of large-scale screening of bacteriophages to better understand the emergence of multi-drug resistant bacterial.},
}

Humans
*Methicillin-Resistant Staphylococcus aureus
Virome
*Bacteriophages
*Siphoviridae
*Gastroenteritis
*Staphylococcal Infections/microbiology

@article {pmid35485976,
year = {2023},
author = {Jiang, Y and Balaban, M and Zhu, Q and Mirarab, S},
title = {DEPP: Deep Learning Enables Extending Species Trees using Single Genes.},
journal = {Systematic biology},
volume = {72},
number = {1},
pages = {17-34},
pmid = {35485976},
issn = {1076-836X},
support = {R35 GM142725/GM/NIGMS NIH HHS/United States ; 1R35GM142725/NH/NIH HHS/United States ; },
mesh = {Phylogeny ; *Deep Learning ; RNA, Ribosomal, 16S/genetics ; Algorithms ; *Microbiota/genetics ; },
abstract = {Placing new sequences onto reference phylogenies is increasingly used for analyzing environmental samples, especially microbiomes. Existing placement methods assume that query sequences have evolved under specific models directly on the reference phylogeny. For example, they assume single-gene data (e.g., 16S rRNA amplicons) have evolved under the GTR model on a gene tree. Placement, however, often has a more ambitious goal: extending a (genome-wide) species tree given data from individual genes without knowing the evolutionary model. Addressing this challenging problem requires new directions. Here, we introduce Deep-learning Enabled Phylogenetic Placement (DEPP), an algorithm that learns to extend species trees using single genes without prespecified models. In simulations and on real data, we show that DEPP can match the accuracy of model-based methods without any prior knowledge of the model. We also show that DEPP can update the multilocus microbial tree-of-life with single genes with high accuracy. We further demonstrate that DEPP can combine 16S and metagenomic data onto a single tree, enabling community structure analyses that take advantage of both sources of data. [Deep learning; gene tree discordance; metagenomics; microbiome analyses; neural networks; phylogenetic placement.].},
}

Phylogeny
*Deep Learning
RNA, Ribosomal, 16S/genetics
Algorithms
*Microbiota/genetics

@article {pmid37194081,
year = {2023},
author = {Gallet, A and Halary, S and Duval, C and Huet, H and Duperron, S and Marie, B},
title = {Disruption of fish gut microbiota composition and holobiont's metabolome during a simulated Microcystis aeruginosa (Cyanobacteria) bloom.},
journal = {Microbiome},
volume = {11},
number = {1},
pages = {108},
pmid = {37194081},
issn = {2049-2618},
mesh = {Animals ; *Microcystis/physiology ; *Gastrointestinal Microbiome ; *Cyanobacteria/genetics ; Lakes/microbiology ; Metabolome ; *Oryzias/physiology ; },
abstract = {BACKGROUND: Cyanobacterial blooms are one of the most common stressors encountered by metazoans living in freshwater lentic systems such as lakes and ponds. Blooms reportedly impair fish health, notably through oxygen depletion and production of bioactive compounds including cyanotoxins. However, in the times of the "microbiome revolution", it is surprising that so little is still known regarding the influence of blooms on fish microbiota. In this study, an experimental approach is used to demonstrate that blooms affect fish microbiome composition and functions, as well as the metabolome of holobionts. To this end, the model teleost Oryzias latipes is exposed to simulated Microcystis aeruginosa blooms of various intensities in a microcosm setting, and the response of bacterial gut communities is evaluated in terms of composition and metabolome profiling. Metagenome-encoded functions are compared after 28 days between control individuals and those exposed to highest bloom level.

RESULTS: The gut bacterial community of O. latipes exhibits marked responses to the presence of M. aeruginosa blooms in a dose-dependent manner. Notably, abundant gut-associated Firmicutes almost disappear, while potential opportunists increase. The holobiont's gut metabolome displays major changes, while functions encoded in the metagenome of bacterial partners are more marginally affected. Bacterial communities tend to return to original composition after the end of the bloom and remain sensitive in case of a second bloom, reflecting a highly reactive gut community.

CONCLUSION: Gut-associated bacterial communities and holobiont functioning are affected by both short and long exposure to M. aeruginosa, and show evidence of post-bloom resilience. These findings point to the significance of bloom events to fish health and fitness, including survival and reproduction, through microbiome-related effects. In the context of increasingly frequent and intense blooms worldwide, potential outcomes relevant to conservation biology as well as aquaculture warrant further investigation. Video Abstract.},
}

Animals
*Microcystis/physiology
*Gastrointestinal Microbiome
*Cyanobacteria/genetics
Lakes/microbiology
Metabolome
*Oryzias/physiology

@article {pmid37194043,
year = {2023},
author = {Yao, S and Jin, T and Zhang, L and Zhang, Y and Chen, R and Wang, Q and Lv, M and Hu, C and Ma, T and Xia, W},
title = {N/S element transformation modulating lithospheric microbial communities by single-species manipulation.},
journal = {Microbiome},
volume = {11},
number = {1},
pages = {107},
pmid = {37194043},
issn = {2049-2618},
mesh = {Nitrates/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Petroleum/metabolism/microbiology ; Sulfur/metabolism ; Nitrogen/metabolism ; Sulfates ; },
abstract = {BACKGROUND: The lithospheric microbiome plays a vital role in global biogeochemical cycling, yet their mutual modulation mechanisms remain largely uncharted. Petroleum reservoirs are important lithosphere ecosystems that provide desirable resources for understanding microbial roles in element cycling. However, the strategy and mechanism of modulating indigenous microbial communities for the optimization of community structures and functions are underexplored, despite its significance in energy recovery and environmental remediation.

RESULTS: Here we proposed a novel selective stimulation of indigenous functional microbes by driving nitrogen and sulfur cycling in petroleum reservoirs using injections of an exogenous heterocycle-degrading strain of Pseudomonas. We defined such bacteria capable of removing and releasing organically bound sulfur and nitrogen from heterocycles as "bioredox triggers". High-throughput 16S rRNA amplicon sequencing, metagenomic, and gene transcription-level analyses of extensive production water and sandstone core samples spanning the whole oil production process clarified the microbiome dynamics following the intervention. These efforts demonstrated the feasibility of in situ N/S element release and electron acceptor generation during heterocycle degradation, shifting microbiome structures and functions and increasing phylogenetic diversity and genera engaged in sulfur and nitrogen cycling, such as Desulfovibrio, Shewanella, and Sulfurospirillum. The metabolic potentials of sulfur- and nitrogen-cycling processes, particularly dissimilatory sulfate reduction and dissimilatory nitrate reduction, were elevated in reservoir microbiomes. The relative expression of genes involved in sulfate reduction (dsrA, dsrB) and nitrate reduction (napA) was upregulated by 85, 28, and 22 folds, respectively. Field trials showed significant improvements in oil properties, with a decline in asphaltenes and aromatics, hetero-element contents, and viscosity, hence facilitating the effective exploitation of heavy oil.

CONCLUSIONS: The interactions between microbiomes and element cycling elucidated in this study will contribute to a better understanding of microbial metabolic involvement in, and response to, biogeochemical processes in the lithosphere. The presented findings demonstrated the immense potential of our microbial modulation strategy for green and enhanced heavy oil recovery. Video Abstract.},
}

Nitrates/metabolism
Phylogeny
RNA, Ribosomal, 16S/genetics
*Microbiota
*Petroleum/metabolism/microbiology
Sulfur/metabolism
Nitrogen/metabolism
Sulfates

@article {pmid37189387,
year = {2023},
author = {Aljuraiban, GS and Alfhili, MA and Aldhwayan, MM and Aljazairy, EA and Al-Musharaf, S},
title = {Metagenomic Shotgun Sequencing Reveals Specific Human Gut Microbiota Associated with Insulin Resistance and Body Fat Distribution in Saudi Women.},
journal = {Biomolecules},
volume = {13},
number = {4},
pages = {},
pmid = {37189387},
issn = {2218-273X},
mesh = {Humans ; Female ; *Insulin Resistance ; Saudi Arabia ; *Gastrointestinal Microbiome/genetics ; Body Fat Distribution ; Obesity ; Insulin ; },
abstract = {(1) Background: Gut microbiota dysbiosis may lead to diseases such as insulin resistance and obesity. We aimed to investigate the relationship between insulin resistance, body fat distribution, and gut microbiota composition. (2) Methods: The present study included 92 Saudi women (18-25 years) with obesity (body mass index (BMI) ≥ 30 kg/m[2], n = 44) and with normal weight (BMI 18.50-24.99 kg/m[2], n = 48). Body composition indices, biochemical data, and stool samples were collected. The whole-genome shotgun sequencing technique was used to analyze the gut microbiota. Participants were divided into subgroups stratified by the homeostatic model assessment for insulin resistance (HOMA-IR) and other adiposity indices. (3) Results: HOMA-IR was inversely correlated with Actinobacteria (r = -0.31, p = 0.003), fasting blood glucose was inversely correlated with Bifidobacterium kashiwanohense (r = -0.22, p = 0.03), and insulin was inversely correlated with Bifidobacterium adolescentis (r = -0.22, p = 0.04). There were significant differences in α- and β-diversities in those with high HOMA-IR and waist-hip ratio (WHR) compared to low HOMA-IR and WHR (p = 0.02, 0.03, respectively). (4) Conclusions: Our findings highlight the relationship between specific gut microbiota at different taxonomic levels and measures of glycemic control in Saudi Arabian women. Future studies are required to determine the role of the identified strains in the development of insulin resistance.},
}

Humans
Female
*Insulin Resistance
Saudi Arabia
*Gastrointestinal Microbiome/genetics
Body Fat Distribution
Obesity
Insulin

@article {pmid37148792,
year = {2023},
author = {Wang, Y and Tian, X and Song, T and Jiang, Z and Zhang, G and He, C and Li, P},
title = {Linking DOM characteristics to microbial community: The potential role of DOM mineralization for arsenic release in shallow groundwater.},
journal = {Journal of hazardous materials},
volume = {454},
number = {},
pages = {131566},
doi = {10.1016/j.jhazmat.2023.131566},
pmid = {37148792},
issn = {1873-3336},
mesh = {Dissolved Organic Matter ; *Arsenic/analysis ; *Groundwater/chemistry ; Carbon ; *Microbiota ; Nitrogen/analysis ; },
abstract = {Dissolved organic matter (DOM) play critical roles in arsenic (As) biotransformation in groundwater, but its compositional characteristics and interactions with indigenous microbial communities remain unclear. In this study, DOM signatures coupled with taxonomy and functions of microbial community were characterized in As-enriched groundwater by excitation-emission matrix, Fourier transform ion cyclotron resonance mass spectrometry and metagenomic sequencing. Results showed that As concentrations were significantly positively correlated with DOM humification (r = 0.707, p < 0.01) and the most dominant humic acid-like DOM components (r = 0.789, p < 0.01). Molecular characterization further demonstrated high DOM oxidation degree, with the prevalence of unsaturated oxygen-low aromatics, nitrogen (N1/N2)-containing compounds and unique CHO molecules in high As groundwater. These DOM properties were consistent with microbial composition and functional potentials. Both taxonomy and binning analyses demonstrated the dominance of Pseudomonas stutzeri, Microbacterium and Sphingobium xenophagum in As-enriched groundwater which possessed abundant As-reducing gene, with organic carbon degrading genes capable of labile to recalcitrant compounds degradation and high potentials of organic nitrogen mineralization to generate ammonium. Besides, most assembled bins in high As groundwater presented strong fermentation potentials which could facilitate carbon utilization by heterotrophic microbes. This study provides better insight into the potential role of DOM mineralization for As release in groundwater system.},
}

Dissolved Organic Matter
*Arsenic/analysis
*Groundwater/chemistry
Carbon
*Microbiota
Nitrogen/analysis

@article {pmid37137392,
year = {2023},
author = {Jin, Y and Xiong, W and Liu, D and Wu, Z and Xiao, G and Wang, S and Su, H},
title = {Responses of straw foam-based aerobic granular sludge to atrazine: Insights from metagenomics and microbial community variations.},
journal = {Chemosphere},
volume = {331},
number = {},
pages = {138828},
doi = {10.1016/j.chemosphere.2023.138828},
pmid = {37137392},
issn = {1879-1298},
mesh = {Sewage/chemistry ; Waste Disposal, Fluid/methods ; *Atrazine ; Metagenomics ; Bioreactors/microbiology ; Aerobiosis ; *Microbiota ; Bacteria/genetics ; Nitrogen ; },
abstract = {Atrazine (ATZ) has caused serious environmental pollution, but the biodegradation of ATZ is relatively slow and inefficient. Herein, a straw foam-based aerobic granular sludge (SF-AGS) was developed, the spatially ordered architectures of which could greatly improve the drug tolerance and biodegradation efficiency of ATZ. The results showed that, in the presence of ATZ, chemical oxygen demand (COD), ammonium nitrogen (NH4[+]-N), total phosphorus (TP), and total nitrogen (TN) were effectively removed within 6 h, and the removal efficiencies were as high as 93.37%, 85.33%, 84.7%, and 70%, respectively. Furthermore, ATZ stimulated microbial consortia to secrete three times more extracellular polymers compared to without ATZ. Illumina MiSeq sequencing results showed that bacterial diversity and richness decreased, leading to significant changes in microbial population structure and composition. ATZ-resistant bacteria including Proteobacteria, Actinobacteria, and Burkholderia laid the biological basis for the stability of aerobic particles, efficient removal of pollutants, and degradation of ATZ. The study demonstrated that SF-AGS is feasible for ATZ-laden low-strength wastewater treatment.},
}

Sewage/chemistry
Waste Disposal, Fluid/methods
*Atrazine
Metagenomics
Bioreactors/microbiology
Aerobiosis
*Microbiota
Bacteria/genetics
Nitrogen

@article {pmid37100380,
year = {2023},
author = {Tang, H and Zhou, T and Jin, W and Zong, S and Mamtimin, T and Salama, ES and Jeon, BH and Liu, P and Han, H and Li, X},
title = {Tumor-targeting engineered probiotic Escherichia coli Nissle 1917 inhibits colorectal tumorigenesis and modulates gut microbiota homeostasis in mice.},
journal = {Life sciences},
volume = {324},
number = {},
pages = {121709},
doi = {10.1016/j.lfs.2023.121709},
pmid = {37100380},
issn = {1879-0631},
mesh = {Animals ; Mice ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; *Azurin/adverse effects ; Carcinogenesis ; Cell Transformation, Neoplastic ; *Probiotics/therapeutic use ; *Colorectal Neoplasms/metabolism ; Escherichia coli/genetics ; Dextran Sulfate/pharmacology ; Disease Models, Animal ; *Colitis/chemically induced ; },
abstract = {AIMS: Preliminary studies have identified the use of probiotics as a potential treatment strategy against colorectal cancer (CRC). However, natural probiotics lack direct tumor-targeting and tumor-killing activity in the intestine. This study aimed to construct a tumor-targeting engineered probiotic to combat CRC.

MAIN METHODS: Standard adhesion assay was performed to analyze the adherence ability of tumor-binding protein HlpA to CT26 cells. CCK-8 assay, Hoechst 33258 staining and flow cytometry analysis were used for examining cytotoxicity of tumoricidal protein azurin toward CT26 cells. An engineered probiotic Ep-AH harboring azurin and hlpA genes was developed using Escherichia coli Nissle 1917 (EcN) chassis. Antitumor effects of Ep-AH were evaluated in the azoxymethane (AOM) and dextran sodium sulfate salt (DSS)-induced CRC mice. Moreover, analysis of gut microbiota was conducted via fecal 16S rRNA gene sequencing and shotgun metagenomic sequencing.

KEY FINDINGS: Azurin caused a dose-dependent increase of apoptosis in CT26 cells. Ep-AH treatment reversed weight loss (p < 0.001), fecal occult blood (p < 0.01), and shortening of colon length (p < 0.001) than model group, as well as reducing tumorigenesis by 36 % (p < 0.001). Both Ep-H and Ep-A (EcN expressing HlpA or azurin) were less effective than Ep-AH. Furthermore, Ep-AH enriched the members of beneficial bacteria (e.g., Blautia and Bifidobacterium) and reversed abnormal changes of genes associated with several metabolic pathways (e.g., lipopolysaccharide biosynthesis).

SIGNIFICANCE: These results demonstrated that Ep-AH had excellent therapeutic benefits on cancer remission and gut microbiota modulation. Our study provides an effective strategy for anti-CRC treatment.},
}

Animals
Mice
*Gastrointestinal Microbiome
RNA, Ribosomal, 16S/genetics
*Azurin/adverse effects
Carcinogenesis
Cell Transformation, Neoplastic
*Probiotics/therapeutic use
*Colorectal Neoplasms/metabolism
Escherichia coli/genetics
Dextran Sulfate/pharmacology
Disease Models, Animal
*Colitis/chemically induced

@article {pmid36694293,
year = {2023},
author = {Wang, G and Jin, Z and George, TS and Feng, G and Zhang, L},
title = {Arbuscular mycorrhizal fungi enhance plant phosphorus uptake through stimulating hyphosphere soil microbiome functional profiles for phosphorus turnover.},
journal = {The New phytologist},
volume = {238},
number = {6},
pages = {2578-2593},
doi = {10.1111/nph.18772},
pmid = {36694293},
issn = {1469-8137},
mesh = {*Mycorrhizae/metabolism ; Phosphorus/metabolism ; Soil ; Phytic Acid/metabolism ; Fungi/metabolism ; *Microbiota ; Bacteria/metabolism ; Plant Roots/metabolism ; Soil Microbiology ; },
abstract = {The extraradical hyphae of arbuscular mycorrhizal (AM) fungi are colonized by different bacteria in natural and agricultural systems, but the mechanisms by which AM fungi interact with the hyphosphere soil microbiome and influence soil organic phosphorus (P) mobilization remain unclear. We grew Medicago in two-compartment microcosms, inoculated with Rhizophagus irregularis, or not, in the root compartment and set up P treatments (without P, with P addition as KH2 PO4 or nonsoluble phytate) in the hyphal compartment. We studied the processes of soil P turnover and characterized the microbiome functional profiles for P turnover in the hyphosphere soil by metagenomic sequencing. Compared with the bulk soil, the hyphosphere soil of R. irregularis was inhabited by a specific bacterial community and their functional profiles for P turnover was stimulated. At the species level, the shift in hyphosphere soil microbiome was characterized by the recruitment of the genome bin2.39 harbouring both gcd and phoD genes and genome bin2.97 harbouring the phoD gene, which synergistically drove nonsoluble phytate mobilization in the hyphosphere soil. Our results suggest that AM fungi recruits a specific hyphosphere soil microbiome and stimulated their functional profiles for P turnover to enhance utilization of phytate.},
}

*Mycorrhizae/metabolism
Phosphorus/metabolism
Soil
Phytic Acid/metabolism
Fungi/metabolism
*Microbiota
Bacteria/metabolism
Plant Roots/metabolism
Soil Microbiology

@article {pmid36082501,
year = {2023},
author = {Özdemir, A and Yozgat, A and Işgın-Atıcı, K and Avcı, E and Yıldız, BD and Gündoğdu, A and Nalbantoğlu, U and Turhan, T and Doğruman-Al, F and Büyüktuncer, Z},
title = {Potential associations between alterations in gut microbiome and obesity-related traits after the bariatric surgery.},
journal = {Journal of human nutrition and dietetics : the official journal of the British Dietetic Association},
volume = {36},
number = {3},
pages = {981-996},
doi = {10.1111/jhn.13087},
pmid = {36082501},
issn = {1365-277X},
mesh = {Humans ; *Obesity, Morbid/surgery ; *Gastrointestinal Microbiome ; *Bariatric Surgery ; Diet ; Cholesterol ; },
abstract = {BACKGROUND: This study aimed to examine the effects of both obesity and bariatric surgery on gut microbiome, dietary intake, as well as metabolic and inflammatory parameters.

METHODS: All participants (15 with morbid obesity who had bariatric surgery, 8 with morbid obesity and 11 non-obese) were followed up for a 6-month period with interviews at baseline (M0), at the end of 3 (M3) and 6 months (M6). Dietary assessment was done, and blood and faecal samples were collected.

RESULTS: Dietary energy and nutrient intakes as well as serum glucose levels, total cholesterol, low-density lipoprotein (LDL)-cholesterol and high sensitivity C-reactive protein (hs-CRP) levels decreased after surgery (p < 0.05, for each). Participants with morbid obesity had higher levels of Firmicutes and lower levels of Bacteroidetes at M0 compared to non-obese participants. The abundances of Bacteroidetes increased (p = 0.02), whereas that of Firmicutes decreased (p > 0.05) after the surgery, leading to a significant decrease in Firmicutes/Bacteroidetes ratio (p = 0.01). At sub-phylum level, the abundances of Lactobacillus and Bifidobacterium decreased, whereas those of Akkermansia increased after the surgery (p < 0.01, for each). Although participants who were morbidly obese had a distinct profile according to ß-diversity indices at M0, it became similar with the profile of non-obese participants (p > 0.05) at M3 and M6. Similarly, α-diversity indices were lower in subjects with morbid obesity at M0, but became similar to levels in non-obese controls at M6.

CONCLUSION: This study confirmed that bariatric surgery has substantial impacts on gut microbiome's composition and diversity, as well as anthropometrical measurements and biochemical parameters, which were associated with the alterations in dietary intake patterns.},
}

Humans
*Obesity, Morbid/surgery
*Gastrointestinal Microbiome
*Bariatric Surgery
Diet
Cholesterol

@article {pmid37189337,
year = {2023},
author = {Dossey, AT and Oppert, B and Chu, FC and Lorenzen, MD and Scheffler, B and Simpson, S and Koren, S and Johnston, JS and Kataoka, K and Ide, K},
title = {Genome and Genetic Engineering of the House Cricket (Acheta domesticus): A Resource for Sustainable Agriculture.},
journal = {Biomolecules},
volume = {13},
number = {4},
pages = {},
pmid = {37189337},
issn = {2218-273X},
mesh = {Animals ; *Gryllidae/genetics/metabolism ; Agriculture ; Crops, Agricultural ; Allergens/metabolism ; Genetic Engineering ; },
abstract = {Background: The house cricket, Acheta domesticus, is one of the most farmed insects worldwide and the foundation of an emerging industry using insects as a sustainable food source. Edible insects present a promising alternative for protein production amid a plethora of reports on climate change and biodiversity loss largely driven by agriculture. As with other crops, genetic resources are needed to improve crickets for food and other applications. Methods: We present the first high quality annotated genome assembly of A. domesticus from long read data and scaffolded to chromosome level, providing information needed for genetic manipulation. Results: Gene groups related to immunity were annotated and will be useful for improving value to insect farmers. Metagenome scaffolds in the A. domesticus assembly, including Invertebrate Iridescent Virus 6 (IIV6), were submitted as host-associated sequences. We demonstrate both CRISPR/Cas9-mediated knock-in and knock-out of A. domesticus and discuss implications for the food, pharmaceutical, and other industries. RNAi was demonstrated to disrupt the function of the vermilion eye-color gene producing a useful white-eye biomarker phenotype. Conclusions: We are utilizing these data to develop technologies for downstream commercial applications, including more nutritious and disease-resistant crickets, as well as lines producing valuable bioproducts, such as vaccines and antibiotics.},
}

Animals
*Gryllidae/genetics/metabolism
Agriculture
Crops, Agricultural
Allergens/metabolism
Genetic Engineering

@article {pmid37189333,
year = {2023},
author = {Cres, CM and Tritt, A and Bouchard, KE and Zhang, Y},
title = {DL-TODA: A Deep Learning Tool for Omics Data Analysis.},
journal = {Biomolecules},
volume = {13},
number = {4},
pages = {},
pmid = {37189333},
issn = {2218-273X},
mesh = {Humans ; *Deep Learning ; Neural Networks, Computer ; Bacteria/genetics ; Metagenome ; *Microbiota/genetics ; Algorithms ; },
abstract = {Metagenomics is a technique for genome-wide profiling of microbiomes; this technique generates billions of DNA sequences called reads. Given the multiplication of metagenomic projects, computational tools are necessary to enable the efficient and accurate classification of metagenomic reads without needing to construct a reference database. The program DL-TODA presented here aims to classify metagenomic reads using a deep learning model trained on over 3000 bacterial species. A convolutional neural network architecture originally designed for computer vision was applied for the modeling of species-specific features. Using synthetic testing data simulated with 2454 genomes from 639 species, DL-TODA was shown to classify nearly 75% of the reads with high confidence. The classification accuracy of DL-TODA was over 0.98 at taxonomic ranks above the genus level, making it comparable with Kraken2 and Centrifuge, two state-of-the-art taxonomic classification tools. DL-TODA also achieved an accuracy of 0.97 at the species level, which is higher than 0.93 by Kraken2 and 0.85 by Centrifuge on the same test set. Application of DL-TODA to the human oral and cropland soil metagenomes further demonstrated its use in analyzing microbiomes from diverse environments. Compared to Centrifuge and Kraken2, DL-TODA predicted distinct relative abundance rankings and is less biased toward a single taxon.},
}

Humans
*Deep Learning
Neural Networks, Computer
Bacteria/genetics
Metagenome
*Microbiota/genetics
Algorithms

@article {pmid36631002,
year = {2023},
author = {Hsu, CL and Lang, S and Demir, M and Fouts, DE and Stärkel, P and Schnabl, B},
title = {Any alcohol use in NAFLD patients is associated with significant changes to the intestinal virome.},
journal = {Hepatology (Baltimore, Md.)},
volume = {77},
number = {6},
pages = {2073-2083},
pmid = {36631002},
issn = {1527-3350},
support = {P30 DK120515/DK/NIDDK NIH HHS/United States ; T32 DK007202/DK/NIDDK NIH HHS/United States ; },
mesh = {Humans ; *Non-alcoholic Fatty Liver Disease ; Virome ; Alcohol Drinking/adverse effects ; *Alcoholism ; Ethanol ; *Liver Diseases, Alcoholic ; },
abstract = {BACKGROUND AND AIMS: The prevalence of alcohol use disorder (AUD) and metabolic dysfunction-associated fatty liver disease (MAFLD) are increasing worldwide, leading to the increasing likelihood of both etiologies contributing to a patient's liver disease. However, the effects of modest alcohol use in NAFLD are controversial and more studies are needed. We compared the intestinal viromes of patients with AUD and NAFLD in order to evaluate the effect of alcohol consumption on the intestinal viromes of NAFLD patients by extracting virus-like particles and performing metagenomic sequencing.

APPROACH AND RESULTS: Viral nucleic acids were extracted from fecal samples and subjected to metagenomic sequencing. We demonstrate significant differences in the intestinal viromes of NAFLD and AUD patients, and that alcohol use in NAFLD patients reclassified to MAFLD accounted for significant differences in the intestinal viromes. The relative abundance of several Lactococcus phages was more similar between AUD patients and alcohol-consuming MAFLD patients than non-alcohol-consuming MAFLD patients and control subjects, and multivariate modeling using the most discriminating Lactococcus phages could better predict alcohol use in the MAFLD population than the alcohol-associated liver disease/NAFLD Index. Significant differences in the viral composition and diversity were also seen between MAFLD patients with low and moderate alcohol consumption compared with no alcohol consumption.

CONCLUSIONS: The intestinal virome of MAFLD patients who consume low to moderate amounts of alcohol are significantly different from those who do not, and many features of the intestinal virome of alcohol-consuming MAFLD patients resemble that of AUD patients.},
}

Humans
*Non-alcoholic Fatty Liver Disease
Virome
Alcohol Drinking/adverse effects
*Alcoholism
Ethanol
*Liver Diseases, Alcoholic

@article {pmid37189332,
year = {2023},
author = {Smith, L and Goldobina, E and Govi, B and Shkoporov, AN},
title = {Bacteriophages of the Order Crassvirales: What Do We Currently Know about This Keystone Component of the Human Gut Virome?.},
journal = {Biomolecules},
volume = {13},
number = {4},
pages = {},
pmid = {37189332},
issn = {2218-273X},
support = {101001684/ERC_/European Research Council/International ; 220646/Z/20/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Animals ; Humans ; *Bacteriophages/genetics ; Virome ; Metagenomics ; Genomics ; DNA ; Mammals/genetics ; },
abstract = {The order Crassvirales comprises dsDNA bacteriophages infecting bacteria in the phylum Bacteroidetes that are found in a variety of environments but are especially prevalent in the mammalian gut. This review summarises available information on the genomics, diversity, taxonomy, and ecology of this largely uncultured viral taxon. With experimental data available from a handful of cultured representatives, the review highlights key properties of virion morphology, infection, gene expression and replication processes, and phage-host dynamics.},
}

Animals
Humans
*Bacteriophages/genetics
Virome
Metagenomics
Genomics
DNA
Mammals/genetics

@article {pmid37188713,
year = {2023},
author = {Orihara, K and Yahagi, K and Saito, Y and Watanabe, Y and Sasai, T and Hara, T and Tsukuda, N and Oki, K and Fujimoto, J and Matsuki, T},
title = {Characterization of Bifidobacterium kashiwanohense that utilizes both milk- and plant-derived oligosaccharides.},
journal = {Gut microbes},
volume = {15},
number = {1},
pages = {2207455},
pmid = {37188713},
issn = {1949-0984},
mesh = {Infant ; Child ; Humans ; Phylogeny ; *Gastrointestinal Microbiome ; Milk, Human/metabolism ; Oligosaccharides/metabolism ; alpha-L-Fucosidase/metabolism ; },
abstract = {Bifidobacteria are prominent members of the human gut microbiota throughout life. The ability to utilize milk- and plant-derived carbohydrates is important for bifidobacterial colonization of the infant and adult gut. The Bifidobacterium catenulatum subspecies kashiwanohense (B. kashiwanohense) was originally isolated from infant feces. However, only a few strains have been described, and the characteristics of this subspecies have been poorly investigated. Here, we characterized genotypes and phenotypes of 23 B. kashiwanohense-associated strains, including 12 newly sequenced isolates. Genome-based analysis clarified the phylogenetic relationship between these strains, revealing that only 13 strains are genuine B. kashiwanohense. We defined specific marker sequences and investigated the worldwide prevalence of B. kashiwanohense based on metagenome data. This revealed that not only infants but also adults and weaning children harbor this subspecies in the gut. Most B. kashiwanohense strains utilize long-chain xylans and possess genes for extracellular xylanase (GH10), arabinofuranosidase and xylosidase (GH43), and ABC transporters that contribute to the utilization of xylan-derived oligosaccharides. We also confirmed that B. kashiwanohense strains utilize short- and long-chain human milk oligosaccharides and possess genes for fucosidase (GH95 and GH29) and specific ABC transporter substrate-binding proteins that contribute to the utilization of a wide range of human milk oligosaccharides. Collectively, we found that B. kashiwanohense strains utilize both plant- and milk-derived carbohydrates and identified key genetic factors that allow them to assimilate various carbohydrates.},
}

Infant
Child
Humans
Phylogeny
*Gastrointestinal Microbiome
Milk, Human/metabolism
Oligosaccharides/metabolism
alpha-L-Fucosidase/metabolism

@article {pmid37187470,
year = {2023},
author = {Wu, C and Yi, H and Hu, Y and Luo, D and Tang, Z and Wen, X and Zhang, Y and Tang, M and Zhang, L and Wu, S and Chen, M},
title = {Effects of second-line anti-tuberculosis drugs on the intestinal microbiota of patients with rifampicin-resistant tuberculosis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {13},
number = {},
pages = {1127916},
pmid = {37187470},
issn = {2235-2988},
mesh = {Humans ; Antitubercular Agents/pharmacology/therapeutic use ; Rifampin/pharmacology/therapeutic use ; *Gastrointestinal Microbiome ; Cross-Sectional Studies ; Tryptophan ; *Tuberculosis, Multidrug-Resistant/drug therapy ; *Tuberculosis/drug therapy ; *Mycobacterium tuberculosis ; },
abstract = {OBJECTIVE: To determine the effects of second-line anti-tuberculosis (TB) drugs on the composition and functions of intestinal microbiota in patients with rifampicin-resistant TB (RR-TB).

METHODS: In this cross-sectional study, stool samples and relevant clinical information were collected from patients with RR-TB admitted to the Drug-resistant Specialty Department at Hunan Chest Hospital (Hunan Institute For Tuberculosis Control). The composition and functions of intestinal microbiota were analyzed using metagenomic sequencing and bioinformatics methods.

RESULTS: Altered structural composition of the intestinal microbiota was found when patients from the control, intensive phase treatment, and continuation phase treatment groups were compared (P<0.05). Second-line anti-TB treatment resulted in a decrease in the relative abundance of species, such as Prevotella copri, compared with control treatment. However, the relative abundance of Escherichia coli, Salmonella enterica, and 11 other conditionally pathogenic species increased significantly in the intensive phase treatment group. Based on differential functional analysis, some metabolism-related functions, such as the biosynthesises of phenylalanine, tyrosine, and tryptophan, were significantly inhibited during second-line anti-TB drug treatment, while other functions, such as phenylalanine metabolism, were significantly promoted during the intensive phase of treatment.

CONCLUSION: Second-line anti-TB drug treatment caused changes in the structural composition of the intestinal microbiota in patients with RR-TB. In particular, this treatment induced a significant increase in the relative abundance of 11 conditionally pathogenic species, including Escherichia coli. Functional analysis revealed significantly decreased biosynthesises of phenylalanine, tyrosine, and tryptophan and significantly increased phenylalanine metabolism.},
}

Humans
Antitubercular Agents/pharmacology/therapeutic use
Rifampin/pharmacology/therapeutic use
*Gastrointestinal Microbiome
Cross-Sectional Studies
Tryptophan
*Tuberculosis, Multidrug-Resistant/drug therapy
*Tuberculosis/drug therapy
*Mycobacterium tuberculosis

@article {pmid37186231,
year = {2023},
author = {Stach, TL and Sieber, G and Shah, M and Simon, SA and Soares, A and Bornemann, TLV and Plewka, J and Künkel, J and Becker, C and Meyer, F and Boenigk, J and Probst, AJ},
title = {Temporal disturbance of a model stream ecosystem by high microbial diversity from treated wastewater.},
journal = {MicrobiologyOpen},
volume = {12},
number = {2},
pages = {e1347},
pmid = {37186231},
issn = {2045-8827},
mesh = {*Ecosystem ; Rivers/microbiology ; Wastewater ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; *Microbiota/genetics ; },
abstract = {Microbial communities in freshwater streams play an essential role in ecosystem functioning via biogeochemical cycling. Yet, the impacts of treated wastewater influx into stream ecosystems on microbial strain diversity remain mostly unexplored. Here, we coupled full-length 16S ribosomal RNA gene Nanopore sequencing and strain-resolved metagenomics to investigate the impact of treated wastewater on a mesocosm system (AquaFlow) run with restored river water. Over 10 days, community Bray-Curtis dissimilarities between treated and control mesocosm decreased (0.57 ± 0.058 to 0.26 ± 0.046) based on ribosomal protein S3 gene clustering, finally converging to nearly identical communities. Similarly, strain-resolved metagenomics revealed a high diversity of bacteria and viruses after the introduction of treated wastewater; these microbes also decreased over time resulting in the same strain clusters in control and treatment at the end of the experiment. Specifically, 39.2% of viral strains detected in all samples were present after the introduction of treated wastewater only. Although bacteria present at low abundance in the treated wastewater introduced additional antibiotic resistance genes, signals of naturally occurring ARG-encoding organisms resembled the resistome at the endpoint. Our results suggest that the previously stressed freshwater stream and its microbial community are resilient to a substantial introduction of treated wastewater.},
}

*Ecosystem
Rivers/microbiology
Wastewater
RNA, Ribosomal, 16S/genetics
Bacteria/genetics
*Microbiota/genetics

@article {pmid37180439,
year = {2023},
author = {Niu, C and Tu, Y and Jin, Q and Chen, Z and Yuan, K and Wang, M and Zhang, P and Luo, J and Li, H and Yang, Y and Liu, X and Mao, M and Dong, T and Tan, W and Hu, X and Pan, Y and Hou, L and Ma, R and Huang, Z},
title = {Mapping the human oral and gut fungal microbiota in patients with metabolic dysfunction-associated fatty liver disease.},
journal = {Frontiers in cellular and infection microbiology},
volume = {13},
number = {},
pages = {1157368},
pmid = {37180439},
issn = {2235-2988},
mesh = {Humans ; *Mycobiome ; Fungi/genetics ; *Gastrointestinal Microbiome ; Feces/microbiology ; Saliva ; *Non-alcoholic Fatty Liver Disease ; },
abstract = {Metabolic dysfunction-associated fatty liver disease (MAFLD) is a phenotype of liver diseases associated with metabolic syndrome. The pathogenesis MAFLD remains unclear. The liver maintains is located near the intestine and is physiologically interdependent with the intestine via metabolic exchange and microbial transmission, underpinning the recently proposed "oral-gut-liver axis" concept. However, little is known about the roles of commensal fungi in the disease development. This study aimed to characterize the alterations of oral and gut mycobiota and their roles in MAFLD. Twenty-one MAFLD participants and 20 healthy controls were enrolled. Metagenomics analyses of saliva, supragingival plaques, and feces revealed significant alterations in the gut fungal composition of MAFLD patients. Although no statistical difference was evident in the oral mycobiome diversity within MAFLD and healthy group, significantly decreased diversities were observed in fecal samples of MAFLD patients. The relative abundance of one salivary species, five supragingival species, and seven fecal species was significantly altered in MAFLD patients. Twenty-two salivary, 23 supragingival, and 22 fecal species were associated with clinical parameters. Concerning the different functions of fungal species, pathways involved in metabolic pathways, biosynthesis of secondary metabolites, microbial metabolism in diverse environments, and carbon metabolism were abundant both in the oral and gut mycobiomes. Moreover, different fungal contributions in core functions were observed between MAFLD patients and the healthy controls, especially in the supragingival plaque and fecal samples. Finally, correlation analysis between oral/gut mycobiome and clinical parameters identified correlations of certain fungal species in both oral and gut niches. Particularly, Mucor ambiguus, which was abundant both in saliva and feces, was positively correlated with body mass index, total cholesterol, low-density lipoprotein, alanine aminotransferase, and aspartate aminotransferase, providing evidence of a possible "oral-gut-liver" axis. The findings illustrate the potential correlation between core mycobiome and the development of MAFLD and could propose potential therapeutic strategies.},
}

Humans
*Mycobiome
Fungi/genetics
*Gastrointestinal Microbiome
Feces/microbiology
Saliva
*Non-alcoholic Fatty Liver Disease

@article {pmid37121198,
year = {2023},
author = {Li, L and Yan, W and Zhang, B and Zhang, H and Geng, R and Sun, S and Guan, X},
title = {Coupling of selenate reduction and pyrrhotite oxidation by indigenous microbial consortium in natural aquifer.},
journal = {Water research},
volume = {238},
number = {},
pages = {119987},
doi = {10.1016/j.watres.2023.119987},
pmid = {37121198},
issn = {1879-2448},
mesh = {Selenic Acid ; *Microbial Consortia ; Ferric Compounds ; Oxidation-Reduction ; Ferrous Compounds ; *Groundwater ; },
abstract = {Pyrrhotite is ubiquitously found in natural environment and involved in diverse (bio)processes. However, the pyrrhotite-driven bioreduction of toxic selenate [Se(VI)] remains largely unknown. This study demonstrates that Se(VI) is successfully bioreduced under anaerobic condition with the participation of pyrrhotite for the first time. Completely removal of Se(VI) was achieved at initial concentration of 10 mg/L Se(VI) and 0.56 mL/min flow rate in continuous column experiment with indigenous microbial consortium and pyrrhotite. Variation in hydrochemistry and hydrodynamics affected Se(VI) removal performance. Se(VI) was reduced to insoluble Se(0) while elements in pyrrhotite were oxidized to Fe(III) and SO4[2-]. Breakthrough study indicated that biotic activity contributed 81.4 ± 1.07% to Se(VI) transformation. Microbial community analysis suggested that chemoautotrophic genera (e.g., Thiobacillus) could realize pyrrhotite oxidation and Se(VI) reduction independently, while heterotrophic genera (e.g., Bacillus, Pseudomonas) contributed to Se(VI) detoxification by utilizing metabolic intermediates generated through Fe(II) and S(-II) oxidation, which were further verified by pure culture tests. Metagenomic and qPCR analyses indicated genes encoding enzymes for Se(VI) reduction (e.g., serA, napA and srdBAC), S oxidation (e.g., soxB) and Fe oxidation (e.g., mtrA) were upregulated. The elevated electron transporters (e.g., nicotinamide adenine dinucleotide, cytochrome c) promoted electron transfer from pyrrhotite to Se(VI). This study gains insights into Se biogeochemistry under the effect of Fe(II)-bearing minerals and provides a sustainable strategy for Se(VI) bioremediation in natural aquifer.},
}

Selenic Acid
*Microbial Consortia
Ferric Compounds
Oxidation-Reduction
Ferrous Compounds
*Groundwater

@article {pmid37041035,
year = {2023},
author = {Sun, Y and Cheng, Z and Li, X and Yang, Q and Zhao, B and Wu, Z and Xia, Y},
title = {Genome enrichment of rare and unknown species from complicated microbiomes by nanopore selective sequencing.},
journal = {Genome research},
volume = {33},
number = {4},
pages = {612-621},
doi = {10.1101/gr.277266.122},
pmid = {37041035},
issn = {1549-5469},
mesh = {Humans ; *Nanopores ; *Microbiota/genetics ; Metagenome ; Metagenomics ; },
abstract = {Rare species are vital members of a microbial community, but retrieving their genomes is difficult because of their low abundance. The ReadUntil (RU) approach allows nanopore devices to sequence specific DNA molecules selectively in real time, which provides an opportunity for enriching rare species. Despite the robustness of enriching rare species by reducing the sequencing depth of known host sequences, such as the human genome, there is still a gap in RU-based enriching of rare species in environmental samples whose community composition is unclear, and many rare species have poor or incomplete reference genomes in public databases. Therefore, here we present metaRUpore to overcome this challenge. When we applied metaRUpore to a thermophilic anaerobic digester (TAD) community and human gut microbial community, it reduced coverage of the high-abundance populations and modestly increased (∼2×) the genome coverage of the rare taxa, facilitating successful recovery of near-finished metagenome-assembled genomes (nf-MAGs) of rare species. The simplicity and robustness of the approach make it accessible for laboratories with moderate computational resources, and hold the potential to become the standard practice in future metagenomic sequencing of complicated microbiomes.},
}

Humans
*Nanopores
*Microbiota/genetics
Metagenome
Metagenomics

@article {pmid37016727,
year = {2023},
author = {Tilves, C and Tanaka, T and Differding, MK and Spira, AP and Chia, CW and Ferrucci, L and Mueller, NT},
title = {The gut microbiome and regional fat distribution: Findings from the Baltimore Longitudinal Study of Aging.},
journal = {Obesity (Silver Spring, Md.)},
volume = {31},
number = {5},
pages = {1425-1435},
doi = {10.1002/oby.23717},
pmid = {37016727},
issn = {1930-739X},
support = {K01 HL141589/HL/NHLBI NIH HHS/United States ; T32 HL007024/HL/NHLBI NIH HHS/United States ; R01 AG050507/AG/NIA NIH HHS/United States ; },
mesh = {Humans ; Female ; Male ; Body Mass Index ; Longitudinal Studies ; *Gastrointestinal Microbiome ; Cross-Sectional Studies ; Baltimore ; Aging ; Absorptiometry, Photon ; },
abstract = {OBJECTIVE: The aim of this study was to examine associations of gut microbiome diversity and composition with directly measured regional fat distribution, including central fat, in a large community-based cohort.

METHODS: A cross-sectional investigation was conducted in the Baltimore Longitudinal Study of Aging (N = 815, 55.2% female, 65.9% White). The fecal microbiome was assessed using whole-genome shotgun metagenomic sequencing, and trunk and leg fat was measured using dual x-ray absorptiometry. Multivariable-adjusted associations of regional fat measures, BMI, or waist circumference with microbiome alpha diversity metrics, microbiome beta diversity metrics, and species differential abundance (verified using two compositional statistical approaches) were examined.

RESULTS: Trunk fat, leg fat, BMI, and waist circumference all significantly explained similar amounts of variance in microbiome structure. Differential abundance testing identified 11 bacterial species significantly associated with at least one measure of body composition or anthropometry. Ruminococcus gnavus was strongly and consistently associated with trunk fat mass, which is congruent with prior literature.

CONCLUSIONS: Microbiome diversity and composition, in particular higher abundance of Ruminococcus gnavus, were associated with greater trunk fat, in addition to other measures of obesity. Longitudinal studies are needed to replicate these findings, and if replicated, randomized trials are needed to determine whether interventions targeting microbiome features such as abundance of Ruminococcus gnavus can lead to reductions in trunk fat and its metabolic sequelae.},
}

Humans
Female
Male
Body Mass Index
Longitudinal Studies
*Gastrointestinal Microbiome
Cross-Sectional Studies
Baltimore
Aging
Absorptiometry, Photon

@article {pmid37003055,
year = {2023},
author = {Jamal, R and Messaoudene, M and de Figuieredo, M and Routy, B},
title = {Future indications and clinical management for fecal microbiota transplantation (FMT) in immuno-oncology.},
journal = {Seminars in immunology},
volume = {67},
number = {},
pages = {101754},
doi = {10.1016/j.smim.2023.101754},
pmid = {37003055},
issn = {1096-3618},
mesh = {Humans ; Animals ; Mice ; Fecal Microbiota Transplantation/adverse effects ; Immune Checkpoint Inhibitors ; Treatment Outcome ; *Microbiota ; *Neoplasms/therapy/etiology ; },
abstract = {The gut microbiota has rapidly emerged as one of the "hallmarks of cancers" and a key contributor to cancer immunotherapy. Metagenomics profiling has established the link between microbiota compositions and immune checkpoint inhibitors response and toxicity, while murine experiments demonstrating the synergistic benefits of microbiota modification with immune checkpoint inhibitors (ICIs) pave a clear path for translation. Fecal microbiota transplantation (FMT) is one of the most effective treatments for patients with Clostridioides difficile, but its utility in other disease contexts has been limited. Nonetheless, promising data from the first trials combining FMT with ICIs have provided strong clinical rationale to pursue this strategy as a novel therapeutic avenue. In addition to the safety considerations surrounding new and emerging pathogens potentially transmissible by FMT, several other challenges must be overcome in order to validate the use of FMT as a therapeutic option in oncology. In this review, we will explore how the lessons learned from FMT in other specialties will help shape the design and development of FMT in the immuno-oncology arena.},
}

Humans
Animals
Mice
Fecal Microbiota Transplantation/adverse effects
Immune Checkpoint Inhibitors
Treatment Outcome
*Microbiota
*Neoplasms/therapy/etiology

@article {pmid36946508,
year = {2023},
author = {Mannan, A and Hoque, MN and Noyon, SH and Mehedi, HMH and Foysal, MJ and Salauddin, A and Islam, SMR and Sharmen, F and Tanni, AA and Siddiki, AZ and Tay, A and Siddique, MM and Rahman, MS and Galib, SM and Akter, F},
title = {SARS-CoV-2 infection alters the gut microbiome in diabetes patients: A cross-sectional study from Bangladesh.},
journal = {Journal of medical virology},
volume = {95},
number = {4},
pages = {e28691},
doi = {10.1002/jmv.28691},
pmid = {36946508},
issn = {1096-9071},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Diabetes Mellitus, Type 2/complications ; Cross-Sectional Studies ; RNA, Ribosomal, 16S/genetics ; Dysbiosis/microbiology ; Bangladesh/epidemiology ; *COVID-19 ; SARS-CoV-2/genetics ; Bacteria/genetics ; },
abstract = {Populations of different South Asian nations including Bangladesh reportedly have a high risk of developing diabetes in recent years. This study aimed to investigate the differences in the gut microbiome of COVID-19-positive participants with or without type 2 diabetes mellitus (T2DM) compared with healthy control subjects. Microbiome data of 30 participants with T2DM were compared with 22 age-, sex-, and body mass index (BMI)-matched individuals. Clinical features were recorded while fecal samples were collected aseptically from the participants. Amplicon-based (16S rRNA) metagenome analyses were employed to explore the dysbiosis of gut microbiota and its correlation with genomic and functional features in COVID-19 patients with or without T2DM. Comparing the detected bacterial genera across the sample groups, 98 unique genera were identified, of which 9 genera had unique association with COVID-19 T2DM patients. Among different bacterial groups, Shigella (25%), Bacteroides (23.45%), and Megamonas (15.90%) had higher mean relative abundances in COVID-19 patients with T2DM. An elevated gut microbiota dysbiosis in T2DM patients with COVID-19 was observed while some metabolic functional changes correlated with bidirectional microbiome dysbiosis between diabetes and non-diabetes humans gut were also found. These results further highlight the possible association of COVID-19 infection that might be linked with alteration of gut microbiome among T2DM patients.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Diabetes Mellitus, Type 2/complications
Cross-Sectional Studies
RNA, Ribosomal, 16S/genetics
Dysbiosis/microbiology
Bangladesh/epidemiology
*COVID-19
SARS-CoV-2/genetics
Bacteria/genetics

@article {pmid36929732,
year = {2023},
author = {Ma, ZS},
title = {Virome comparison (VC): A novel approach to comparing viromes based on virus species specificity and virome specificity diversity.},
journal = {Journal of medical virology},
volume = {95},
number = {4},
pages = {e28682},
doi = {10.1002/jmv.28682},
pmid = {36929732},
issn = {1096-9071},
mesh = {Humans ; *Virome/genetics ; Species Specificity ; *Viruses/genetics ; Metagenomics ; },
abstract = {The human virome, or the viral communities distributed on or in our body, is estimated to contain about 380 trillion of viruses (individuals), which has far reaching influences on our health and diseases. Obviously, the sheer numbers of viruses alone make the comparisons of two or multiple viromes extremely challenging. In fact, the theory of computation in computer science for so-termed NP-hard problems stipulates that the problem is unsolvable when the size of virome is sufficiently large even with fastest supercomputers. Practically, one has to develop heuristic and approximate algorithms to obtain practically satisfactory solutions for NP-hard problems. Here, we extend the species-specificity and specificity-diversity framework to develop a method for virome comparison (VC). The VC method consists of a pair of metrics: virus species specificity (VS) and virome specificity diversity (VSD) and corresponding pair of random search algorithms. Specifically, the VS and VS permutation (VSP) test can detect unique virus species (US) or enriched virus species (ES) in each virome (treatment), and the VSD and VSD permutation (VSDP) test can further determine holistic differences between two viromes or their subsets (assemblages of viruses). The test with four virome data sets demonstrated that the VC method is effective, efficient, and robust.},
}

Humans
*Virome/genetics
Species Specificity
*Viruses/genetics
Metagenomics

@article {pmid37180114,
year = {2023},
author = {Britto, AMA and Siqueira, JD and Curty, G and Goes, LR and Policarpo, C and Meyrelles, AR and Furtado, Y and Almeida, G and Giannini, ALM and Machado, ES and Soares, MA},
title = {Microbiome analysis of Brazilian women cervix reveals specific bacterial abundance correlation to RIG-like receptor gene expression.},
journal = {Frontiers in immunology},
volume = {14},
number = {},
pages = {1147950},
pmid = {37180114},
issn = {1664-3224},
mesh = {Humans ; Female ; Cervix Uteri/microbiology ; *Uterine Cervical Neoplasms/genetics ; Toll-Like Receptor 3/genetics ; *Papillomavirus Infections/genetics ; Brazil ; Gene Expression ; *Microbiota/genetics ; },
abstract = {The relationship among microbiome, immunity and cervical cancer has been targeted by several studies, yet many questions remain unanswered. We characterized herein the virome and bacteriome from cervical samples and correlated these findings with innate immunity gene expression in a Brazilian convenience sample of HPV-infected (HPV+) and uninfected (HPV-) women. For this purpose, innate immune gene expression data were correlated to metagenomic information. Correlation analysis showed that interferon (IFN) is able to differentially modulate pattern recognition receptors (PRRs) expression based on HPV status. Virome analysis indicated that HPV infection correlates to the presence of Anellovirus (AV) and seven complete HPV genomes were assembled. Bacteriome results unveiled that vaginal community state types (CST) distribution was independent of HPV or AV status, although bacterial phyla distribution differed between groups. Furthermore, TLR3 and IFNαR2 levels were higher in the Lactobacillus no iners-dominated mucosa and we detected correlations among RIG-like receptors (RLR) associated genes and abundance of specific anaerobic bacteria. Collectively, our data show an intriguing connection between HPV and AV infections that could foster cervical cancer development. Besides that, TLR3 and IFNαR2 seem to create a protective milieu in healthy cervical mucosa (L. no iners-dominated), and RLRs, known to recognize viral RNA, were correlated to anaerobic bacteria suggesting that they might be related to dysbiosis.},
}

Humans
Female
Cervix Uteri/microbiology
*Uterine Cervical Neoplasms/genetics
Toll-Like Receptor 3/genetics
*Papillomavirus Infections/genetics
Brazil
Gene Expression
*Microbiota/genetics

@article {pmid37179329,
year = {2023},
author = {Anderson, AC and von Ohle, C and Frese, C and Boutin, S and Bridson, C and Schoilew, K and Peikert, SA and Hellwig, E and Pelz, K and Wittmer, A and Wolff, D and Al-Ahmad, A},
title = {The oral microbiota is a reservoir for antimicrobial resistance: resistome and phenotypic resistance characteristics of oral biofilm in health, caries, and periodontitis.},
journal = {Annals of clinical microbiology and antimicrobials},
volume = {22},
number = {1},
pages = {37},
pmid = {37179329},
issn = {1476-0711},
mesh = {Humans ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Dental Caries Susceptibility ; *Microbiota/genetics ; *Periodontitis/genetics ; Bacteria ; Genes, Bacterial ; },
abstract = {BACKGROUND: Antimicrobial resistance (AMR) is an ever-growing threat to modern medicine and, according to the latest reports, it causes nearly twice as many deaths globally as AIDS or malaria. Elucidating reservoirs and dissemination routes of antimicrobial resistance genes (ARGs) are essential in fighting AMR. Human commensals represent an important reservoir, which is underexplored for the oral microbiota. Here, we set out to investigate the resistome and phenotypic resistance of oral biofilm microbiota from 179 orally healthy (H), caries active (C), and periodontally diseased (P) individuals (TRN: DRKS00013119, Registration date: 22.10.2022). The samples were analysed using shotgun metagenomic sequencing combined, for the first time, with culture technique. A selection of 997 isolates was tested for resistance to relevant antibiotics.

RESULTS: The shotgun metagenomics sequencing resulted in 2,069,295,923 reads classified into 4856 species-level OTUs. PERMANOVA analysis of beta-diversity revealed significant differences between the groups regarding their microbiota composition and their ARG profile. The samples were clustered into three ecotypes based on their microbial composition. The bacterial composition of H and C samples greatly overlapped and was based on ecotypes 1 and 2 whereas ecotype 3 was only detected in periodontitis. We found 64 ARGs conveying resistance to 36 antibiotics, particularly to tetracycline, macrolide-lincosamide-streptogramin, and beta-lactam antibiotics, and a correspondingly high prevalence of phenotypic resistance. Based on the microbiota composition, these ARGs cluster in different resistotypes, and a higher prevalence is found in healthy and caries active than in periodontally diseased individuals. There was a significant association between the resistotypes and the ecotypes. Although numerous associations were found between specific antibiotic resistance and bacterial taxa, only a few taxa showed matching associations with both genotypic and phenotypic analyses.

CONCLUSIONS: Our findings show the importance of the oral microbiota from different niches within the oral cavity as a reservoir for antibiotic resistance. Additionally, the present study showed the need for using more than one method to reveal antibiotic resistance within the total oral biofilm, as a clear mismatch between the shotgun metagenomics method and the phenotypic resistance characterization was shown.},
}

Humans
Anti-Bacterial Agents/pharmacology
Drug Resistance, Bacterial/genetics
Dental Caries Susceptibility
*Microbiota/genetics
*Periodontitis/genetics
Bacteria
Genes, Bacterial

@article {pmid37177963,
year = {2023},
author = {Luo, ZM and Liu, JX and Hu, YQ and He, L and Zhou, YY and Zheng, QR and Chai, BF},
title = {[Taxonomic and Functional Diversity of Soil Microbial Communities in Subalpine Meadow with Different Degradation Degrees in Mount Wutai].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {44},
number = {5},
pages = {2918-2927},
doi = {10.13227/j.hjkx.202204330},
pmid = {37177963},
issn = {0250-3301},
mesh = {*Ecosystem ; Grassland ; Carbon ; Soil ; Soil Microbiology ; *Microbiota ; Bacteria/genetics ; },
abstract = {Although soil microbes play a key role in grassland ecosystem functioning, the response of their diversity to grassland degradation has not been fully investigated. Here, we used shotgun metagenomic sequencing to analyze the characteristics and influencing factors of soil microbial taxonomic and functional diversity at four different degradation stages[i.e., non-degraded (ND), lightly degraded (LD), moderately degraded (MD), and heavily degraded (HD)]of subalpine meadow in the Mount Wutai. The results showed that there were significant differences in the relative abundances of Actinobacteria, Bacteroidetes, Nitrospirae, and Parcubacteria among the four subalpine grasslands with different degradation degrees (P<0.05).Compared with that in ND, the degraded meadows increased the proportion of genes related to carbon metabolism, biosynthesis of amino acids, pyruvate metabolism, citric acid cycle, propanoate metabolism, butanoate metabolism, and fatty acid metabolism (P<0.05), indicating that the degradation of subalpine grassland changed the metabolic potential of energy metabolism and the nutrient cycle of the soil microbial community. Grassland degradation changed soil microbial taxonomic and functional α diversity, especially in MD and HD.Grassland degradation resulted in significant changes in the taxonomic and functional compositions of the microbial communities. The total nitrogen, pH, and soil organic carbon significantly affected the taxonomic and functional compositions of the microbial communities.The β diversity of the plant community was significantly correlated with the taxonomic and functional β diversity of the microbial community (P<0.05), indicating strong coupling. The results of this study revealed the changes and driving mechanisms of subsurface microbial taxonomic and functional diversity during grassland degradation, which can provide a theoretical basis for subalpine meadow protection and ecological restoration.},
}

*Ecosystem
Grassland
Carbon
Soil
Soil Microbiology
*Microbiota
Bacteria/genetics

@article {pmid37175775,
year = {2023},
author = {Kazakova, P and Abasolo, N and de Cripan, SM and Marquès, E and Cereto-Massagué, A and Garcia, L and Canela, N and Tormo, R and Torrell, H},
title = {Gut Microbiome and Small RNA Integrative-Omic Perspective of Meconium and Milk-FED Infant Stool Samples.},
journal = {International journal of molecular sciences},
volume = {24},
number = {9},
pages = {},
pmid = {37175775},
issn = {1422-0067},
mesh = {Infant, Newborn ; Humans ; Infant ; *Meconium ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Milk, Human ; Bacteria/genetics ; DNA, Viral ; },
abstract = {The human gut microbiome plays an important role in health, and its initial development is conditioned by many factors, such as feeding. It has also been claimed that this colonization is guided by bacterial populations, the dynamic virome, and transkingdom interactions between host and microbial cells, partially mediated by epigenetic signaling. In this article, we characterized the bacteriome, virome, and smallRNome and their interaction in the meconium and stool samples from infants. Bacterial and viral DNA and RNA were extracted from the meconium and stool samples of 2- to 4-month-old milk-fed infants. The bacteriome, DNA and RNA virome, and smallRNome were assessed using 16S rRNA V4 sequencing, viral enrichment sequencing, and small RNA sequencing protocols, respectively. Data pathway analysis and integration were performed using the R package mixOmics. Our findings showed that the bacteriome differed among the three groups, while the virome and smallRNome presented significant differences, mainly between the meconium and stool of milk-fed infants. The gut environment is rapidly acquired after birth, and it is highly adaptable due to the interaction of environmental factors. Additionally, transkingdom interactions between viruses and bacteria can influence host and smallRNome profiles. However, virome characterization has several protocol limitations that must be considered.},
}

Infant, Newborn
Humans
Infant
*Meconium
*Gastrointestinal Microbiome/genetics
RNA, Ribosomal, 16S/genetics
Feces/microbiology
Milk, Human
Bacteria/genetics
DNA, Viral

@article {pmid37175619,
year = {2023},
author = {Even, G and Mouray, A and Vandenabeele, N and Martel, S and Merlin, S and Lebrun-Ruer, S and Chabé, M and Audebert, C},
title = {Bact-to-Batch: A Microbiota-Based Tool to Determine Optimal Animal Allocation in Experimental Designs.},
journal = {International journal of molecular sciences},
volume = {24},
number = {9},
pages = {},
pmid = {37175619},
issn = {1422-0067},
mesh = {Mice ; Animals ; *Research Design ; RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; Pilot Projects ; *Microbiota/genetics ; Feces ; },
abstract = {The basis of any animal experimentation begins with the housing of animals that should take into account the need for splitting animals into similar groups. Even if it is generally recommended to use the minimum number of animals necessary to obtain reliable and statistically significant results (3Rs rule), the allocation of animals is currently mostly based on randomness. Since variability in gut microbiota is an important confounding factor in animal experiments, the main objective of this study was to develop a new approach based on 16S rRNA gene sequencing analysis of the gut microbiota of animals participating in an experiment, in order to correctly assign the animals across batches. For this purpose, a pilot study was performed on 20 mouse faecal samples with the aim of establishing two groups of 10 mice as similar as possible in terms of their faecal microbiota fingerprinting assuming that this approach limits future analytical bias and ensures reproducibility. The suggested approach was challenged with previously published data from a third-party study. This new method allows to embrace the unavoidable microbiota variability between animals in order to limit artefacts and to provide an additional assurance for the reproducibility of animal experiments.},
}

Mice
Animals
*Research Design
RNA, Ribosomal, 16S/genetics
Reproducibility of Results
Pilot Projects
*Microbiota/genetics
Feces

@article {pmid37173775,
year = {2023},
author = {Vigneron, A and Cruaud, P and Lovejoy, C and Vincent, WF},
title = {Genomic insights into cryptic cycles of microbial hydrocarbon production and degradation in contiguous freshwater and marine microbiomes.},
journal = {Microbiome},
volume = {11},
number = {1},
pages = {104},
pmid = {37173775},
issn = {2049-2618},
mesh = {Canada ; *Hydrocarbons/metabolism ; *Microbiota/genetics ; Alkanes/metabolism ; Bacteria/genetics ; Genomics ; Water ; Lakes/microbiology ; Oxygen/metabolism ; Sulfur/metabolism ; },
abstract = {BACKGROUND: Cyanobacteria and eukaryotic phytoplankton produce long-chain alkanes and generate around 100 times greater quantities of hydrocarbons in the ocean compared to natural seeps and anthropogenic sources. Yet, these compounds do not accumulate in the water column, suggesting rapid biodegradation by co-localized microbial populations. Despite their ecological importance, the identities of microbes involved in this cryptic hydrocarbon cycle are mostly unknown. Here, we identified genes encoding enzymes involved in the hydrocarbon cycle across the salinity gradient of a remote, vertically stratified, seawater-containing High Arctic lake that is isolated from anthropogenic petroleum sources and natural seeps. Metagenomic analysis revealed diverse hydrocarbon cycling genes and populations, with patterns of variation along gradients of light, salinity, oxygen, and sulfur that are relevant to freshwater, oceanic, hadal, and anoxic deep sea ecosystems.

RESULTS: Analyzing genes and metagenome-assembled genomes down the water column of Lake A in the Canadian High Arctic, we detected microbial hydrocarbon production and degradation pathways at all depths, from surface freshwaters to dark, saline, anoxic waters. In addition to Cyanobacteria, members of the phyla Flavobacteria, Nitrospina, Deltaproteobacteria, Planctomycetes, and Verrucomicrobia had pathways for alkane and alkene production, providing additional sources of biogenic hydrocarbons. Known oil-degrading microorganisms were poorly represented in the system, while long-chain hydrocarbon degradation genes were identified in various freshwater and marine lineages such as Actinobacteria, Schleiferiaceae, and Marinimicrobia. Genes involved in sulfur and nitrogen compound transformations were abundant in hydrocarbon producing and degrading lineages, suggesting strong interconnections with nitrogen and sulfur cycles and a potential for widespread distribution in the ocean.

CONCLUSIONS: Our detailed metagenomic analyses across water column gradients in a remote petroleum-free lake derived from the Arctic Ocean suggest that the current estimation of bacterial hydrocarbon production in the ocean could be substantially underestimated by neglecting non-phototrophic production and by not taking low oxygen zones into account. Our findings also suggest that biogenic hydrocarbons may sustain a large fraction of freshwater and oceanic microbiomes, with global biogeochemical implications for carbon, sulfur, and nitrogen cycles. Video Abstract.},
}

Canada
*Hydrocarbons/metabolism
*Microbiota/genetics
Alkanes/metabolism
Bacteria/genetics
Genomics
Water
Lakes/microbiology
Oxygen/metabolism
Sulfur/metabolism

@article {pmid37169816,
year = {2023},
author = {La Reau, AJ and Strom, NB and Filvaroff, E and Mavrommatis, K and Ward, TL and Knights, D},
title = {Shallow shotgun sequencing reduces technical variation in microbiome analysis.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {7668},
pmid = {37169816},
issn = {2045-2322},
mesh = {Humans ; Reproducibility of Results ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Bacteria/genetics ; Sequence Analysis, DNA ; High-Throughput Nucleotide Sequencing ; Metagenomics ; },
abstract = {The microbiome is known to play a role in many human diseases, but identifying key microbes and their functions generally requires large studies due to the vast number of species and genes, and the high levels of intra-individual and inter-individual variation. 16S amplicon sequencing of the rRNA gene is commonly used for large studies due to its comparatively low sequencing cost, but it has poor taxonomic and functional resolution. Deep shotgun sequencing is a more accurate and comprehensive alternative for small studies, but can be cost-prohibitive for biomarker discovery in large populations. Shallow or moderate-depth shotgun metagenomics may serve as a viable alternative to 16S sequencing for large-scale and/or dense longitudinal studies, but only if resolution and reproducibility are comparable. Here we applied both 16S and shallow shotgun stool microbiome sequencing to a cohort of 5 subjects sampled twice daily and weekly, with technical replication at the DNA extraction and the library preparation/sequencing steps, for a total of 80 16S samples and 80 shallow shotgun sequencing samples. We found that shallow shotgun sequencing produced lower technical variation and higher taxonomic resolution than 16S sequencing, at a much lower cost than deep shotgun sequencing. These findings suggest that shallow shotgun sequencing provides a more specific and more reproducible alternative to 16S sequencing for large-scale microbiome studies where costs prohibit deep shotgun sequencing and where bacterial species are expected to have good coverage in whole-genome reference databases.},
}

Humans
Reproducibility of Results
RNA, Ribosomal, 16S/genetics
*Microbiota/genetics
Bacteria/genetics
Sequence Analysis, DNA
High-Throughput Nucleotide Sequencing
Metagenomics

@article {pmid37169786,
year = {2023},
author = {Lugli, GA and Mancabelli, L and Milani, C and Fontana, F and Tarracchini, C and Alessandri, G and van Sinderen, D and Turroni, F and Ventura, M},
title = {Comprehensive insights from composition to functional microbe-based biodiversity of the infant human gut microbiota.},
journal = {NPJ biofilms and microbiomes},
volume = {9},
number = {1},
pages = {25},
pmid = {37169786},
issn = {2055-5008},
mesh = {Humans ; Infant ; Infant, Newborn ; Adult ; *Gastrointestinal Microbiome ; *Microbiota ; Bacteria/genetics ; Metagenome ; Biodiversity ; },
abstract = {During infancy, gut microbiota development is a crucial process involved in the establishment of microbe-host interactions which may persist throughout adulthood, and which are believed to influence host health. To fully understand the complexities of such interactions, it is essential to assess gut microbiota diversity of newborns and its associated microbial dynamics and relationships pertaining to health and disease. To explore microbial biodiversity during the first 3 years of human life, 10,935 shotgun metagenomic datasets were taxonomically and functionally classified. Microbial species distribution between infants revealed the presence of eight major Infant Community State Types (ICSTs), being dominated by 17 bacterial taxa, whose distribution was shown to correspond to the geographical origin and infant health status. In total, 2390 chromosomal sequences of the predominant taxa were reconstructed from metagenomic data and used in combination with 44,987 publicly available genomes to trace the distribution of microbial Population Subspecies (PS) within the different infant groups, revealing patterns of multistrain coexistence among ICSTs. Finally, implementation of a metagenomic- and metatranscriptomic-based metabolic profiling highlighted different enzymatic expression patterns of the gut microbiota that allowed us to acquire insights into mechanistic aspects of health-gut microbiota interplay in newborns. Comparison between metagenomic and metatranscriptomic data highlights how a complex environment like the human gut must be investigated by employing both sequencing methodologies and possibly supplemented with metabolomics approaches. While metagenomic analyses are very useful for microbial classification aimed at unveiling key players driving microbiota balances, using these data to explain functionalities of the microbiota is not always warranted.},
}

Humans
Infant
Infant, Newborn
Adult
*Gastrointestinal Microbiome
*Microbiota
Bacteria/genetics
Metagenome
Biodiversity

@article {pmid37158970,
year = {2023},
author = {Hu, J and Chen, J and Xu, X and Hou, Q and Ren, J and Yan, X},
title = {Gut microbiota-derived 3-phenylpropionic acid promotes intestinal epithelial barrier function via AhR signaling.},
journal = {Microbiome},
volume = {11},
number = {1},
pages = {102},
pmid = {37158970},
issn = {2049-2618},
mesh = {Animals ; Mice ; Swine ; *Gastrointestinal Microbiome ; Receptors, Aryl Hydrocarbon/genetics ; DNA, Ribosomal ; Fecal Microbiota Transplantation ; },
abstract = {BACKGROUND: The intestinal epithelial barrier confers protection against the intestinal invasion by pathogens and exposure to food antigens and toxins. Growing studies have linked the gut microbiota to the intestinal epithelial barrier function. The mining of the gut microbes that facilitate the function of intestinal epithelial barrier is urgently needed.

RESULTS: Here, we studied a landscape of the gut microbiome of seven pig breeds using metagenomics and 16S rDNA gene amplicon sequencing. The results indicated an obvious difference in the gut microbiome between Congjiang miniature (CM) pigs (a native Chinese breed) and commercial Duroc × [Landrace × Yorkshire] (DLY) pigs. CM finishing pigs had stronger intestinal epithelial barrier function than the DLY finishing pigs. Fecal microbiota transplantation from CM and DLY finishing pigs to germ-free (GF) mice transferred the intestinal epithelial barrier characteristics. By comparing the gut microbiome of the recipient GF mice, we identified and validated Bacteroides fragilis as a microbial species that contributes to the intestinal epithelial barrier. B. fragilis-derived 3-phenylpropionic acid metabolite had an important function on the enhancement of intestinal epithelial barrier. Furthermore, 3-phenylpropionic acid facilitated the intestinal epithelial barrier by activating aryl hydrocarbon receptor (AhR) signaling.

CONCLUSIONS: These findings suggest that manipulation of B. fragilis and 3-phenylpropionic acid is a promising strategy for improving intestinal epithelial barrier. Video Abstract.},
}

Animals
Mice
Swine
*Gastrointestinal Microbiome
Receptors, Aryl Hydrocarbon/genetics
DNA, Ribosomal
Fecal Microbiota Transplantation

@article {pmid37158954,
year = {2023},
author = {Ettinger, CL and Saunders, M and Selbmann, L and Delgado-Baquerizo, M and Donati, C and Albanese, D and Roux, S and Tringe, S and Pennacchio, C and Del Rio, TG and Stajich, JE and Coleine, C},
title = {Highly diverse and unknown viruses may enhance Antarctic endoliths' adaptability.},
journal = {Microbiome},
volume = {11},
number = {1},
pages = {103},
pmid = {37158954},
issn = {2049-2618},
mesh = {Antarctic Regions ; *Acclimatization ; Bicycling ; Climate ; *Microbiota/genetics ; },
abstract = {BACKGROUND: Rock-dwelling microorganisms are key players in ecosystem functioning of Antarctic ice free-areas. Yet, little is known about their diversity and ecology, and further still, viruses in these communities have been largely unexplored despite important roles related to host metabolism and nutrient cycling. To begin to address this, we present a large-scale viral catalog from Antarctic rock microbial communities.

RESULTS: We performed metagenomic analyses on rocks from across Antarctica representing a broad range of environmental and spatial conditions, and which resulted in a predicted viral catalog comprising > 75,000 viral operational taxonomic units (vOTUS). We found largely undescribed, highly diverse and spatially structured virus communities which had predicted auxiliary metabolic genes (AMGs) with functions indicating that they may be potentially influencing bacterial adaptation and biogeochemistry.

CONCLUSION: This catalog lays the foundation for expanding knowledge of virosphere diversity, function, spatial ecology, and dynamics in extreme environments. This work serves as a step towards exploring adaptability of microbial communities in the face of a changing climate. Video Abstract.},
}

Antarctic Regions
*Acclimatization
Bicycling
Climate
*Microbiota/genetics

@article {pmid37119735,
year = {2023},
author = {Palmu, J and Börschel, CS and Ortega-Alonso, A and Markó, L and Inouye, M and Jousilahti, P and Salido, RA and Sanders, K and Brennan, C and Humphrey, GC and Sanders, JG and Gutmann, F and Linz, D and Salomaa, V and Havulinna, AS and Forslund, SK and Knight, R and Lahti, L and Niiranen, T and Schnabel, RB},
title = {Gut microbiome and atrial fibrillation-results from a large population-based study.},
journal = {EBioMedicine},
volume = {91},
number = {},
pages = {104583},
pmid = {37119735},
issn = {2352-3964},
mesh = {Humans ; *Atrial Fibrillation/etiology/complications ; *Gastrointestinal Microbiome ; Heart ; Bacteria/genetics ; Aging ; Incidence ; },
abstract = {BACKGROUND: Atrial fibrillation (AF) is an important heart rhythm disorder in aging populations. The gut microbiome composition has been previously related to cardiovascular disease risk factors. Whether the gut microbial profile is also associated with the risk of AF remains unknown.

METHODS: We examined the associations of prevalent and incident AF with gut microbiota in the FINRISK 2002 study, a random population sample of 6763 individuals. We replicated our findings in an independent case-control cohort of 138 individuals in Hamburg, Germany.

FINDINGS: Multivariable-adjusted regression models revealed that prevalent AF (N = 116) was associated with nine microbial genera. Incident AF (N = 539) over a median follow-up of 15 years was associated with eight microbial genera with false discovery rate (FDR)-corrected P < 0.05. Both prevalent and incident AF were associated with the genera Enorma and Bifidobacterium (FDR-corrected P < 0.001). AF was not significantly associated with bacterial diversity measures. Seventy-five percent of top genera (Enorma, Paraprevotella, Odoribacter, Collinsella, Barnesiella, Alistipes) in Cox regression analyses showed a consistent direction of shifted abundance in an independent AF case-control cohort that was used for replication.

INTERPRETATION: Our findings establish the basis for the use of microbiome profiles in AF risk prediction. However, extensive research is still warranted before microbiome sequencing can be used for prevention and targeted treatment of AF.

FUNDING: This study was funded by European Research Council, German Ministry of Research and Education, Academy of Finland, Finnish Medical Foundation, and the Finnish Foundation for Cardiovascular Research, the Emil Aaltonen Foundation, and the Paavo Nurmi Foundation.},
}

Humans
*Atrial Fibrillation/etiology/complications
*Gastrointestinal Microbiome
Heart
Bacteria/genetics
Aging
Incidence

@article {pmid37118882,
year = {2023},
author = {Ceylani, T},
title = {Effect of SCD probiotics supplemented with tauroursodeoxycholic acid (TUDCA) application on the aged rat gut microbiota composition.},
journal = {Journal of applied microbiology},
volume = {134},
number = {5},
pages = {},
doi = {10.1093/jambio/lxad092},
pmid = {37118882},
issn = {1365-2672},
mesh = {Rats ; Animals ; Rats, Sprague-Dawley ; *Gastrointestinal Microbiome ; Taurochenodeoxycholic Acid/pharmacology ; *Probiotics/pharmacology ; },
abstract = {AIMS: In this study, the effects of SCD Probiotics with tauroursodeoxycholic acid (TUDCA) application on the aged rat gut microbiota (GM) composition were investigated.

METHODS AND RESULTS: Twenty-four-month-old Sprague-Dawley rats were given 300 mg/kg of TUDCA along with 3 mL (1 × 108 CFU) of SCD probiotics for 7 days. The bacterial profile was determined by the metagenome applied to the cecum content. TUDCA, SCD probiotics, and TUDCA with SCD probiotics designed GM differently. TUDCA and SCD probiotics have the most different dominant species profiles.

CONCLUSIONS: SCD probiotics and TUDCA have their own unique effects on the species found in GM, and when they are evaluated together, the species found in GM are restructured differently.},
}

Rats
Animals
Rats, Sprague-Dawley
*Gastrointestinal Microbiome
Taurochenodeoxycholic Acid/pharmacology
*Probiotics/pharmacology

@article {pmid37039875,
year = {2023},
author = {Chen, Y and Li, X and Yu, C and Wang, E and Luo, C and Jin, Y and Zhang, L and Ma, Y and Jin, Y and Yang, L and Sun, B and Qiao, J and Zhou, X and Rasche, L and Einsele, H and Song, J and Bai, T and Hou, X},
title = {Gut microbiome alterations in patients with COVID-19-related coagulopathy.},
journal = {Annals of hematology},
volume = {102},
number = {6},
pages = {1589-1598},
pmid = {37039875},
issn = {1432-0584},
mesh = {Humans ; *Gastrointestinal Microbiome ; Cross-Sectional Studies ; *COVID-19/complications ; *Blood Coagulation Disorders/etiology ; *Microbiota ; },
abstract = {COVID-19 is characterized by a predominantly prothrombotic state, which underlies severe disease and poor outcomes. Imbalances of the gut microbiome have been linked with abnormal hemostatic processes. Understanding the relationship between the gut microbiome and abnormal coagulation parameters in COVID-19 could provide a novel framework for the diagnosis and management of COVID-related coagulopathies (CRC). This cross-sectional study used shotgun metagenomic sequencing to examine the gut microbiota of patients with CRC (n = 66) and compared it to COVID control (CCs) (n = 27) and non-COVID control (NCs) (n = 22) groups. Three, 1, and 3 taxa were found enriched in CRCs, CCs, and NCs. Next, random forest models using 7 microbial biomarkers and differential clinical characteristics were constructed and achieved strong diagnostic potential in distinguishing CRC. Specifically, the most promising biomarker species for CRC were Streptococcus thermophilus, Enterococcus faecium, and Citrobacter portucalensis. Conversely, Enterobacteriaceae family and Fusicatenibacter genus are potentially protective against CRC in COVID patients. We further identified 4 species contributing to 20 MetaCyc pathways that were differentially abundant among groups, with S. thermophilus as the main coding species in CRCs. Our findings suggest that the alterations of gut microbiota compositional and functional profiles may influence the pathogenesis of CRC and that microbiota-based diagnosis and treatment could potentially benefit COVID patients in preventing and alleviating thrombosis-related clinical outcomes.},
}

Humans
*Gastrointestinal Microbiome
Cross-Sectional Studies
*COVID-19/complications
*Blood Coagulation Disorders/etiology
*Microbiota

@article {pmid37037312,
year = {2023},
author = {Wang, H and Min, C and Xia, F and Xia, Y and Tang, M and Li, J and Hu, Y and Zou, M},
title = {Metagenomic analysis reveals the short-term influences on conjugation of blaNDM-1 and microbiome in hospital wastewater by silver nanoparticles at environmental-related concentration.},
journal = {Environmental research},
volume = {228},
number = {},
pages = {115866},
doi = {10.1016/j.envres.2023.115866},
pmid = {37037312},
issn = {1096-0953},
mesh = {Wastewater ; Silver ; Metagenome ; *Metal Nanoparticles ; Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; *Microbiota ; Hospitals ; },
abstract = {Hospital wastewater contains large amounts of antibiotic-resistant bacteria and serves as an important reservoir for horizontal gene transfer (HGT). However, the response of the microbiome in hospital wastewater to silver remains unclear. In this study, the short-term impacts of silver on the microbiome in hospital wastewater were investigated by metagenome next-generation sequencing. The influence of silver on the conjugation of plasmid carrying blaNDM-1 was further examined. Our results showed that in hospital wastewater, high abundances of antibiotic resistance genes (ARGs) were detected. The distribution tendencies of certain ARG types on chromosomes or plasmids were different. Clinically important ARGs were identified in phage-like contigs, indicating potential transmission via transduction. Pseudomonadales, Enterobacterales, and Bacteroidales were the major ARG hosts. Mobile genetic elements were mainly detected in plasmids and associated with various types of ARGs. The binning approach identified 29 bins that were assigned to three phyla. Various ARGs and virulence factors were identified in 14 and 11 bins, respectively. MetaCHIP identified 49 HGT events. The transferred genes were annotated as ARGs, mobile genetic elements, and functional genes, and they mainly originated from donors belonging to Bacteroides and Pseudomonadales. In addition, 20 nm AgNPs reduced microbial diversity and enhanced the relative abundance of Acinetobacter. The changes induced by 20 nm AgNPs included increases in the abundances of ARGs and genes involved lipid metabolism pathway. Conjugation experiments showed that Ag[+] and 20 nm AgNPs caused 2.38-, 3.31-, 4.72-, and 4.57-fold and 1.46-, 1.61-, 3.86-, and 2.16-fold increases in conjugation frequencies of plasmid with blaNDM-1 at 0.1, 1, 10, and 100 μg/L, respectively. Our findings provide insight into the response of the microbiome in hospital wastewater to silver, emphasize the adaptation capability of Acinetobacter inhabiting hospitals against adverse environments, and highlight the promotion of silver for antibiotic resistance.},
}

Wastewater
Silver
Metagenome
*Metal Nanoparticles
Anti-Bacterial Agents/pharmacology
Genes, Bacterial
*Microbiota
Hospitals

@article {pmid37011797,
year = {2023},
author = {Wang, L and Zhu, M and Li, Y and Zhao, Z},
title = {Assessing the effects of aquaculture on tidal flat ecological status using multi-metrics interaction-based index of biotic integrity (Mt-IBI).},
journal = {Environmental research},
volume = {228},
number = {},
pages = {115789},
doi = {10.1016/j.envres.2023.115789},
pmid = {37011797},
issn = {1096-0953},
mesh = {Humans ; *Ecosystem ; Benchmarking ; Environmental Monitoring/methods ; *Microbiota ; Nitrogen ; Aquaculture ; Rivers ; China ; },
abstract = {Given tidal flat special environmental conditions and the degree of pollution caused by human activities, there is an urgent need to quantitatively assess their ecological status. Bioindication has become an indispensable part of environmental quality monitoring on account of its sensitivity to environmental disturbance. Thus, this study used bio-indicators to establish a multi-metrics-based index of biotic integrity (Mt-IBI) to evaluate the ecological status of the tidal flats with/without aquaculture through metagenomic sequencing. Four core indexes that were significantly correlated to other indexes with redundancy (p < 0.05), including Escherichia, beta-lactam antibiotic resistance genes, cellulase and xyloglucanases and the keystone species with 21° in the network, were selected after the screening processes. By implementing Mt-IBI in the tidal flats, the ecological health of the sampling sites was categorized into three levels, with Mt-IBI values of 2.01-2.63 (severe level), 2.81-2.93 (moderate level) and 3.23-4.18 (mild level), respectively. Through SEM analysis, water chemical oxygen demand and antibiotics were determined to be the primary controlling factors of the ecological status of tidal flat regions influenced by aquaculture, followed by salinity and total nitrogen. It is worth noting that the alteration of microbial communities impacted ecological status through the mediation of antibiotics. It is hoped that the results of our study will provide a theoretical basis for coastal environment restoration and that the use of Mt-IBI to assess ecosystem status in different aquatic environments will be further popularized in the future.},
}

Humans
*Ecosystem
Benchmarking
Environmental Monitoring/methods
*Microbiota
Nitrogen
Aquaculture
Rivers
China

@article {pmid36965360,
year = {2023},
author = {Li, Z and Qing, Y and Cui, G and Li, M and Liu, T and Zeng, Y and Zhou, C and Hu, X and Jiang, J and Wang, D and Gao, Y and Zhang, J and Cai, C and Wang, T and Wan, C},
title = {Shotgun metagenomics reveals abnormal short-chain fatty acid-producing bacteria and glucose and lipid metabolism of the gut microbiota in patients with schizophrenia.},
journal = {Schizophrenia research},
volume = {255},
number = {},
pages = {59-66},
doi = {10.1016/j.schres.2023.03.005},
pmid = {36965360},
issn = {1573-2509},
mesh = {Humans ; *Gastrointestinal Microbiome ; Lipid Metabolism ; Metagenomics ; Glucose ; *Schizophrenia ; Bacteria/metabolism ; Fatty Acids, Volatile/metabolism ; },
abstract = {Evidence has shown that the gut microbiota is closely related to the pathogenesis of schizophrenia, but temporal changes in the gut microbiota of patients with schizophrenia (SZ) during treatment remain unclear. Here, to evaluate temporal changes in the gut microbiota in schizophrenia, we performed whole-genome shotgun metagenomics on fecal samples from 36 healthy controls (HCs) and 19 baseline-period patients, and followed up with patients upon treatment. Compared to that in HCs, beta diversity in SZ was significantly distinct. The genera Bacteroides, Prevotella and Clostridium were the top 3 altered genera between SZ and HCs, and the Bacteroides-Prevotella ratio was significantly increased in SZ. Thirty-three percent of differentially abundant species were short-chain fatty acid (SCFA)-producing bacteria. Functional analysis showed that glucose and lipid metabolism of the gut microbiota was decreased in SZ compared with those in HCs. The abundances of two rate-limiting enzymes in glucose and lipid metabolism, phosphofructokinase (PFK) and acetyl-CoA carboxylase (ACC), were significantly decreased in SZ, and differentially abundant metabolism-related enzymes were significantly associated with SCFA-producing bacteria. Next, we found that the abundance of SCFA-producing bacteria also changed after treatment and that Clostridium was significantly negatively correlated with the total positive and negative syndrome scale (PANSS) score in patients. Functional analysis showed that glycoside hydrolase family 30 incrementally increased in abundance during treatment and were significantly associated with SCFA-producing bacteria. Our findings help to provide evidence for the role of gut microbiota in the occurrence and development of schizophrenia.},
}

Humans
*Gastrointestinal Microbiome
Lipid Metabolism
Metagenomics
Glucose
*Schizophrenia
Bacteria/metabolism
Fatty Acids, Volatile/metabolism

@article {pmid37155494,
year = {2023},
author = {Gomez-Alvarez, V and Siponen, S and Kauppinen, A and Hokajärvi, AM and Tiwari, A and Sarekoski, A and Miettinen, IT and Torvinen, E and Pitkänen, T},
title = {A comparative analysis employing a gene- and genome-centric metagenomic approach reveals changes in composition, function, and activity in waterworks with different treatment processes and source water in Finland.},
journal = {Water research},
volume = {229},
number = {},
pages = {119495},
pmid = {37155494},
issn = {1879-2448},
support = {EPA999999/ImEPA/Intramural EPA/United States ; },
mesh = {Metagenome ; *Drinking Water/microbiology ; Finland ; Bacteria/metabolism ; *Microbiota/genetics ; Archaea/genetics ; *Disinfectants ; Metagenomics ; },
abstract = {The emergence and development of next-generation sequencing technologies (NGS) has made the analysis of the water microbiome in drinking water distribution systems (DWDSs) more accessible and opened new perspectives in microbial ecology studies. The current study focused on the characterization of the water microbiome employing a gene- and genome-centric metagenomic approach to five waterworks in Finland with different raw water sources, treatment methods, and disinfectant. The microbial communities exhibit a distribution pattern of a few dominant taxa and a large representation of low-abundance bacterial species. Changes in the community structure may correspond to the presence or absence and type of disinfectant residual which indicates that these conditions exert selective pressure on the microbial community. The Archaea domain represented a small fraction (up to 2.5%) and seemed to be effectively controlled by the disinfection of water. Their role particularly in non-disinfected DWDS may be more important than previously considered. In general, non-disinfected DWDSs harbor higher microbial richness and maintaining disinfectant residual is significantly important for ensuring low microbial numbers and diversity. Metagenomic binning recovered 139 (138 bacterial and 1 archaeal) metagenome-assembled genomes (MAGs) that had a >50% completeness and <10% contamination consisting of 20 class representatives in 12 phyla. The presence and occurrence of nitrite-oxidizing bacteria (NOB)-like microorganisms have significant implications for nitrogen biotransformation in drinking water systems. The metabolic and functional complexity of the microbiome is evident in DWDSs ecosystems. A comparative analysis found a set of differentially abundant taxonomic groups and functional traits in the active community. The broader set of transcribed genes may indicate an active and diverse community regardless of the treatment methods applied to water. The results indicate a highly dynamic and diverse microbial community and confirm that every DWDS is unique, and the community reflects the selection pressures exerted at the community structure, but also at the levels of functional properties and metabolic potential.},
}

Metagenome
*Drinking Water/microbiology
Finland
Bacteria/metabolism
*Microbiota/genetics
Archaea/genetics
*Disinfectants
Metagenomics

@article {pmid37149537,
year = {2023},
author = {Ferrillo, A and Kobel, CM and Vera-Ponce de León, A and La Rosa, SL and Kunath, BJ and Pope, PB and Hagen, LH},
title = {Long-Read Metagenomics and CAZyme Discovery.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2657},
number = {},
pages = {253-284},
pmid = {37149537},
issn = {1940-6029},
mesh = {*Metagenomics/methods ; *Microbiota ; Metagenome ; Carbohydrates ; High-Throughput Nucleotide Sequencing ; },
abstract = {Microorganisms play a primary role in regulating biogeochemical cycles and are a valuable source of enzymes that have biotechnological applications, such as carbohydrate-active enzymes (CAZymes). However, the inability to culture the majority of microorganisms that exist in natural ecosystems restricts access to potentially novel bacteria and beneficial CAZymes. While commonplace molecular-based culture-independent methods such as metagenomics enable researchers to study microbial communities directly from environmental samples, recent progress in long-read sequencing technologies are advancing the field. We outline key methodological stages that are required as well as describe specific protocols that are currently used for long-read metagenomic projects dedicated to CAZyme discovery.},
}

*Metagenomics/methods
*Microbiota
Metagenome
Carbohydrates
High-Throughput Nucleotide Sequencing

@article {pmid37149185,
year = {2023},
author = {Palladino, G and Rampelli, S and Scicchitano, D and Nanetti, E and Iuffrida, L and Wathsala, RHGR and Interino, N and Marini, M and Porru, E and Turroni, S and Fiori, J and Franzellitti, S and Candela, M},
title = {Seasonal dynamics of the microbiome-host response to pharmaceuticals and pesticides in Mytilus galloprovincialis farmed in the Northwestern Adriatic Sea.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {163948},
doi = {10.1016/j.scitotenv.2023.163948},
pmid = {37149185},
issn = {1879-1026},
abstract = {Marine mussels, especially Mytilus galloprovincialis, are well-established sentinel species, being naturally resistant to the exposure to multiple xenobiotics of natural and anthropogenic origin. Even if the response to multiple xenobiotic exposure is well known at the host level, the role of the mussel-associated microbiome in the animal response to environmental pollution is poorly explored, despite its potential in xenobiotic detoxification and its important role in host development, protection, and adaptation. Here, we characterized the microbiome-host integrative response of M. galloprovincialis in a real-world setting, involving exposure to a complex pattern of emerging pollutants, as occurs in the Northwestern Adriatic Sea. A total of 387 mussel individuals from 3 commercial farms, spanning about 200 km along the Northwestern Adriatic coast, and in 3 different seasons, were collected. Multiresidue analysis (for quantitative xenobiotic determination), transcriptomics (for host physiological response), and metagenomics (for host-associated microbial taxonomical and functional features) analyses were performed on the digestive glands. According to our findings, M. galloprovincialis responds to the presence of the complex pattern of multiple emerging pollutants - including the antibiotics sulfamethoxazole, erythromycin, and tetracycline, the herbicides atrazine and metolachlor, and the insecticide N,N-diethyl-m-toluamide - integrating host defense mechanisms, e.g., through upregulation of transcripts involved in animal metabolic activity, and microbiome-mediated detoxification functions, including microbial functionalities involved in multidrug or tetracycline resistance. Overall, our data highlight the importance of the mussel-associated microbiome as a strategic player for the orchestration of resistance to the multixenobiotic exposure at the holobiont level, providing strategic functionalities for the detoxification of multiple xenobiotic substances, as occurring in real world exposure settings. Complementing the host with microbiome-dependent xenobiotic degradative and resistance genes, the M. galloprovincialis digestive gland associated microbiome can have an important role in the detoxification of emerging pollutants in a context of high anthropogenic pressure, supporting the relevance of mussel systems as potential animal-based bioremediation tool.},
}

@article {pmid37140125,
year = {2023},
author = {Li, M and Liu, J and Zhu, J and Wang, H and Sun, C and Gao, NL and Zhao, XM and Chen, WH},
title = {Performance of Gut Microbiome as an Independent Diagnostic Tool for 20 Diseases: Cross-Cohort Validation of Machine-Learning Classifiers.},
journal = {Gut microbes},
volume = {15},
number = {1},
pages = {2205386},
pmid = {37140125},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Machine Learning ; Research Design ; Metagenome ; Metagenomics/methods ; },
abstract = {Cross-cohort validation is essential for gut-microbiome-based disease stratification but was only performed for limited diseases. Here, we systematically evaluated the cross-cohort performance of gut microbiome-based machine-learning classifiers for 20 diseases. Using single-cohort classifiers, we obtained high predictive accuracies in intra-cohort validation (~0.77 AUC), but low accuracies in cross-cohort validation, except the intestinal diseases (~0.73 AUC). We then built combined-cohort classifiers trained on samples combined from multiple cohorts to improve the validation of non-intestinal diseases, and estimated the required sample size to achieve validation accuracies of >0.7. In addition, we observed higher validation performance for classifiers using metagenomic data than 16S amplicon data in intestinal diseases. We further quantified the cross-cohort marker consistency using a Marker Similarity Index and observed similar trends. Together, our results supported the gut microbiome as an independent diagnostic tool for intestinal diseases and revealed strategies to improve cross-cohort performance based on identified determinants of consistent cross-cohort gut microbiome alterations.},
}

Humans
*Gastrointestinal Microbiome/genetics
Machine Learning
Research Design
Metagenome
Metagenomics/methods

@article {pmid37002522,
year = {2023},
author = {Wagh, MS and Sivarajan, S and Osborne, WJ},
title = {A new paradigm in the bioremoval of lead, nickel, and cadmium using a cocktail of biosystems: a metagenomic approach.},
journal = {Environmental science and pollution research international},
volume = {30},
number = {20},
pages = {58967-58985},
pmid = {37002522},
issn = {1614-7499},
mesh = {Animals ; Cadmium/analysis ; Nickel/analysis ; Lead/analysis ; RNA, Ribosomal, 16S ; *Metals, Heavy/analysis ; Biodegradation, Environmental ; *Microbiota ; Bacteria ; Soil/chemistry ; *Oligochaeta ; *Soil Pollutants/analysis ; },
abstract = {Lead (Pb), nickel (Ni), and cadmium (Cd) are known for its harmful effects on the environment. Microbial community related to soil plays a pivotal role in configuring several properties of the ecosystem. Thus, remediation of such heavy metals using multiple biosystems had shown excellent bioremoval potential. The current study demonstrates the integrated approach of Chrysopogon zizanioides in combination with earthworm Eisenia fetida augmented with VITMSJ3 potent strain for the uptake of metals like Pb, Ni, and Cd from the contaminated soil. For the uptake of heavy metals, Pb, Ni, and Cd with the concentrations of 50, 100, and 150 mg kg[-1] were supplemented in pots with plants and earthworms. C. zizanioides was used for bioremoval due to their massive fibrous root system which can absorb heavy metals. A substantial increase of 70-80% Pb, Ni, and Cd was found for VITMSJ3 augmented setup. A total of 12 earthworms were introduced in each setup and were tested for the toxicity and damages in the various internal structures. Reduction in malondialdehyde (MDA) content was observed in the earthworms with VITMSJ3 strain proving less toxicity and damages. Metagenomic analysis of the soil associated bacterial diversity was assessed by amplifying the V3V4 region of the 16S rRNA gene and the annotations were studied. Firmicutes were found to be the predominant genus with 56.65% abundance in the bioaugmented soil R (60) proving the detoxification of metals in the bioaugmented soil. Our study proved that a synergistic effect of plant and earthworm in association with potent bacterial strain had higher uptake of Pb, Ni, and Cd. Metagenomic analysis revealed the changes in microbial abundance in the soil before and after treatment.},
}

Animals
Cadmium/analysis
Nickel/analysis
Lead/analysis
RNA, Ribosomal, 16S
*Metals, Heavy/analysis
Biodegradation, Environmental
*Microbiota
Bacteria
Soil/chemistry
*Oligochaeta
*Soil Pollutants/analysis

@article {pmid36916422,
year = {2023},
author = {Wang, AJ and Song, D and Hong, YM and Liu, NN},
title = {Multi-omics insights into the interplay between gut microbiota and colorectal cancer in the "microworld" age.},
journal = {Molecular omics},
volume = {19},
number = {4},
pages = {283-296},
doi = {10.1039/d2mo00288d},
pmid = {36916422},
issn = {2515-4184},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Multiomics ; *Microbiota ; Metabolomics/methods ; *Colorectal Neoplasms/genetics ; },
abstract = {Colorectal cancer (CRC) is a multifactorial heterogeneous disease largely due to both genetic predisposition and environmental factors including the gut microbiota, a dynamic microbial ecosystem inhabiting the gastrointestinal tract. Elucidation of the molecular mechanisms by which the gut microbiota interacts with the host may contribute to the pathogenesis, diagnosis, and promotion of CRC. However, deciphering the influence of genetic variants and interactions with the gut microbial ecosystem is rather challenging. Despite recent advancements in single omics analysis, the application of multi-omics approaches to integrate multiple layers of information in the microbiome and host to introduce effective prevention, diagnosis, and treatment strategies is still in its infancy. Here, we integrate host- and microbe-based multi-omics studies, respectively, to provide a strategy to explore potential causal relationships between gut microbiota and colorectal cancer. Specifically, we summarize the recent multi-omics studies such as metagenomics combined with metabolomics and metagenomics combined with genomics. Meanwhile, the sample size and sample types commonly used in multi-omics research, as well as the methods of data analysis, were also generalized. We highlight multiple layers of information from multi-omics that need to be verified by different types of models. Together, this review provides new insights into the clinical diagnosis and treatment of colorectal cancer patients.},
}

Humans
*Gastrointestinal Microbiome/genetics
Multiomics
*Microbiota
Metabolomics/methods
*Colorectal Neoplasms/genetics

@article {pmid36349836,
year = {2023},
author = {Yuan, ZA and Zhong, LQ and Du, HR and Feng, JN and Liu, XX and Yuan, HY and Guo, JH and Liu, P and Zhang, MH},
title = {Effects of vegetation type differences induced by human disturbance on the nutrition strategy and gut microbiota of Siberian roe deer.},
journal = {Molecular ecology},
volume = {32},
number = {10},
pages = {2534-2550},
doi = {10.1111/mec.16775},
pmid = {36349836},
issn = {1365-294X},
mesh = {Humans ; Animals ; *Deer/physiology ; *Gastrointestinal Microbiome/genetics ; Forests ; Diet/veterinary ; *Microbiota ; },
abstract = {The Siberian roe deer (Capreolus pygargus) is a widely distributed ungulate in northeast China. Due to a series of human disturbance activities such as large-scale forest cutting, deforestation and reclamation, road construction in the past, the appearance and internal structure of forest vegetation in the habitat of Siberian roe have changed significantly. At the same time, Siberian roe population had a series of ecological adaptation responses in the face of such habitat changes. Therefore, two typical vegetation types with differences were selected in the Muling Forest, China. We used nutritional ecology and microbial metagenomic analysis techniques to compare the nutritional selection strategy and the structure and functional characteristics of faecal microbiota of Siberian roe groups in two vegetation types. The results showed that the α diversity of dietary and gut microbes of deer in Natural Forest was higher than that in Plantation Forest. However, the gut microbes of the Plantation Forest group contained more unique enzymes in the functional pathways of carbon metabolism and biosynthesis of amino acids. This study suggests that habitat type is associated with plant community composition, and contributes to changes in the intake proportions of major macronutrients by altering the availability, quality, and composition of certain edible plants. Feeding behaviour may be an important regulatory factor of gut microbiota structure and function of deer. The metabolic function of gut microbiota to different nutrients may affect the microbial community structure. Therefore, our results suggest that the gut microbes of Siberian roe may have coevolved with their diets, and reflect the adaptability of deer populations to environmental changes (e.g., vegetation type). Our study provides new insights into how spatial heterogeneity affects nutrition and microecosystems by describing the interactions among the environment, diet, and symbiotic gut microbes in wild ungulates.},
}

Humans
Animals
*Deer/physiology
*Gastrointestinal Microbiome/genetics
Forests
Diet/veterinary
*Microbiota

@article {pmid35562600,
year = {2023},
author = {Greene, LK and McKenney, EA and Gasper, W and Wrampelmeier, C and Hayer, S and Ehmke, EE and Clayton, JB},
title = {Gut Site and Gut Morphology Predict Microbiome Structure and Function in Ecologically Diverse Lemurs.},
journal = {Microbial ecology},
volume = {85},
number = {4},
pages = {1608-1619},
pmid = {35562600},
issn = {1432-184X},
mesh = {Animals ; *Lemur ; Retrospective Studies ; *Lemuridae ; *Microbiota ; *Strepsirhini ; },
abstract = {Most studies of wildlife gut microbiotas understandably rely on feces to approximate consortia along the gastrointestinal tract. We therefore compared microbiome structure and predicted metagenomic function in stomach, small intestinal, cecal, and colonic samples from 52 lemurs harvested during routine necropsies. The lemurs represent seven genera (Cheirogaleus, Daubentonia, Varecia, Hapalemur, Eulemur, Lemur, Propithecus) characterized by diverse feeding ecologies and gut morphologies. In particular, the hosts variably depend on fibrous foodstuffs and show correlative morphological complexity in their large intestines. Across host lineages, microbiome diversity, variability, membership, and function differed between the upper and lower gut, reflecting regional tradeoffs in available nutrients. These patterns related minimally to total gut length but were modulated by fermentation capacity (i.e., the ratio of small to large intestinal length). Irrespective of feeding strategy, host genera with limited fermentation capacity harbored more homogenized microbiome diversity along the gut, whereas those with expanded fermentation capacity harbored cecal and colonic microbiomes with greater diversity and abundant fermentative Ruminococcaceae taxa. While highlighting the value of curated sample repositories for retrospective comparisons, our results confirm that the need to survive on fibrous foods, either routinely or in hypervariable environments, can shape the morphological and microbial features of the lower gut.},
}

Animals
*Lemur
Retrospective Studies
*Lemuridae
*Microbiota
*Strepsirhini

@article {pmid35503575,
year = {2023},
author = {Dick, JM and Tan, J},
title = {Chemical Links Between Redox Conditions and Estimated Community Proteomes from 16S rRNA and Reference Protein Sequences.},
journal = {Microbial ecology},
volume = {85},
number = {4},
pages = {1338-1355},
pmid = {35503575},
issn = {1432-184X},
mesh = {RNA, Ribosomal, 16S/genetics ; *Proteome ; *Microbiota/genetics ; Metagenome ; Oxidation-Reduction ; Phylogeny ; },
abstract = {Environmental influences on community structure are often assessed through multivariate analyses in order to relate microbial abundances to separately measured physicochemical variables. However, genes and proteins are themselves chemical entities; in combination with genome databases, differences in microbial abundances directly encode for chemical variability. We predicted that the carbon oxidation state of estimated community proteomes, obtained by combining taxonomic abundances from published 16S rRNA gene sequencing datasets with reference microbial proteomes from the NCBI Reference Sequence (RefSeq) database, would reflect environmental oxidation-reduction conditions. Analysis of multiple datasets confirms the geobiochemical predictions for environmental redox gradients in hydrothermal systems, stratified lakes and marine environments, and shale gas wells. The geobiochemical signal is largest for the steep redox gradients associated with hydrothermal systems and between injected water and produced fluids from shale gas wells, demonstrating that microbial community composition can be a chemical proxy for environmental redox gradients. Although estimates of oxidation state from 16S amplicon and metagenomic sequences are correlated, the 16S-based estimates show stronger associations with redox gradients in some environments.},
}

RNA, Ribosomal, 16S/genetics
*Proteome
*Microbiota/genetics
Metagenome
Oxidation-Reduction
Phylogeny

@article {pmid35318755,
year = {2023},
author = {Peimbert, M and Alcaraz, LD},
title = {Where environmental microbiome meets its host: Subway and passenger microbiome relationships.},
journal = {Molecular ecology},
volume = {32},
number = {10},
pages = {2602-2618},
doi = {10.1111/mec.16440},
pmid = {35318755},
issn = {1365-294X},
mesh = {Humans ; *Railroads ; *Microbiota/genetics ; Metagenome ; Cities ; Bacteria/genetics ; },
abstract = {Subways are urban transport systems with high capacity. Every day around the world, there are more than 150 million subway passengers. Since 2013, thousands of microbiome samples from various subways worldwide have been sequenced. Skin bacteria and environmental organisms dominate the subway microbiomes. The literature has revealed common bacterial groups in subway systems; even so, it is possible to identify cities by their microbiome. Low frequency bacteria are responsible for specific bacterial fingerprints of each subway system. Furthermore, daily subway commuters leave their microbial clouds and interact with other passengers. Microbial exchange is quite fast; the hand microbiome changes within minutes, and after cleaning the handrails, the bacteria are re-established within minutes. To investigate new taxa and metabolic pathways of subway microbial communities, several high-quality metagenomic-assembled genomes (MAG) have been described. Subways are harsh environments unfavorable for microorganism growth. However, recent studies have observed a wide diversity of viable and metabolically active bacteria. Understanding which bacteria are living, dormant, or dead allows us to propose realistic ecological interactions. Questions regarding the relationship between humans and the subway microbiome, particularly the microbiome effects on personal and public health, remain unanswered. This review summarizes our knowledge of subway microbiomes and their relationship with passenger microbiomes.},
}

Humans
*Railroads
*Microbiota/genetics
Metagenome
Cities
Bacteria/genetics

@article {pmid37134153,
year = {2023},
author = {Schwartz, DJ and Shalon, N and Wardenburg, K and DeVeaux, A and Wallace, MA and Hall-Moore, C and Ndao, IM and Sullivan, JE and Radmacher, P and Escobedo, M and Burnham, CD and Warner, BB and Tarr, PI and Dantas, G},
title = {Gut pathogen colonization precedes bloodstream infection in the neonatal intensive care unit.},
journal = {Science translational medicine},
volume = {15},
number = {694},
pages = {eadg5562},
doi = {10.1126/scitranslmed.adg5562},
pmid = {37134153},
issn = {1946-6242},
mesh = {Infant ; Infant, Newborn ; Humans ; Infant, Premature ; *Gastrointestinal Microbiome/genetics ; Intensive Care Units, Neonatal ; Vancomycin/pharmacology/therapeutic use ; *Sepsis/microbiology ; *Bacterial Infections ; Bacteria/genetics ; Gentamicins ; Ampicillin ; },
abstract = {Bacterial bloodstream infections (BSIs) resulting in late-onset sepsis affect up to half of extremely preterm infants and have substantial morbidity and mortality. Bacterial species associated with BSIs in neonatal intensive care units (NICUs) commonly colonize the preterm infant gut microbiome. Accordingly, we hypothesized that the gut microbiome is a reservoir of BSI-causing pathogenic strains that increase in abundance before BSI onset. We analyzed 550 previously published fecal metagenomes from 115 hospitalized neonates and found that recent ampicillin, gentamicin, or vancomycin exposure was associated with increased abundance of Enterobacteriaceae and Enterococcaceae in infant guts. We then performed shotgun metagenomic sequencing on 462 longitudinal fecal samples from 19 preterm infants (cases) with BSI and 37 non-BSI controls, along with whole-genome sequencing of the BSI isolates. Infants with BSI caused by Enterobacteriaceae were more likely than infants with BSI caused by other organisms to have had ampicillin, gentamicin, or vancomycin exposure in the 10 days before BSI. Relative to controls, gut microbiomes of cases had increased relative abundance of the BSI-causing species and clustered by Bray-Curtis dissimilarity according to BSI pathogen. We demonstrated that 11 of 19 (58%) of gut microbiomes before BSI, and 15 of 19 (79%) of gut microbiomes at any time, harbored the BSI isolate with fewer than 20 genomic substitutions. Last, BSI strains from the Enterobacteriaceae and Enterococcaceae families were detected in multiple infants, indicating BSI-strain transmission. Our findings support future studies to evaluate BSI risk prediction strategies based on gut microbiome abundance in hospitalized preterm infants.},
}

Infant
Infant, Newborn
Humans
Infant, Premature
*Gastrointestinal Microbiome/genetics
Intensive Care Units, Neonatal
Vancomycin/pharmacology/therapeutic use
*Sepsis/microbiology
*Bacterial Infections
Bacteria/genetics
Gentamicins
Ampicillin

@article {pmid37080086,
year = {2023},
author = {Usié, A and Leão, C and Gaspar, D and Monteiro, H and Tábuas, L and Bettencourt, E and Caetano, P and Padre, L and Carolino, N and Ramos, AM and de Matos, C and Branco, S},
title = {A metagenomics approach to characterize the footrot microbiome in Merino sheep.},
journal = {Veterinary microbiology},
volume = {281},
number = {},
pages = {109745},
doi = {10.1016/j.vetmic.2023.109745},
pmid = {37080086},
issn = {1873-2542},
mesh = {Animals ; Sheep ; *Sheep Diseases/microbiology ; *Foot Rot/microbiology ; Fusobacterium necrophorum ; *Dichelobacter nodosus/genetics ; Bacteria/genetics ; Sheep, Domestic ; *Microbiota/genetics ; *Gram-Negative Bacterial Infections/microbiology/veterinary ; },
abstract = {In the Portuguese Alentejo region, Merino sheep breed is the most common breed, reared for the production of meat, dairy, and wool. Footrot is responsible for lameness, decreased animal welfare, and higher production losses, generating a negative economic impact. The disease is caused by Dichelobacter nodosus that interacts with the sheep foot microbiome, to date largely uncharacterized. In fact, Dichelobacter nodosus is not able to induce footrot by itself being required the presence of a second pathogen known as Fusobacterium necrophorum. To understand and characterize the footrot microbiome dynamics of different footrot lesion scores, a whole metagenome sequencing (WMGS) approach was used. Foot tissue samples were collected from 212 animals with different degrees of footrot lesion scores, ranging from 0 to 5. Distinct bacterial communities were associated with feet with different footrot scores identifying a total of 63 phyla and 504 families. As the severity of footrot infection increases the microorganisms' diversity decreases triggering a shift in the composition of the microbiome from a dominant gram-positive in mild stages to a dominant gram-negative in the severe stages. Several species previously associated with footrot and other polymicrobial diseases affecting the epidermis and provoking inflammatory responses such as Treponema spp., Staphylococcus spp., Streptococcus spp. and Campylobacter spp. were identified proliferating along with the lesions' severity. Although these bacteria are not able to initiate footrot, several evidences have been described supporting their association with the severity and incidence increase of footrot lesions caused by Dichelobacter nodosus and Fusobacterium necrophorum. Further investigation is required to establish the roles of particular taxa and identify which of them play a role in the disease process and which are opportunistic pathogens.},
}

Animals
Sheep
*Sheep Diseases/microbiology
*Foot Rot/microbiology
Fusobacterium necrophorum
*Dichelobacter nodosus/genetics
Bacteria/genetics
Sheep, Domestic
*Microbiota/genetics
*Gram-Negative Bacterial Infections/microbiology/veterinary

@article {pmid37069399,
year = {2023},
author = {Fan, Y and Støving, RK and Berreira Ibraim, S and Hyötyläinen, T and Thirion, F and Arora, T and Lyu, L and Stankevic, E and Hansen, TH and Déchelotte, P and Sinioja, T and Ragnarsdottir, O and Pons, N and Galleron, N and Quinquis, B and Levenez, F and Roume, H and Falony, G and Vieira-Silva, S and Raes, J and Clausen, L and Telléus, GK and Bäckhed, F and Oresic, M and Ehrlich, SD and Pedersen, O},
title = {The gut microbiota contributes to the pathogenesis of anorexia nervosa in humans and mice.},
journal = {Nature microbiology},
volume = {8},
number = {5},
pages = {787-802},
pmid = {37069399},
issn = {2058-5276},
mesh = {Humans ; Female ; Animals ; Mice ; Male ; *Gastrointestinal Microbiome ; *Anorexia Nervosa/microbiology ; Metabolomics ; Feces/microbiology ; Feeding Behavior ; Bacteria/genetics ; },
abstract = {Anorexia nervosa (AN) is an eating disorder with a high mortality. About 95% of cases are women and it has a population prevalence of about 1%, but evidence-based treatment is lacking. The pathogenesis of AN probably involves genetics and various environmental factors, and an altered gut microbiota has been observed in individuals with AN using amplicon sequencing and relatively small cohorts. Here we investigated whether a disrupted gut microbiota contributes to AN pathogenesis. Shotgun metagenomics and metabolomics were performed on faecal and serum samples, respectively, from a cohort of 77 females with AN and 70 healthy females. Multiple bacterial taxa (for example, Clostridium species) were altered in AN and correlated with estimates of eating behaviour and mental health. The gut virome was also altered in AN including a reduction in viral-bacterial interactions. Bacterial functional modules associated with the degradation of neurotransmitters were enriched in AN and various structural variants in bacteria were linked to metabolic features of AN. Serum metabolomics revealed an increase in metabolites associated with reduced food intake (for example, indole-3-propionic acid). Causal inference analyses implied that serum bacterial metabolites are potentially mediating the impact of an altered gut microbiota on AN behaviour. Further, we performed faecal microbiota transplantation from AN cases to germ-free mice under energy-restricted feeding to mirror AN eating behaviour. We found that the reduced weight gain and induced hypothalamic and adipose tissue gene expression were related to aberrant energy metabolism and eating behaviour. Our 'omics' and mechanistic studies imply that a disruptive gut microbiome may contribute to AN pathogenesis.},
}

Humans
Female
Animals
Mice
Male
*Gastrointestinal Microbiome
*Anorexia Nervosa/microbiology
Metabolomics
Feces/microbiology
Feeding Behavior
Bacteria/genetics

@article {pmid37052633,
year = {2023},
author = {Nagar, S and Bharti, M and Negi, RK},
title = {Genome-resolved metagenomics revealed metal-resistance, geochemical cycles in a Himalayan hot spring.},
journal = {Applied microbiology and biotechnology},
volume = {107},
number = {10},
pages = {3273-3289},
pmid = {37052633},
issn = {1432-0614},
mesh = {*Hot Springs/microbiology ; Metagenomics ; Bacteria/genetics/metabolism ; Archaea/genetics/metabolism ; Metagenome ; *Microbiota ; Metals/metabolism ; Sulfur/metabolism ; Nitrogen/metabolism ; Phylogeny ; },
abstract = {The hot spring microbiome is a complex assemblage of micro- and macro-organisms; however, the understanding and projection of enzymatic repertoire that access earth's integral ecosystem processes remains ambivalent. Here, the Khirganga hot spring characterized with white microbial mat and ions rich in sulfate, chlorine, sodium, and magnesium ions is investigated and displayed the examination of 41 high and medium qualified metagenome-assembled genomes (MAGs) belonged to at least 12 bacterial and 2 archaeal phyla which aids to drive sulfur, oxygen, iron, and nitrogen cycles with metabolic mechanisms involved in heavy metal tolerance. These MAGs possess over 1749 genes putatively involved in crucial metabolism of elements viz. nitrogen, phosphorus, and sulfur and 598 genes encoding enzymes for czc efflux system, chromium, arsenic, and copper heavy metals resistance. The MAGs also constitute 229 biosynthetic gene clusters classified abundantly as bacteriocins and terpenes. The metabolic roles possibly involved in altering linkages in nitrogen biogeochemical cycles and explored a discerned rate of carbon fixation exclusively in archaeal member Methanospirillum hungatei inhabited in microbial mat. Higher Pfam entropy scores of biogeochemical cycling in Proteobacteria members assuring their major contribution in assimilation of ammonia and sequestration of nitrate and sulfate components as electron acceptors. This study will readily improve the understanding of the composite relationship between bacterial species owning metal resistance genes (MRGs) and underline the exploration of adaptive mechanism of these MAGs in multi-metal contaminated environment. KEY POINTS: • Identification of 41 novel bacterial and archaeal species in habitats of hot spring • Genome-resolved metagenomics revealed MRGs (n = 598) against Cr, Co, Zn, Cd, As, and Cu • Highest entropies of N (0.48) and Fe (0.44) cycles were detected within the MAGs.},
}

*Hot Springs/microbiology
Metagenomics
Bacteria/genetics/metabolism
Archaea/genetics/metabolism
Metagenome
*Microbiota
Metals/metabolism
Sulfur/metabolism
Nitrogen/metabolism
Phylogeny

@article {pmid37037943,
year = {2023},
author = {Shah, SA and Deng, L and Thorsen, J and Pedersen, AG and Dion, MB and Castro-Mejía, JL and Silins, R and Romme, FO and Sausset, R and Jessen, LE and Ndela, EO and Hjelmsø, M and Rasmussen, MA and Redgwell, TA and Leal Rodríguez, C and Vestergaard, G and Zhang, Y and Chawes, B and Bønnelykke, K and Sørensen, SJ and Bisgaard, H and Enault, F and Stokholm, J and Moineau, S and Petit, MA and Nielsen, DS},
title = {Expanding known viral diversity in the healthy infant gut.},
journal = {Nature microbiology},
volume = {8},
number = {5},
pages = {986-998},
pmid = {37037943},
issn = {2058-5276},
support = {143924//CIHR/Canada ; },
mesh = {Infant ; Humans ; Prospective Studies ; *Bacteriophages/genetics ; Lysogeny ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Bacteria/genetics ; },
abstract = {The gut microbiome is shaped through infancy and impacts the maturation of the immune system, thus protecting against chronic disease later in life. Phages, or viruses that infect bacteria, modulate bacterial growth by lysis and lysogeny, with the latter being especially prominent in the infant gut. Viral metagenomes (viromes) are difficult to analyse because they span uncharted viral diversity, lacking marker genes and standardized detection methods. Here we systematically resolved the viral diversity in faecal viromes from 647 1-year-olds belonging to Copenhagen Prospective Studies on Asthma in Childhood 2010, an unselected Danish cohort of healthy mother-child pairs. By assembly and curation we uncovered 10,000 viral species from 248 virus family-level clades (VFCs). Most (232 VFCs) were previously unknown, belonging to the Caudoviricetes viral class. Hosts were determined for 79% of phage using clustered regularly interspaced short palindromic repeat spacers within bacterial metagenomes from the same children. Typical Bacteroides-infecting crAssphages were outnumbered by undescribed phage families infecting Clostridiales and Bifidobacterium. Phage lifestyles were conserved at the viral family level, with 33 virulent and 118 temperate phage families. Virulent phages were more abundant, while temperate ones were more prevalent and diverse. Together, the viral families found in this study expand existing phage taxonomy and provide a resource aiding future infant gut virome research.},
}

Infant
Humans
Prospective Studies
*Bacteriophages/genetics
Lysogeny
Feces/microbiology
*Gastrointestinal Microbiome/genetics
Bacteria/genetics

@article {pmid37001571,
year = {2023},
author = {Song, C and Ma, Y and Wang, Y and Li, P and Chen, Y and Liu, H and Zhang, Z},
title = {Diosgenin reduces bone loss through the regulation of gut microbiota in ovariectomized rats.},
journal = {Gene},
volume = {869},
number = {},
pages = {147383},
doi = {10.1016/j.gene.2023.147383},
pmid = {37001571},
issn = {1879-0038},
mesh = {Female ; Rats ; Animals ; Humans ; Rats, Sprague-Dawley ; Bone Density ; *Gastrointestinal Microbiome ; *Diosgenin/pharmacology/therapeutic use ; *Bone Diseases, Metabolic ; *Osteoporosis/drug therapy/metabolism ; Estradiol/pharmacology ; Ovariectomy ; },
abstract = {Diosgenin (DIO) is an aglycone of steroid saponins acquired from plants, including Dioscorea alata, Smilax China, and Trigonella foenum graecum, acting as an anti-osteoporosis, anti-diabetic, anti-hyperlipidemic, anti-inflammatory. Recent studies have demonstrated that DIO reduces bone loss. This study aimed to investigate the effects of DIO on the gut microbiota (GM) of ovariectomized (OVX) osteoporotic rats. Female Sprague-Dawley rats were randomly divided into sham operation (sham + vehicle group) or ovariectomy. For 12 weeks, OVX rats were treated using a vehicle (OVX + vehicle group) and DIO (OVX + DIO group). Subsequently, ELISA was conducted to determine serum estradiol levels, micro-CT scanning was performed to evaluate bone quality, and feces were collected for metagenomics sequencing to examine the structure and function of GM. Raw reads were filtered to remove chimera sequences. Operational taxonomic units (OTUs) were clustered in the filtered reads. A Venn diagram analysis was conducted to study the common and unique OTUs in the sham + vehicle, OVX + vehicle, and OVX + DIO groups. LEfSe analysis was conducted to evaluate the specific GM of the three groups. The GM functions were analyzed using the KEGG and CAZy databases. After a 12-week treatment, DIO administration prevented OVX-induced weight gain and increased the estradiol levels. DIO treatment improved the bone microstructure and structural parameters of rat tibias. Metagenomics sequencing results identified 1139, 1207, and 1235 operational taxonomic units (OTUs) in the sham + vehicle, OVX + vehicle, and OVX + DIO groups, respectively. The percentage of common OTUs was 41.2%. Treatment with DIO restored the composition of GM in OVX rats by increasing the abundance of Coriobacteriia Adlercreutzia, Romboutsia, and Romboutsia_idealis and reducing the abundance of Betaproteobacteria, Gammaproteobacteria, Methanobacteria, Bacteroides, Phocaeicola, Alistipes, Bacteroids_uniformis, Bacteroids_xylanisolvens. The anti-osteoporosis effect of DIO can be regulated through environmental information processing, organismal Systems, Cellular Processes, human diseases, metabolism, and genetic information processing. Meanwhile, treatment with DIO improved GM homeostasis by increasing the metabolism of carbohydrates, other amino acids, and glycans and reducing translation, energy metabolism, and nucleotide metabolism. DIO can reduce bone loss by regulating the structural composition and function of GM, a novel strategy for preventing osteoporosis.},
}

Female
Rats
Animals
Humans
Rats, Sprague-Dawley
Bone Density
*Gastrointestinal Microbiome
*Diosgenin/pharmacology/therapeutic use
*Bone Diseases, Metabolic
*Osteoporosis/drug therapy/metabolism
Estradiol/pharmacology
Ovariectomy

@article {pmid36899176,
year = {2023},
author = {von Takach, B and Sargent, H and Penton, CE and Rick, K and Murphy, BP and Neave, G and Davies, HF and Hill, BM and Banks, SC},
title = {Population genomics and conservation management of the threatened black-footed tree-rat (Mesembriomys gouldii) in northern Australia.},
journal = {Heredity},
volume = {130},
number = {5},
pages = {278-288},
pmid = {36899176},
issn = {1365-2540},
mesh = {Animals ; Rats ; Australia ; *Conservation of Natural Resources ; *Metagenomics ; Biodiversity ; Ecosystem ; },
abstract = {Genomic diversity is a fundamental component of Earth's total biodiversity, and requires explicit consideration in efforts to conserve biodiversity. To conserve genomic diversity, it is necessary to measure its spatial distribution, and quantify the contribution that any intraspecific evolutionary lineages make to overall genomic diversity. Here, we describe the range-wide population genomic structure of a threatened Australian rodent, the black-footed tree-rat (Mesembriomys gouldii), aiming to provide insight into the timing and extent of population declines across a large region with a dearth of long-term monitoring data. By estimating recent trajectories in effective population sizes at four localities, we confirm widespread population decline across the species' range, but find that the population in the peri-urban area of the Darwin region has been more stable. Based on current sampling, the Melville Island population made the greatest contribution to overall allelic richness of the species, and the prioritisation analysis suggested that conservation of the Darwin and Cobourg Peninsula populations would be the most cost-effective scenario to retain more than 90% of all alleles. Our results broadly confirm current sub-specific taxonomy, and provide crucial data on the spatial distribution of genomic diversity to help prioritise limited conservation resources. Along with additional sampling and genomic analysis from the far eastern and western edges of the black-footed tree-rat distribution, we suggest a range of conservation and research priorities that could help improve black-footed tree-rat population trajectories at large and fine spatial scales, including the retention and expansion of structurally complex habitat patches.},
}

Animals
Rats
Australia
*Conservation of Natural Resources
*Metagenomics
Biodiversity
Ecosystem

@article {pmid35953094,
year = {2023},
author = {Kong, C and Liang, L and Liu, G and Du, L and Yang, Y and Liu, J and Shi, D and Li, X and Ma, Y},
title = {Integrated metagenomic and metabolomic analysis reveals distinct gut-microbiome-derived phenotypes in early-onset colorectal cancer.},
journal = {Gut},
volume = {72},
number = {6},
pages = {1129-1142},
doi = {10.1136/gutjnl-2022-327156},
pmid = {35953094},
issn = {1468-3288},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Colorectal Neoplasms/diagnosis ; *Microbiota ; Phenotype ; Choline ; },
abstract = {OBJECTIVE: The incidence of early-onset colorectal cancer (EO-CRC) is steadily increasing. Here, we aimed to characterise the interactions between gut microbiome, metabolites and microbial enzymes in EO-CRC patients and evaluate their potential as non-invasive biomarkers for EO-CRC.

DESIGN: We performed metagenomic and metabolomic analyses, identified multiomics markers and constructed CRC classifiers for the discovery cohort with 130 late-onset CRC (LO-CRC), 114 EO-CRC subjects and age-matched healthy controls (97 LO-Control and 100 EO-Control). An independent cohort of 38 LO-CRC, 24 EO-CRC, 22 LO-Controls and 24 EO-Controls was analysed to validate the results.

RESULTS: Compared with controls, reduced alpha-diversity was apparent in both, LO-CRC and EO-CRC subjects. Although common variations existed, integrative analyses identified distinct microbiome-metabolome associations in LO-CRC and EO-CRC. Fusobacterium nucleatum enrichment and short-chain fatty acid depletion, including reduced microbial GABA biosynthesis and a shift in acetate/acetaldehyde metabolism towards acetyl-CoA production characterises LO-CRC. In comparison, multiomics signatures of EO-CRC tended to be associated with enriched Flavonifractor plauti and increased tryptophan, bile acid and choline metabolism. Notably, elevated red meat intake-related species, choline metabolites and KEGG orthology (KO) pldB and cbh gene axis may be potential tumour stimulators in EO-CRC. The predictive model based on metagenomic, metabolomic and KO gene markers achieved a powerful classification performance for distinguishing EO-CRC from controls.

CONCLUSION: Our large-sample multiomics data suggest that altered microbiome-metabolome interplay helps explain the pathogenesis of EO-CRC and LO-CRC. The potential of microbiome-derived biomarkers as promising non-invasive tools could be used for the accurate detection and distinction of individuals with EO-CRC.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Colorectal Neoplasms/diagnosis
*Microbiota
Phenotype
Choline

@article {pmid37132662,
year = {2023},
author = {Bos, RP and Kaul, D and Zettler, ER and Hoffman, JM and Dupont, CL and Amaral-Zettler, LA and Mincer, TJ},
title = {Plastics select for distinct early colonizing microbial populations with reproducible traits across environmental gradients.},
journal = {Environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1462-2920.16391},
pmid = {37132662},
issn = {1462-2920},
abstract = {Little is known about early plastic biofilm assemblage dynamics and successional changes over time. By incubating virgin microplastics along oceanic transects and comparing adhered microbial communities with those of naturally occurring plastic litter at the same locations, we constructed gene catalogues to contrast the metabolic differences between early and mature biofilm communities. Early colonization incubations were reproducibly dominated by Alteromonadaceae and harboured significantly higher proportions of genes associated with adhesion, biofilm formation, chemotaxis, hydrocarbon degradation and motility. Comparative genomic analyses among the Alteromonadaceae metagenome assembled genomes (MAGs) highlighted the importance of the mannose-sensitive hemagglutinin (MSHA) operon, recognized as a key factor for intestinal colonization, for early colonization of hydrophobic plastic surfaces. Synteny alignments of MSHA also demonstrated positive selection for mshA alleles across all MAGs, suggesting that mshA provides a competitive advantage for surface colonization and nutrient acquisition. Large-scale genomic characteristics of early colonizers varied little, despite environmental variability. Mature plastic biofilms were composed of predominantly Rhodobacteraceae and displayed significantly higher proportions of carbohydrate hydrolysis enzymes and genes for photosynthesis and secondary metabolism. Our metagenomic analyses provide insight into early biofilm formation on plastics in the ocean and how early colonizers self-assemble, compared to mature, phylogenetically and metabolically diverse biofilms.},
}

@article {pmid37125210,
year = {2023},
author = {Rzoska-Smith, E and Stelzer, R and Monterio, M and Cary, SC and Williamson, A},
title = {DNA repair enzymes of the Antarctic Dry Valley metagenome.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1156817},
pmid = {37125210},
issn = {1664-302X},
abstract = {Microbiota inhabiting the Dry Valleys of Antarctica are subjected to multiple stressors that can damage deoxyribonucleic acid (DNA) such as desiccation, high ultraviolet light (UV) and multiple freeze-thaw cycles. To identify novel or highly-divergent DNA-processing enzymes that may enable effective DNA repair, we have sequenced metagenomes from 30 sample-sites which are part of the most extensive Antarctic biodiversity survey undertaken to date. We then used these to construct wide-ranging sequence similarity networks from protein-coding sequences and identified candidate genes involved in specialized repair processes including unique nucleases as well as a diverse range of adenosine triphosphate (ATP) -dependent DNA ligases implicated in stationary-phase DNA repair processes. In one of the first direct investigations of enzyme function from these unique samples, we have heterologously expressed and assayed a number of these enzymes, providing insight into the mechanisms that may enable resident microbes to survive these threats to their genomic integrity.},
}

@article {pmid36735064,
year = {2023},
author = {Tessler, M and Cunningham, SW and Ingala, MR and Warring, SD and Brugler, MR},
title = {An Environmental DNA Primer for Microbial and Restoration Ecology.},
journal = {Microbial ecology},
volume = {85},
number = {3},
pages = {796-808},
pmid = {36735064},
issn = {1432-184X},
mesh = {*DNA, Environmental/genetics ; DNA Primers ; DNA Barcoding, Taxonomic/methods ; Ecology ; DNA/genetics ; Environmental Monitoring ; Biodiversity ; },
abstract = {Environmental DNA (eDNA) sequencing-DNA collected from the environment from living cells or shed DNA-was first developed for working with microbes and has greatly benefitted microbial ecologists for decades since. These tools have only become increasingly powerful with the advent of metabarcoding and metagenomics. Most new studies that examine diverse assemblages of bacteria, archaea, protists, fungi, and viruses lean heavily into eDNA using these newer technologies, as the necessary sequencing technology and bioinformatic tools have become increasingly affordable and user friendly. However, eDNA methods are rapidly evolving, and sometimes it can feel overwhelming to simply keep up with the basics. In this review, we provide a starting point for microbial ecologists who are new to DNA-based methods by detailing the eDNA methods that are most pertinent, including study design, sample collection and storage, selecting the right sequencing technology, lab protocols, equipment, and a few bioinformatic tools. Furthermore, we focus on how eDNA work can benefit restoration and what modifications are needed when working in this subfield.},
}

*DNA, Environmental/genetics
DNA Primers
DNA Barcoding, Taxonomic/methods
Ecology
DNA/genetics
Environmental Monitoring
Biodiversity

@article {pmid36695828,
year = {2023},
author = {Hilderbrand, RH and Bambakidis, T and Crump, BC},
title = {The Roles of Microbes in Stream Restorations.},
journal = {Microbial ecology},
volume = {85},
number = {3},
pages = {853-861},
pmid = {36695828},
issn = {1432-184X},
mesh = {Animals ; *Ecosystem ; Rivers ; Fishes ; Biomass ; *Microbiota ; Biofilms ; },
abstract = {The goods and services provided by riverine systems are critical to humanity, and our reliance increases with our growing population and demands. As our activities expand, these systems continue to degrade throughout the world even as we try to restore them, and many efforts have not met expectations. One way to increase restoration effectiveness could be to explicitly design restorations to promote microbial communities, which are responsible for much of the organic matter breakdown, nutrient removal or transformation, pollutant removal, and biomass production in river ecosystems. In this paper, we discuss several design concepts that purposefully create conditions for these various microbial goods and services, and allow microbes to act as ecological restoration engineers. Focusing on microbial diversity and function could improve restoration effectiveness and overall ecosystem resilience to the stressors that caused the need for the restoration. Advances in next-generation sequencing now allow the use of microbial 'omics techniques (e.g., metagenomics, metatranscriptomics) to assess stream ecological conditions in similar fashion to fish and benthic macroinvertebrates. Using representative microbial communities from stream sediments, biofilms, and the water column may greatly advance assessment capabilities. Microbes can assess restorations and ecosystem function where animals may not currently be present, and thus may serve as diagnostics for the suitability of animal reintroductions. Emerging applications such as ecological metatranscriptomics may further advance our understanding of the roles of specific restoration designs towards ecological services as well as assess restoration effectiveness.},
}

Animals
*Ecosystem
Rivers
Fishes
Biomass
*Microbiota
Biofilms

@article {pmid36346444,
year = {2023},
author = {Palmer, B and Lawson, D and Lipson, DA},
title = {Years After a Fire, Biocrust Microbial Communities are Similar to Unburned Communities in a Coastal Grassland.},
journal = {Microbial ecology},
volume = {85},
number = {3},
pages = {1028-1044},
pmid = {36346444},
issn = {1432-184X},
mesh = {Ecosystem ; Grassland ; *Microbiota ; *Fires ; Bacteria/genetics ; Chlorophyll ; Soil ; },
abstract = {Microbial communities are integral for ecosystem processes and their taxonomic composition and function may be altered by a disturbance such as fire. Biocrusts are composed of macroscopic and microscopic organisms and are important for a variety of ecosystem functions, such as nutrient cycling and erosion control. We sought to understand if biocrust community composition and function were altered 1 year after a prescribed fire and 6 years after a wildfire in a coastal California grassland on San Clemente Island. We used shotgun metagenomic sequencing and measurements of chlorophyll content, exopolysaccharide production related to soil stability, and nitrogen fixation. There were no differences in the community composition between unburned samples and the samples burned in the prescribed fire and wildfire. Chlorophyll content differed between the prescribed fire and the controls; however, there were no measured differences in exopolysaccharide production, and nitrogen fixation. However, the wildfire and their respective unburned samples had different functions based on the gene annotations. We compiled one Actinobacteria metagenome-assembled genome from the shotgun sequences which had genes for oxidative and heat stress tolerance. These results suggest that the biocrust community can reach a community composition and function similar to the unburned biocrusts within a year after a prescribed burn and 6 years after a wildfire. However, legacy effects of the wildfire may present themselves in the differences between functional gene sequences. Due to their ability to match the undisturbed community composition and function within years and without intervention, future restoration work should consider the biocrusts in their restoration plans as they may provide valuable ecosystem functions after a disturbance.},
}

Ecosystem
Grassland
*Microbiota
*Fires
Bacteria/genetics
Chlorophyll
Soil

@article {pmid36322790,
year = {2023},
author = {Battat, R and Scherl, EJ and Lukin, D and Charilaou, P and Mahtani, P and Gerber, J and Gandara, JA and , and Dündar, F and Zumbo, P and Betel, D and Guo, CJ and Longman, RS},
title = {Increased Primary Bile Acids with Ileocolonic Resection Impact Ileal Inflammation and Gut Microbiota in Inflammatory Bowel Disease.},
journal = {Journal of Crohn's & colitis},
volume = {17},
number = {5},
pages = {795-803},
pmid = {36322790},
issn = {1876-4479},
support = {UL1 TR002384/TR/NCATS NIH HHS/United States ; UL1TR002384/TR/NCATS NIH HHS/United States ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Inflammatory Bowel Diseases/surgery/microbiology ; Inflammation ; *Ileitis/surgery/microbiology ; Colectomy ; Bile Acids and Salts ; },
abstract = {BACKGROUND: Most Crohn's disease [CD] patients require surgery. Ileitis recurs after most ileocolectomies and is a critical determinant for outcomes. The impacts of ileocolectomy-induced bile acid [BA] perturbations on intestinal microbiota and inflammation are unknown. We characterized the relationships between ileocolectomy, stool BAs, microbiota and intestinal inflammation in inflammatory bowel disease [IBD].

METHODS: Validated IBD clinical and endoscopic assessments were prospectively collected. Stool primary and secondary BA concentrations were compared based on ileocolectomy and ileitis status. Primary BA thresholds for ileitis were evaluated. Metagenomic sequencing was use to profile microbial composition and function. Relationships between ileocolectomy, BAs and microbiota were assessed.

RESULTS: In 166 patients, elevated primary and secondary BAs existed with ileocolectomy. With ileitis, only primary BAs [795 vs 398 nmol/g, p = 0.009] were higher compared to without ileitis. The optimal primary BA threshold [≥228 nmol/g] identified ileitis on multivariable analysis [odds ratio = 2.3, p = 0.04]. Microbial diversity, Faecalibacterium prausnitzii and O-acetylhomoserine aminocarboxypropyltransferase [MetY] were decreased with elevated primary BAs. Amongst ileocolectomy patients, only those with elevated primary BAs had diversity, F. prausnitzii and MetY reductions. Those with both ileocolectomy and intermediate [p = 0.002] or high [≥228 nmol/g, p = 9.1e-11]] primary BA concentrations had reduced F. prausnitzii compared to without ileocolectomy. Those with ileocolectomy and low [<29.2 nmol/g] primary BA concentrations had similar F. prausnitzii to those without ileocolectomy [p = 0.13]. MetY was reduced with ileitis [p = 0.02].

CONCLUSIONS: Elevated primary BAs were associated with ileitis, and reduced microbial diversity, F. prausnitzii abundance and enzymatic abundance of MetY [acetate and l-methionine-producing enzyme expressed by F. prausnitzii], and were the only factors associated with these findings after ileocolectomy.},
}

Humans
*Gastrointestinal Microbiome
*Inflammatory Bowel Diseases/surgery/microbiology
Inflammation
*Ileitis/surgery/microbiology
Colectomy
Bile Acids and Salts

@article {pmid37022232,
year = {2023},
author = {Zimmerman, S and Tierney, BT and Patel, CJ and Kostic, AD},
title = {Quantifying Shared and Unique Gene Content across 17 Microbial Ecosystems.},
journal = {mSystems},
volume = {8},
number = {2},
pages = {e0011823},
pmid = {37022232},
issn = {2379-5077},
mesh = {Humans ; *Microbiota/genetics ; Metagenome/genetics ; *Gastrointestinal Microbiome/genetics ; Metagenomics/methods ; Genome, Bacterial ; },
abstract = {Measuring microbial diversity is traditionally based on microbe taxonomy. Here, in contrast, we aimed to quantify heterogeneity in microbial gene content across 14,183 metagenomic samples spanning 17 ecologies, including 6 human associated, 7 nonhuman host associated, and 4 in other nonhuman host environments. In total, we identified 117,629,181 nonredundant genes. The vast majority of genes (66%) occurred in only one sample (i.e., "singletons"). In contrast, we found 1,864 sequences present in every metagenome, but not necessarily every bacterial genome. Additionally, we report data sets of other ecology-associated genes (e.g., abundant in only gut ecosystems) and simultaneously demonstrated that prior microbiome gene catalogs are both incomplete and inaccurately cluster microbial genetic life (e.g., at gene sequence identities that are too restrictive). We provide our results and the sets of environmentally differentiating genes described above at http://www.microbial-genes.bio. IMPORTANCE The amount of shared genetic elements has not been quantified between the human microbiome and other host- and non-host-associated microbiomes. Here, we made a gene catalog of 17 different microbial ecosystems and compared them. We show that most species shared between environment and human gut microbiomes are pathogens and that prior gene catalogs described as "nearly complete" are far from it. Additionally, over two-thirds of all genes only appear in a single sample, and only 1,864 genes (0.001%) are found in all types of metagenomes. These results highlight the large diversity between metagenomes and reveal a new, rare class of genes, those found in every type of metagenome, but not every microbial genome.},
}

Humans
*Microbiota/genetics
Metagenome/genetics
*Gastrointestinal Microbiome/genetics
Metagenomics/methods
Genome, Bacterial

@article {pmid37010293,
year = {2023},
author = {Maranga, M and Szczerbiak, P and Bezshapkin, V and Gligorijevic, V and Chandler, C and Bonneau, R and Xavier, RJ and Vatanen, T and Kosciolek, T},
title = {Comprehensive Functional Annotation of Metagenomes and Microbial Genomes Using a Deep Learning-Based Method.},
journal = {mSystems},
volume = {8},
number = {2},
pages = {e0117822},
pmid = {37010293},
issn = {2379-5077},
mesh = {Humans ; Metagenome/genetics ; *Deep Learning ; Molecular Sequence Annotation ; *Microbiota/genetics ; Genome, Microbial ; },
abstract = {Comprehensive protein function annotation is essential for understanding microbiome-related disease mechanisms in the host organisms. However, a large portion of human gut microbial proteins lack functional annotation. Here, we have developed a new metagenome analysis workflow integrating de novo genome reconstruction, taxonomic profiling, and deep learning-based functional annotations from DeepFRI. This is the first approach to apply deep learning-based functional annotations in metagenomics. We validate DeepFRI functional annotations by comparing them to orthology-based annotations from eggNOG on a set of 1,070 infant metagenomes from the DIABIMMUNE cohort. Using this workflow, we generated a sequence catalogue of 1.9 million nonredundant microbial genes. The functional annotations revealed 70% concordance between Gene Ontology annotations predicted by DeepFRI and eggNOG. DeepFRI improved the annotation coverage, with 99% of the gene catalogue obtaining Gene Ontology molecular function annotations, although they are less specific than those from eggNOG. Additionally, we constructed pangenomes in a reference-free manner using high-quality metagenome-assembled genomes (MAGs) and analyzed the associated annotations. eggNOG annotated more genes on well-studied organisms, such as Escherichia coli, while DeepFRI was less sensitive to taxa. Further, we show that DeepFRI provides additional annotations in comparison to the previous DIABIMMUNE studies. This workflow will contribute to novel understanding of the functional signature of the human gut microbiome in health and disease as well as guiding future metagenomics studies. IMPORTANCE The past decade has seen advancement in high-throughput sequencing technologies resulting in rapid accumulation of genomic data from microbial communities. While this growth in sequence data and gene discovery is impressive, the majority of microbial gene functions remain uncharacterized. The coverage of functional information coming from either experimental sources or inferences is low. To solve these challenges, we have developed a new workflow to computationally assemble microbial genomes and annotate the genes using a deep learning-based model DeepFRI. This improved microbial gene annotation coverage to 1.9 million metagenome-assembled genes, representing 99% of the assembled genes, which is a significant improvement compared to 12% Gene Ontology term annotation coverage by commonly used orthology-based approaches. Importantly, the workflow supports pangenome reconstruction in a reference-free manner, allowing us to analyze the functional potential of individual bacterial species. We therefore propose this alternative approach combining deep-learning functional predictions with the commonly used orthology-based annotations as one that could help us uncover novel functions observed in metagenomic microbiome studies.},
}

Humans
Metagenome/genetics
*Deep Learning
Molecular Sequence Annotation
*Microbiota/genetics
Genome, Microbial

@article {pmid36975801,
year = {2023},
author = {Carter, KA and Fodor, AA and Balkus, JE and Zhang, A and Serrano, MG and Buck, GA and Engel, SM and Wu, MC and Sun, S},
title = {Vaginal Microbiome Metagenome Inference Accuracy: Differential Measurement Error according to Community Composition.},
journal = {mSystems},
volume = {8},
number = {2},
pages = {e0100322},
pmid = {36975801},
issn = {2379-5077},
support = {T32 AI007140/AI/NIAID NIH HHS/United States ; P30 ES010126/ES/NIEHS NIH HHS/United States ; },
mesh = {Infant, Newborn ; Pregnancy ; Female ; Humans ; Metagenome/genetics ; RNA, Ribosomal, 16S/genetics ; *Premature Birth/genetics ; *Microbiota/genetics ; Vagina/microbiology ; },
abstract = {Several studies have compared metagenome inference performance in different human body sites; however, none specifically reported on the vaginal microbiome. Findings from other body sites cannot easily be generalized to the vaginal microbiome due to unique features of vaginal microbial ecology, and investigators seeking to use metagenome inference in vaginal microbiome research are "flying blind" with respect to potential bias these methods may introduce into analyses. We compared the performance of PICRUSt2 and Tax4Fun2 using paired 16S rRNA gene amplicon sequencing and whole-metagenome sequencing data from vaginal samples from 72 pregnant individuals enrolled in the Pregnancy, Infection, and Nutrition (PIN) cohort. Participants were selected from those with known birth outcomes and adequate 16S rRNA gene amplicon sequencing data in a case-control design. Cases experienced early preterm birth (<32 weeks of gestation), and controls experienced term birth (37 to 41 weeks of gestation). PICRUSt2 and Tax4Fun2 performed modestly overall (median Spearman correlation coefficients between observed and predicted KEGG ortholog [KO] relative abundances of 0.20 and 0.22, respectively). Both methods performed best among Lactobacillus crispatus-dominated vaginal microbiotas (median Spearman correlation coefficients of 0.24 and 0.25, respectively) and worst among Lactobacillus iners-dominated microbiotas (median Spearman correlation coefficients of 0.06 and 0.11, respectively). The same pattern was observed when evaluating correlations between univariable hypothesis test P values generated with observed and predicted metagenome data. Differential metagenome inference performance across vaginal microbiota community types can be considered differential measurement error, which often causes differential misclassification. As such, metagenome inference will introduce hard-to-predict bias (toward or away from the null) in vaginal microbiome research. IMPORTANCE Compared to taxonomic composition, the functional potential within a bacterial community is more relevant to establishing mechanistic understandings and causal relationships between the microbiome and health outcomes. Metagenome inference attempts to bridge the gap between 16S rRNA gene amplicon sequencing and whole-metagenome sequencing by predicting a microbiome's gene content based on its taxonomic composition and annotated genome sequences of its members. Metagenome inference methods have been evaluated primarily among gut samples, where they appear to perform fairly well. Here, we show that metagenome inference performance is markedly worse for the vaginal microbiome and that performance varies across common vaginal microbiome community types. Because these community types are associated with sexual and reproductive outcomes, differential metagenome inference performance will bias vaginal microbiome studies, obscuring relationships of interest. Results from such studies should be interpreted with substantial caution and the understanding that they may over- or underestimate associations with metagenome content.},
}

Infant, Newborn
Pregnancy
Female
Humans
Metagenome/genetics
RNA, Ribosomal, 16S/genetics
*Premature Birth/genetics
*Microbiota/genetics
Vagina/microbiology

@article {pmid36971593,
year = {2023},
author = {Liu, F and Lu, H and Dong, B and Huang, X and Cheng, H and Qu, R and Hu, Y and Zhong, L and Guo, Z and You, Y and Xu, ZZ},
title = {Systematic Evaluation of the Viable Microbiome in the Human Oral and Gut Samples with Spike-in Gram+/- Bacteria.},
journal = {mSystems},
volume = {8},
number = {2},
pages = {e0073822},
pmid = {36971593},
issn = {2379-5077},
mesh = {Humans ; *Microbiota/genetics ; DNA ; Feces/microbiology ; DNA, Bacterial/genetics ; Bacteria/genetics ; Firmicutes/genetics ; },
abstract = {PMA (propidium monoazide) is one of the few methods that are compatible with metagenomic sequencing to characterize the live/intact microbiota. However, its efficiency in complex communities such as saliva and feces is still controversial. An effective method for depleting host and dead bacterial DNA in human microbiome samples is lacking. Here, we systematically evaluate the efficiency of osmotic lysis and PMAxx treatment (lyPMAxx) in characterizing the viable microbiome with four live/dead Gram+/Gram- microbial strains in simple synthetic and spiked-in complex communities. We show that lyPMAxx-quantitative PCR (qPCR)/sequencing eliminated more than 95% of the host and heat-killed microbial DNA and had a much smaller effect on the live microbes in both simple mock and spiked-in complex communities. The overall microbial load and the alpha diversity of the salivary and fecal microbiome were decreased by lyPMAxx, and the relative abundances of the microbes were changed. The relative abundances of Actinobacteria, Fusobacteria, and Firmicutes in saliva were decreased by lyPMAxx, as was that of Firmicutes in feces. We also found that the frequently used sample storage method, freezing with glycerol, killed or injured 65% and 94% of the living microbial cells in saliva and feces, respectively, with the Proteobacteria phylum affected most in saliva and the Bacteroidetes and Firmicutes phyla affected most in feces. By comparing the absolute abundance variation of the shared species among different sample types and individuals, we found that sample habitat and personal differences affected the response of microbial species to lyPMAxx and freezing. IMPORTANCE The functions and phenotypes of microbial communities are largely defined by viable microbes. Through advanced nucleic acid sequencing technologies and downstream bioinformatic analyses, we gained an insight into the high-resolution microbial community composition of human saliva and feces, yet we know very little about whether such community DNA sequences represent viable microbes. PMA-qPCR was used to characterize the viable microbes in previous studies. However, its efficiency in complex communities such as saliva and feces is still controversial. By spiking-in four live/dead Gram+/Gram- bacterial strains, we demonstrate that lyPMAxx can effectively discriminate between live and dead microbes in the simple synthetic community and complex human microbial communities (saliva and feces). In addition, freezing storage was found to kill or injure the microbes in saliva and feces significantly, as measured with lyPMAxx-qPCR/sequencing. This method has a promising prospect in the viable/intact microbiota detection of complex human microbial communities.},
}

Humans
*Microbiota/genetics
DNA
Feces/microbiology
DNA, Bacterial/genetics
Bacteria/genetics
Firmicutes/genetics

@article {pmid36853013,
year = {2023},
author = {Ren, Y and Hao, L and Liu, J and Wang, P and Ding, Q and Chen, C and Song, Y},
title = {Alterations in the Gut Microbiota in Pregnant Women with Pregestational Type 2 Diabetes Mellitus.},
journal = {mSystems},
volume = {8},
number = {2},
pages = {e0114622},
pmid = {36853013},
issn = {2379-5077},
mesh = {Infant, Newborn ; Humans ; Female ; Pregnancy ; *Gastrointestinal Microbiome/genetics ; *Diabetes Mellitus, Type 2/microbiology ; Pregnant Women ; Dysbiosis/microbiology ; RNA, Ribosomal, 16S/genetics ; Pregnancy Outcome ; *Hyperglycemia ; },
abstract = {Human gut dysbiosis is associated with type 2 diabetes mellitus (T2DM); however, the gut microbiome in pregnant women with pregestational type 2 diabetes mellitus (PGDM) remains unexplored. We investigated the alterations in the gut microbiota composition in pregnant women with or without PGDM. The gut microbiota was examined using 16S rRNA sequencing data of 234 maternal fecal samples that were collected during the first (T1), second (T2), and third (T3) trimesters. The PGDM group presented a reduction in the number of gut bacteria taxonomies as the pregnancies progressed. Linear discriminant analyses revealed that Megamonas, Bacteroides, and Roseburia intestinalis were enriched in the PGDM group, whereas Bacteroides vulgatus, Faecalibacterium prausnitzii, Eubacterium rectale, Bacteroides uniformis, Eubacterium eligens, Subdoligranulum, Bacteroides fragilis, Dialister, Lachnospiraceae, Christensenellaceae R-7, Roseburia inulinivorans, Streptococcus oralis, Prevotella melaninogenica, Neisseria perflava, Bacteroides ovatus, Bacteroides caccae, Veillonella dispar, and Haemophilus parainfluenzae were overrepresented in the control group. Correlation analyses showed that the PGDM-enriched taxa were correlated with higher blood glucose levels during pregnancy, whereas the taxonomic biomarkers of normoglycemic pregnancies exhibited negative correlations with glycemic traits. The microbial networks in the PGDM group comprised weaker microbial interactions than those in the control group. Our study reveals the distinct characteristics of the gut microbiota composition based on gestational ages between normoglycemic and PGDM pregnancies. Further longitudinal research involving women with T2DM at preconception stages and investigations using shotgun metagenomic sequencing should be performed to elucidate the relationships between specific bacterial functions and PGDM metabolic statuses during pregnancy and to identify potential therapeutic targets. IMPORTANCE The incidence of pregestational type 2 diabetes mellitus (PGDM) is increasing, with high rates of serious adverse maternal and neonatal outcomes that are strongly correlated with hyperglycemia. Recent studies have shown that type 2 diabetes mellitus is associated with gut microbial dysbiosis; however, the gut microbiome composition and its associations with the metabolic features of patients with PGDM remain largely unknown. In this study, we investigated the changes in the gut microbiota composition in pregnant women with and without PGDM. We identified differential taxa that may be correlated with maternal metabolic statuses during pregnancy. Additionally, we observed that the number of taxonomic and microbial networks of gut bacteria were distinctly reduced in women with hyperglycemia as their pregnancies progressed. These results extend our understanding of the associations between the gut microbial composition, PGDM-related metabolic changes, and pregnancy outcomes.},
}

Infant, Newborn
Humans
Female
Pregnancy
*Gastrointestinal Microbiome/genetics
*Diabetes Mellitus, Type 2/microbiology
Pregnant Women
Dysbiosis/microbiology
RNA, Ribosomal, 16S/genetics
Pregnancy Outcome
*Hyperglycemia

@article {pmid36809182,
year = {2023},
author = {Olekhnovich, EI and Ivanov, AB and Babkina, AA and Sokolov, AA and Ulyantsev, VI and Fedorov, DE and Ilina, EN},
title = {Consistent Stool Metagenomic Biomarkers Associated with the Response To Melanoma Immunotherapy.},
journal = {mSystems},
volume = {8},
number = {2},
pages = {e0102322},
pmid = {36809182},
issn = {2379-5077},
mesh = {Humans ; Metagenome ; *Melanoma/genetics ; *Microbiota/genetics ; Bacteria/genetics ; Biomarkers ; Immunotherapy/methods ; },
abstract = {The human gut microbiome plays an important role in both health and disease. Recent studies have demonstrated a strong influence of the gut microbiome composition on the efficacy of cancer immunotherapy. However, available studies have not yet succeeded in finding reliable and consistent metagenomic markers that are associated with the response to immunotherapy. Therefore, the reanalysis of the published data may improve our understanding of the association between the composition of the gut microbiome and the treatment response. In this study, we focused on melanoma-related metagenomic data, which are more abundant than are data from other tumor types. We analyzed the metagenomes of 680 stool samples from 7 studies that were published earlier. The taxonomic and functional biomarkers were selected after comparing the metagenomes of patients showing different treatment responses. The list of selected biomarkers was also validated on additional metagenomic data sets that were dedicated to the influence of fecal microbiota transplantation on the response to melanoma immunotherapy. According to our analysis, the resulting cross-study taxonomic biomarkers included three bacterial species: Faecalibacterium prausnitzii, Bifidobacterium adolescentis, and Eubacterium rectale. 101 groups of genes were identified to be functional biomarkers, including those potentially involved in the production of immune-stimulating molecules and metabolites. Moreover, we ranked the microbial species by the number of genes encoding functionally relevant biomarkers that they contained. Thus, we put together a list of potentially the most beneficial bacteria for immunotherapy success. F. prausnitzii, E. rectale, and three species of bifidobacteria stood out as the most beneficial species, even though some useful functions were also present in other bacterial species. IMPORTANCE In this study, we put together a list of potentially the most beneficial bacteria that were associated with a responsiveness to melanoma immunotherapy. Another important result of this study is the list of functional biomarkers of responsiveness to immunotherapy, which are dispersed among different bacterial species. This result possibly explains the existing irregularities between studies regarding the bacterial species that are beneficial to melanoma immunotherapy. Overall, these findings can be utilized to issue recommendations for gut microbiome correction in cancer immunotherapy, and the resulting list of biomarkers might serve as a good stepping stone for the development of a diagnostic test that is aimed at predicting patients' responses to melanoma immunotherapy.},
}

Humans
Metagenome
*Melanoma/genetics
*Microbiota/genetics
Bacteria/genetics
Biomarkers
Immunotherapy/methods

@article {pmid36786595,
year = {2023},
author = {Szóstak, N and Handschuh, L and Samelak-Czajka, A and Tomela, K and Schmidt, M and Pruss, Ł and Milanowska-Zabel, K and Kozlowski, P and Philips, A},
title = {Host Factors Associated with Gut Mycobiome Structure.},
journal = {mSystems},
volume = {8},
number = {2},
pages = {e0098622},
pmid = {36786595},
issn = {2379-5077},
mesh = {Humans ; *Mycobiome ; Cohort Studies ; Fungi/genetics ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; Candida ; *Saccharomyces ; Saccharomyces cerevisiae ; },
abstract = {Recent studies revealed a significant role of the gut fungal community in human health. Here, we investigated the content and variation of gut mycobiota among subjects from the European population. We explored the interplay between gut fungi and various host-related sociodemographic, lifestyle, health, and dietary factors. The study included 923 participants. Fecal DNA samples were analyzed by whole-metagenome high-throughput sequencing. Subsequently, fungi taxonomic profiles were determined and accompanied by computational and statistical analyses of the association with 53 host-related factors. Fungal communities were characterized by a high prevalence of Saccharomyces, Candida, and Sporisorium. Ten factors were found to correlate significantly with the overall mycobiota variation. Most were diet related, including the consumption of chips, meat, sodas, sweetening, processed food, and alcohol, followed by age and marital status. Differences in α- and/or β-diversity were also reported for other factors such as body mass index (BMI), job type, autoimmunological diseases, and probiotics. Differential abundance analysis revealed fungal species that exhibited different patterns of changes under specific conditions. The human gut mycobiota is dominated by yeast, including Saccharomyces, Malassezia, and Candida. Although intervolunteer variability was high, several fungal species persisted across most samples, which may be evidence that a core gut mycobiota exists. Moreover, we showed that host-related factors such as diet, age, and marital status influence the variability of gut mycobiota. To our knowledge, this is the first large and comprehensive study of the European cohort in terms of gut mycobiota associations with such an extensive and differentiated host-related set of factors. IMPORTANCE The human gut is inhabited by many organisms, including bacteria and fungi, that may affect human health. However, research on human gut mycobiome is still rare. Moreover, the large European-based cohort study is missing. Here, we analyzed the first large European cohort in terms of gut mycobiota associations with a differentiated host-related set of factors. Our results showed that chips, meat, sodas, sweetening, processed food, beer, alcohol consumption, age, and marital status were associated with the variability of gut mycobiota. Moreover, our analysis revealed changes in abundances at the fungal species level for many investigated factors. Our results can suggest potentially valuable paths for further, narrowly focused research on gut mycobiome and its impact on human health. In the coming era of gut microbiome-based precision medicine, further research into the relationship between different mycobial structures and host-related factors may result in new preventive approaches or therapeutic procedures.},
}

Humans
*Mycobiome
Cohort Studies
Fungi/genetics
*Gastrointestinal Microbiome/genetics
Feces/microbiology
Candida
*Saccharomyces
Saccharomyces cerevisiae

@article {pmid36786580,
year = {2023},
author = {Gittins, DA and Bhatnagar, S and Hubert, CRJ},
title = {Environmental Selection and Biogeography Shape the Microbiome of Subsurface Petroleum Reservoirs.},
journal = {mSystems},
volume = {8},
number = {2},
pages = {e0088422},
pmid = {36786580},
issn = {2379-5077},
mesh = {*Petroleum/metabolism ; RNA, Ribosomal, 16S/genetics ; Oil and Gas Fields ; *Microbiota/genetics ; Carbon ; },
abstract = {Petroleum reservoirs within the deep biosphere are extreme environments inhabited by diverse microbial communities and represent biogeochemical hot spots in the subsurface. Despite the ecological and industrial importance of oil reservoir microbiomes, systematic study of core microbial taxa and their associated genomic attributes spanning different environmental conditions is limited. Here, we compile and compare 343 16S rRNA gene amplicon libraries and 25 shotgun metagenomic libraries from oil reservoirs in different parts of the world to test for the presence of core taxa and functions. These oil reservoir libraries do not share any core taxa at the species, genus, family, or order levels, and Gammaproteobacteria was the only taxonomic class detected in all samples. Instead, taxonomic composition varies among reservoirs with different physicochemical characteristics and with geographic distance highlighting environmental selection and biogeography in these deep biosphere habitats. Gene-centric metagenomic analysis reveals a functional core of metabolic pathways including carbon acquisition and energy-yielding strategies consistent with biogeochemical cycling in other subsurface environments. Genes for anaerobic hydrocarbon degradation are observed in a subset of the samples and are therefore not considered to represent core functions in oil reservoirs despite hydrocarbons representing an abundant source of carbon in these deep biosphere settings. Overall, this work reveals common and divergent features of oil reservoir microbiomes that are shaped by and responsive to environmental factors, highlighting controls on subsurface microbial community assembly. IMPORTANCE This comprehensive analysis showcases how environmental selection and geographic distance influence the microbiome of subsurface petroleum reservoirs. We reveal substantial differences in the taxonomy of the inhabiting microbes but shared metabolic function between reservoirs with different in situ temperatures and between reservoirs separated by large distances. The study helps understand and advance the field of deep biosphere science by providing an ecological framework and footing for geologists, chemists, and microbiologists studying these habitats to elucidate major controls on deep biosphere microbial ecology.},
}

*Petroleum/metabolism
RNA, Ribosomal, 16S/genetics
Oil and Gas Fields
*Microbiota/genetics
Carbon

@article {pmid36749039,
year = {2023},
author = {Zang, X and Wang, W and Gu, S and Gu, T and Yang, H and Zheng, E and Xu, Z and Huang, S and Li, Z and Cai, G and Hong, L and Wu, Z},
title = {Interaction between Microbes and Host in Sow Vaginas in Early Pregnancy.},
journal = {mSystems},
volume = {8},
number = {2},
pages = {e0119222},
pmid = {36749039},
issn = {2379-5077},
mesh = {Pregnancy ; Animals ; Female ; Swine ; RNA, Ribosomal, 16S/genetics ; *Vagina/chemistry ; Uterus/chemistry ; *Microbiota/genetics ; Metagenome ; },
abstract = {Extensive research has explored the causes of embryo losses during early pregnancy by analyzing interaction mechanisms in sows' uterus, ignoring the importance of the lower reproductive tract in pregnancy development regulation. Despite recent progress in understanding the diversity of vaginal microbes under different physiological states, the dynamic of sows' vaginal microbiotas during pregnancy and the interaction between vaginal microbes and the host are poorly understood. Here, we performed a comprehensive analysis of sows' vaginal microbial communities in early pregnancy coupled with overall patterns of vaginal mucosal epithelium gene expression. The vaginal microbiota was analyzed by 16s rRNA or metagenome sequencing, and the vaginal mucosal epithelium transcriptome was analyzed by RNA sequencing, followed by integration of the data layers. We found that the sows' vaginal microbiotas in early pregnancy develop dynamically, and there is a homeostasis balance of Firmicutes and Proteobacteria. Subsequently, we identified two pregnancy-specific communities, which play diverse roles. The microbes in the vagina stimulate the epithelial cells, while vaginal epithelium changes its structure and functions in response to stimulation. These changes produce specific inflammation responses to promote pregnancy development. Our findings demonstrate the interaction between microbes and host in the sow vagina in early pregnancy to promote pregnancy development, meanwhile providing a reference data set for the study of targeted therapies of microbial homeostasis dysregulation in the female reproductive tract. IMPORTANCE This work sheds light on the dynamics of the sow vaginal microbiotas in early pregnancy and its roles in pregnancy development. Furthermore, this study provides insight into the functional mechanisms of reproductive tract microbes by outlining vaginal microbe-host interactions, which might identify new research and intervention targets for improving pregnancy development by modulating lower reproductive tract microbiota.},
}

Pregnancy
Animals
Female
Swine
RNA, Ribosomal, 16S/genetics
*Vagina/chemistry
Uterus/chemistry
*Microbiota/genetics
Metagenome

@article {pmid36740746,
year = {2023},
author = {Voidaleski, MF and Costa, FF and de Hoog, GS and Gomes, RR and Vicente, VA},
title = {Metagenomics reveals an abundance of black yeast-like fungi in the skin microbiome.},
journal = {Mycoses},
volume = {66},
number = {6},
pages = {488-496},
doi = {10.1111/myc.13574},
pmid = {36740746},
issn = {1439-0507},
mesh = {Humans ; Saccharomyces cerevisiae ; Metagenomics ; Skin/microbiology ; *Exophiala/genetics ; *Microbiota/genetics ; Fungi/genetics ; },
abstract = {BACKGROUND: The skin is the first line of defence against communities of resident viruses, bacteria and fungi. The composition of the microbiome might change with factors related to the environment and host. The microbiome is dominated by bacteria. Dermatophytes and yeasts are the predominant fungi that are also involved in opportunistic infections of skin, hair and nails. Among environmental fungi, Chaetothyriales (black yeasts and relatives) are enriched by hydrocarbon pollution in domesticated habitats and comprise numerous species that cause mild-to-severe disease.

METHODS: We investigated the presence of black fungi in the skin microbiome by conducting an analysis in the publicly available metagenomic SRA database (NCBI). We focused on the causative agents of chromoblastomycosis and phaeohyphomycosis and used barcodes and padlock probe sequences as diagnostic tools.

RESULTS: A total of 132,159,577 MB was analysed and yielded 18,360 reads that matched with 24 species of black fungi. Exophiala was the most prevalent genus, and Cyphellophora europaea was the most abundant species.

CONCLUSION: This study reveals the abundant presence of Chaetothyriales on the skin without necessarily being associated with infection. Most of the detected causal agents are known from mild skin diseases, while also species were revealed that had been reported from CARD9-deficient patients.},
}

Humans
Saccharomyces cerevisiae
Metagenomics
Skin/microbiology
*Exophiala/genetics
*Microbiota/genetics
Fungi/genetics

@article {pmid36468273,
year = {2023},
author = {Hino, A and Fukushima, K and Kusakabe, S and Ueda, T and Sudo, T and Fujita, J and Motooka, D and Takeda, AK and Shinozaki, NO and Watanabe, S and Yokota, T and Shibayama, H and Nakamura, S and Hosen, N},
title = {Prolonged gut microbial alterations in post-transplant survivors of allogeneic haematopoietic stem cell transplantation.},
journal = {British journal of haematology},
volume = {201},
number = {4},
pages = {725-737},
doi = {10.1111/bjh.18574},
pmid = {36468273},
issn = {1365-2141},
mesh = {Humans ; *Gastrointestinal Microbiome ; Dysbiosis/complications ; *Hematopoietic Stem Cell Transplantation/adverse effects ; Patient Discharge ; *Graft vs Host Disease/microbiology ; *Bronchiolitis Obliterans Syndrome ; },
abstract = {Dysbiosis of the gut microbiota has been reported to increase early complications after allogeneic haematopoietic stem cell transplantation (allo-HSCT). However, it remains unclear whether gut microbial alterations persist during late complications, such as chronic graft-versus-host disease (cGVHD) or secondary cancers. Here, we analysed the gut microbiota of 59 patients who survived for 1-21.7 years (median, 6.4 years) after allo-HSCT. Long-term survivors showed lower gut microbial diversity than the age- and sex-matched healthy controls. This decreased diversity was reflected in the reduced abundance of the butyrate-producing bacteria. Patients with a history of grade 3 acute graft-versus-host disease (aGVHD) exhibited higher Veillonella abundance than patients with a history of grade 1-2 or non-aGVHD cases. The abundance of Faecalibacterium showed no decrease only in limited cGVHD cases. Additionally, the microbial structure in the secondary cancer group was significantly different (p < 0.05) from that in the non-secondary cancer group. This study is the first to show that microbial dysbiosis is present over a 10-year lifetime after discharge following allo-HSCT. Our results suggest that these prolonged gut microbial alterations may be associated with the development and exacerbation of late complications in post-transplant survivors.},
}

Humans
*Gastrointestinal Microbiome
Dysbiosis/complications
*Hematopoietic Stem Cell Transplantation/adverse effects
Patient Discharge
*Graft vs Host Disease/microbiology
*Bronchiolitis Obliterans Syndrome

@article {pmid36781125,
year = {2023},
author = {Yang, Z and Wang, H and Yang, S and Wang, X and Shen, Q and Ji, L and Zeng, J and Zhang, W and Gong, H and Shan, T},
title = {Virome diversity of ticks feeding on domestic mammals in China.},
journal = {Virologica Sinica},
volume = {38},
number = {2},
pages = {208-221},
doi = {10.1016/j.virs.2023.02.001},
pmid = {36781125},
issn = {1995-820X},
mesh = {Animals ; Sheep ; Humans ; *Ticks ; Virome ; Phylogeny ; *Viruses/genetics ; *RNA Viruses/genetics ; Mammals ; *Flaviviridae ; China ; },
abstract = {Ticks are considered the second most common pathogen vectors transmitting a broad range of vital human and veterinary viruses. From 2017 to 2018, 640 ticks were collected in eight different provinces in central and western China. Six species were detected, including H.longicornis, De.everestianus, Rh.microplus, Rh.turanicus, Rh.sanguineous, and Hy.asiaticum. Sixty-four viral metagenomic libraries were constructed on the MiSeq Illumina platform, resulting in 13.44 G (5.88 × 10[7]) of 250-bp-end reads, in which 2,437,941 are viral reads. We found 27 nearly complete genome sequences, including 16 genome sequences encoding entire protein-coding regions (lack of 3' or 5' end non-coding regions) and complete viral genomes, distributed in the arboviral family (Chuviridae, Rhabdoviridae, Nairoviridae, Phenuiviridae, Flaviviridae, Iflaviridae) as well as Parvoviridae and Polyomaviridae that cause disease in mammals and even humans. In addition, 13 virus sequences found in Chuviridae, Nairoviridae, Flaviviridae, Iflaviridae, Hepeviridae, Parvoviridae, and Polyomaviridae were identified as belonging to a new virus species in the identified viral genera. Besides, an epidemiological survey shows a high prevalence (9.38% and 15.63%) of two viruses (Ovine Copiparvovirus and Bovine parvovirus 2) in the tick cohort.},
}

Animals
Sheep
Humans
*Ticks
Virome
Phylogeny
*Viruses/genetics
*RNA Viruses/genetics
Mammals
*Flaviviridae
China

@article {pmid36646520,
year = {2023},
author = {Gao, P and Fan, K and Zhang, G and Yin, X and Jia, C and Tian, H},
title = {Coal-mining subsidence changed distribution of the microbiomes and their functional genes in a farmland.},
journal = {Journal of basic microbiology},
volume = {63},
number = {5},
pages = {542-557},
doi = {10.1002/jobm.202200582},
pmid = {36646520},
issn = {1521-4028},
mesh = {Farms ; *Coal Mining ; *Microbiota ; Carbon ; Soil/chemistry ; Coal ; China ; },
abstract = {Land subsidence is a serious geological event, and can trigger severe environmental and ecological issues. In this study, the influences of coal-mining subsidence on distribution of farmland microbiomes and their functional genes were investigated by 16 S ribosomal RNA (rRNA) gene and metagenome sequencing. The results showed the existence of a core microbiome, which determined the community compositions across the subsidence farmland. Subsidence decreased the relative abundances of dominant Streptomyces, Nocardioides, and Rhizophagus, but increased the relative abundances of dominant Bradyrhizobium, Rhizobium, and Trichoderma. Subsidence also decreased the relative abundances of genes related to carbon metabolism, Quorum sensing, aminoacyl-transfer RNA (tRNA) biosynthesis, and oxidative phosphorylation, and increased the relative abundances of genes related to two-component system and bacterial chemotaxis. Furthermore, subsidence weakened the biosynthesis of organic carbons by decreasing the relative abundances of genes encoding glycosyl transferases, and strengthened decomposition of degradable organic carbons of the microbiomes and auxiliary activities by increasing the relative abundances of genes encoding glycoside hydrolases and polysaccharide lyases. The concentrations of total phosphorus, Mg[2+] , and Ca[2+] at the lower areas were significantly higher than those at the upper areas, indicating an associated loss of soil nutrients. Canonical correspondence analysis showed that soil moisture, pH, and the concentrations of NH4 [+] and Ca[2+] were the main factors affecting the distribution of the microbiomes and their functional genes. Collectively, this study shows that coal-mining subsidence alters soil physicochemical properties and distribution of farmland microbiomes and their functional genes.},
}

Farms
*Coal Mining
*Microbiota
Carbon
Soil/chemistry
Coal
China

@article {pmid36565811,
year = {2023},
author = {Li, Y and Cao, L and Han, X and Ma, Y and Liu, Y and Gao, S and Zhang, C},
title = {Altered vaginal eukaryotic virome is associated with different cervical disease status.},
journal = {Virologica Sinica},
volume = {38},
number = {2},
pages = {184-197},
doi = {10.1016/j.virs.2022.12.004},
pmid = {36565811},
issn = {1995-820X},
mesh = {Female ; Humans ; Virome ; *Papillomavirus Infections/microbiology/pathology ; Eukaryota ; *Uterine Cervical Neoplasms/microbiology/pathology ; *Viruses ; Biomarkers ; Papillomaviridae ; },
abstract = {Viruses are important components of the human body. Growing evidence suggests that they are engaged in the physiology and disease status of the host. Even though the vaginal microbiome is involved in human papillomavirus (HPV) infection and cervical cancer (CC) progression, little is known about the role of the vaginal virome. In this pilot exploratory study, using unbiased viral metagenomics, we aim to investigate the vaginal eukaryotic virome in women with different levels of cervical lesions, and examine their associations with different cervical disease status. An altered eukaryotic virome was observed in women with different levels of lesions and Lactobacillus profiles. Anelloviruses and papillomaviruses are the most commonly detected eukaryotic viruses of the vaginal virome. Higher abundance and richness of anelloviruses and papillomaviruses were associated with low-grade squamous intraepithelial lesion (LSIL) and CC. Besides, higher anellovirus abundance was also associated with lactobacillus-depleted microbiome profiles and bacterial community state (CST) type IV. Furthermore, increased correlations between Anelloviridae and Papillomaviridae occurred in the women with increased cervical disease severity level from LSIL to CC. These data suggest underlying interactions between different microbes as well as the host physiology. Higher abundance and diversity of both anelloviruses and papillomaviruses shared by LSIL and CC suggest that anellovirus may be used as a potential adjunct biomarker to predict the risk of HPV persistent infection and/or CC. Future studies need to focus on the clinical relevance of anellovirus abundance with cervical disease status, and the evaluation of their potential as a new adjunct biomarker for the prediction and prognoses of CC.},
}

Female
Humans
Virome
*Papillomavirus Infections/microbiology/pathology
Eukaryota
*Uterine Cervical Neoplasms/microbiology/pathology
*Viruses
Biomarkers
Papillomaviridae