@article {pmid39195462,
year = {2024},
author = {Pan, D and Xiao, P and Li, F and Liu, J and Zhang, T and Zhou, X and Zhang, Y},
title = {High Degree of Polymerization of Chitin Oligosaccharides Produced from Shrimp Shell Waste by Enrichment Microbiota Using Two-Stage Temperature-Controlled Technique of Inducing Enzyme Production and Metagenomic Analysis of Microbiota Succession.},
journal = {Marine drugs},
volume = {22},
number = {8},
pages = {},
doi = {10.3390/md22080346},
pmid = {39195462},
issn = {1660-3397},
support = {32100065//National Natural Science Foundation of China/ ; 32300031//National Natural Science Foundation of China/ ; 2023KJ207//Shandong Province Youth Entrepreneurship Technology Support Program for Higher Education Institutions/ ; ZR2023MB095//Natural Science Foundation of Shandong Province of China/ ; },
mesh = {*Chitin/chemistry ; Animals ; *Oligosaccharides/chemistry ; *Microbiota ; *Chitinases/metabolism ; *Animal Shells/chemistry ; Metagenomics/methods ; Temperature ; Polymerization ; Bacteria ; },
abstract = {The direct enzymatic conversion of untreated waste shrimp and crab shells has been a key problem that plagues the large-scale utilization of chitin biological resources. The microorganisms in soil samples were enriched in two stages with powdered chitin (CP) and shrimp shell powder (SSP) as substrates. The enrichment microbiota XHQ10 with SSP degradation ability was obtained. The activities of chitinase and lytic polysaccharide monooxygenase of XHQ10 were 1.46 and 54.62 U/mL. Metagenomic analysis showed that Chitinolyticbacter meiyuanensis, Chitiniphilus shinanonensis, and Chitinimonas koreensis, with excellent chitin degradation performance, were highly enriched in XHQ10. Chitin oligosaccharides (CHOSs) are produced by XHQ10 through enzyme induction and two-stage temperature control technology, which contains CHOSs with a degree of polymerization (DP) more significant than ten and has excellent antioxidant activity. This work is the first study on the direct enzymatic preparation of CHOSs from SSP using enrichment microbiota, which provides a new path for the large-scale utilization of chitin bioresources.},
}

*Chitin/chemistry
Animals
*Oligosaccharides/chemistry
*Microbiota
*Chitinases/metabolism
*Animal Shells/chemistry
Metagenomics/methods
Temperature
Polymerization
Bacteria

@article {pmid39192682,
year = {2024},
author = {Flynn, PJ and Moreau, CS},
title = {Viral diversity and co-evolutionary dynamics across the ant phylogeny.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e17519},
doi = {10.1111/mec.17519},
pmid = {39192682},
issn = {1365-294X},
support = {2210800//Division of Biological Infrastructure/ ; 1900357//Division of Environmental Biology/ ; //National Science Foundation Graduate Research Fellowship Program/ ; },
abstract = {Knowledge of viral biodiversity within insects, particularly within ants, is extremely limited with only a few environmental viruses from invasive ant species identified to date. This study documents and explores the viral communities in ants. We comprehensively profile the metagenomes of a phylogenetically broad group of 35 ant species with varied ecological traits and report the discovery of 3710 novel and unique ant-associated viral genomes. These previously unknown viruses discovered within this study constitute over 95% of all currently described ant viruses, significantly increasing our knowledge of the ant virosphere. The identified RNA and DNA viruses fill gaps in insect-associated viral phylogenies and uncover evolutionary histories characterized by both frequent host switching and co-divergence. Many ants also host diverse bacterial communities, and we discovered that approximately one-third of these new ant-associated viruses are bacteriophages. Two ecological categories, bacterial abundance in the host and habitat degradation are both correlated with ant viral diversity and help to structure viral communities within ants. These data demonstrate that the ant virosphere is remarkably diverse phylogenetically and genomically and provide a substantial foundation for studies in virus ecology and evolution within eukaryotes. We highlight the importance of studying insect-associated viruses in natural ecosystems in order to more thoroughly and effectively understand host-microbe evolutionary dynamics.},
}

@article {pmid39192352,
year = {2024},
author = {Zeng, G and Zeng, L and Wang, Y and Cao, Z and Zeng, X and Xue, Z and Liu, S and Li, Y and He, L},
title = {Correlation between gut microbiota characteristics and non-small cell lung cancer based on macrogenomics sequencing.},
journal = {Hereditas},
volume = {161},
number = {1},
pages = {26},
pmid = {39192352},
issn = {1601-5223},
support = {No. 2023349//Chengdu Municipal Health Commission/ ; },
mesh = {*Carcinoma, Non-Small-Cell Lung/genetics ; Humans ; *Gastrointestinal Microbiome ; *Lung Neoplasms/genetics/microbiology ; Male ; Middle Aged ; Female ; Feces/microbiology ; Aged ; Metagenome ; Metagenomics/methods ; Bacteria/genetics/classification ; },
abstract = {OBJECTIVE: Non-small cell lung cancer (NSCLC) patients undergoing chemotherapy and immunotherapy experience disturbances in the gut microbiota. This study intends to find out the correlation between gut microbiota and clinical indices before and after radiotherapy for NSCLC.

METHODS: Ten patients with primary NSCLC were screened, and plasma and fecal samples were collected before and after radiotherapy, respectively. Inflammatory indices in plasma were detected. Genomic DNA was extracted from fecal specimens and sequenced on on Illumina HiSeq2000 sequencing platform. Thee sequenced data were subjected to Metagenome assembly, gene prediction, species annotation, and gene function analysis to study and analyze gut microbiota and metabolic functions. The correlation between the diversity of gut microbiota and the clinical indicators of NSCLC patients was evaluated, and the changes of gut microbiota before and after radiotherapy were observed.

RESULTS: The diversity of gut microbiota in NSCLC patients did not correlate with smoking, pathology, and inflammatory markers. The abundance of phylum (p)_Bacteroidetes increased; p_Firmicutes and p_Bacteroidetes accounted for the highest proportion in NSCLC patients, and the abundance of both was dominantly exchanged after radiotherapy. There was a decrease in genus (g)_Bifidobacterium after radiotherapy in NSCLC patients. There was no significant correlation between the diversity of gut microbiota after radiotherapy and radiotherapy sensitivity, and the structural composition and abundance of gut microbiota remained stable.

CONCLUSION: The diversity of gut microbiota is altered after radiotherapy in NSCLC patients, showing an increase in harmful bacteria and a decrease in beneficial bacteria.},
}

*Carcinoma, Non-Small-Cell Lung/genetics
Humans
*Gastrointestinal Microbiome
*Lung Neoplasms/genetics/microbiology
Male
Middle Aged
Female
Feces/microbiology
Aged
Metagenome
Metagenomics/methods
Bacteria/genetics/classification

@article {pmid39192220,
year = {2024},
author = {Samak, ME and Solyman, SM and Hanora, A and Zakeer, S},
title = {Metagenomic mining of two Egyptian Red Sea sponges associated microbial community.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {315},
pmid = {39192220},
issn = {1471-2180},
support = {59/2020//Academy of Scientific Research and Technology/ ; 6420/2009//SIDA/ ; },
mesh = {*Porifera/microbiology ; Animals ; Indian Ocean ; *Metagenomics ; *Microbiota/genetics ; Egypt ; Bacteria/genetics/classification ; Phylogeny ; Biodiversity ; Multigene Family ; Biological Products/metabolism ; Metagenome ; Proteobacteria/genetics/classification/isolation & purification ; },
abstract = {The Red Sea is a promising habitat for the discovery of new bioactive marine natural products. Sponges associated microorganisms represent a wealthy source of compounds with unique chemical structures and diverse biological activities. Metagenomics is an important omics-based culture-independent technique that is used as an effective tool to get genomic and functional information on sponge symbionts. In this study, we used metagenomic analysis of two Egyptian Red Sea sponges Hyrtios erectus and Phorbas topsenti microbiomes to study the biodiversity and the biosynthetic potential of the Red Sea sponges to produce bioactive compounds. Our data revealed high biodiversity of the two sponges' microbiota with phylum Proteobacteria as the most dominant phylum in the associated microbial community with an average of 31% and 70% respectively. The analysis also revealed high biosynthetic potential of sponge Hyrtios erectus microbiome through detecting diverse types of biosynthetic gene clusters (BGCs) with predicted cytotoxic, antibacterial and inhibitory action. Most of these BGCs were predicted to be novel as they did not show any similarity with any MIBiG database known cluster. This study highlights the importance of the microbiome of the collected Red Sea sponge Hyrtios erectus as a valuable source of new bioactive natural products.},
}

*Porifera/microbiology
Animals
Indian Ocean
*Metagenomics
*Microbiota/genetics
Egypt
Bacteria/genetics/classification
Phylogeny
Biodiversity
Multigene Family
Biological Products/metabolism
Metagenome
Proteobacteria/genetics/classification/isolation & purification

@article {pmid39113195,
year = {2024},
author = {Dong, T and Wang, Y and Qi, C and Fan, W and Xie, J and Chen, H and Zhou, H and Han, X},
title = {Sequencing Methods to Study the Microbiome with Antibiotic Resistance Genes in Patients with Pulmonary Infections.},
journal = {Journal of microbiology and biotechnology},
volume = {34},
number = {8},
pages = {1617-1626},
doi = {10.4014/jmb.2402.02004},
pmid = {39113195},
issn = {1738-8872},
mesh = {Humans ; *High-Throughput Nucleotide Sequencing ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; *Bacteria/genetics/drug effects/classification/isolation & purification ; *Microbiota/genetics/drug effects ; Retrospective Studies ; *Drug Resistance, Bacterial/genetics ; Metagenomics/methods ; Microbial Sensitivity Tests ; Respiratory Tract Infections/microbiology/drug therapy ; Genes, Bacterial/genetics ; Male ; Female ; Middle Aged ; },
abstract = {Various antibiotic-resistant bacteria (ARB) are known to induce repeated pulmonary infections and increase morbidity and mortality. A thorough knowledge of antibiotic resistance is imperative for clinical practice to treat resistant pulmonary infections. In this study, we used a reads-based method and an assembly-based method according to the metagenomic next-generation sequencing (mNGS) data to reveal the spectra of ARB and corresponding antibiotic resistance genes (ARGs) in samples from patients with pulmonary infections. A total of 151 clinical samples from 144 patients with pulmonary infections were collected for retrospective analysis. The ARB and ARGs detection performance was compared by the reads-based method and assembly-based method with the culture method and antibiotic susceptibility testing (AST), respectively. In addition, ARGs and the attribution relationship of common ARB were analyzed by the two methods. The comparison results showed that the assembly-based method could assist in determining pathogens detected by the reads-based method as true ARB and improve the predictive capabilities (46% > 13%). ARG-ARB network analysis revealed that assembly-based method could promote determining clear ARG-bacteria attribution and 101 ARGs were detected both in two methods. 25 ARB were obtained by both methods, of which the most predominant ARB and its ARGs in the samples of pulmonary infections were Acinetobacter baumannii (ade), Pseudomonas aeruginosa (mex), Klebsiella pneumoniae (emr), and Stenotrophomonas maltophilia (sme). Collectively, our findings demonstrated that the assembly-based method could be a supplement to the reads-based method and uncovered pulmonary infection-associated ARB and ARGs as potential antibiotic treatment targets.},
}

Humans
*High-Throughput Nucleotide Sequencing
*Anti-Bacterial Agents/pharmacology/therapeutic use
*Bacteria/genetics/drug effects/classification/isolation & purification
*Microbiota/genetics/drug effects
Retrospective Studies
*Drug Resistance, Bacterial/genetics
Metagenomics/methods
Microbial Sensitivity Tests
Respiratory Tract Infections/microbiology/drug therapy
Genes, Bacterial/genetics
Male
Female
Middle Aged

@article {pmid38807549,
year = {2024},
author = {Bae, WY and Jung, WH and Shin, SL and Kim, TR and Sohn, M and Suk, J and Jung, I and Lee, YI and Lee, JH},
title = {Heat-treated Limosilactobacillus fermentum LM1020 with menthol, salicylic acid, and panthenol promotes hair growth and regulates hair scalp microbiome balance in androgenetic alopecia: A double-blind, randomized and placebo-controlled clinical trial.},
journal = {Journal of cosmetic dermatology},
volume = {23},
number = {9},
pages = {2943-2955},
doi = {10.1111/jocd.16357},
pmid = {38807549},
issn = {1473-2165},
support = {S3003957//Ministry of SMEs and Startups/ ; },
mesh = {Humans ; *Alopecia/therapy/microbiology/drug therapy ; Double-Blind Method ; *Scalp/microbiology ; *Microbiota/drug effects ; Adult ; *Limosilactobacillus fermentum/physiology/isolation & purification ; Male ; Female ; Hair/microbiology/growth & development ; Middle Aged ; Hair Follicle/microbiology ; Hot Temperature ; Cell Proliferation/drug effects ; },
abstract = {BACKGROUND: Androgenetic alopecia (AGA) is a common and chronic problem characterized by hair follicle miniaturization.

AIMS: In this study, heat-treated Limosilactobacillus fermentum LM1020 (HT-LM1020) was investigated in human follicle dermal papilla cell (HFDPC), scalp tissue, and clinical trials for patients with AGA.

PATIENTS/METHODS: Cell proliferation and the expression of cyclins and cyclin-dependent kinases (CDKs) were measured in HFDPC. The relative gene expression of 5α-reductase and growth factors were investigated in hair scalp. This double-blind, randomized, placebo-controlled clinical trial was conducted over 24 weeks. Primary efficacy was evaluated by measuring hair density, and secondary efficacy was assessed by experts and self-assessment. Changes in the microbiota of the hair scalps were analyzed using 16S metagenome amplicon sequencing.

RESULTS: HT-LM1020 promoted cell growth (p < 0.001) and cyclin B1 expression, and it reduced 5α-reductase and induced fibroblast growth factor 7 (FGF7), FGF10, and epithelial growth factor7 (EGF7) (p < 0.001). In the clinical trial, the experimental group demonstrated an increase in hair density from 133.70 to 148.87 n/cm[2] at Week 24 (p < 0.001), while also expressing satisfaction with their hair density, reduced hair loss, and hairline. At Week 24, the total ratio of lactic acid bacteria operational taxonomic unit (OTU) in the scalp increased from 6.65% to 26.19%. At the same period, placebo-controlled group decreased Staphylococcus caprae OTU from 77.95% to 14.57% while experimental group decreased from 65.80% to 41.02%.

CONCLUSIONS: These present results showed that HT-LM1020 was a co-effector of ingredients for anti-hair loss contributing to cell proliferation and the expression of CDKs.},
}

Humans
*Alopecia/therapy/microbiology/drug therapy
Double-Blind Method
*Scalp/microbiology
*Microbiota/drug effects
Adult
*Limosilactobacillus fermentum/physiology/isolation & purification
Male
Female
Hair/microbiology/growth & development
Middle Aged
Hair Follicle/microbiology
Hot Temperature
Cell Proliferation/drug effects

@article {pmid39191812,
year = {2024},
author = {Feng, Y and Wei, R and Chen, Q and Shang, T and Zhou, N and Wang, Z and Chen, Y and Chen, G and Zhang, G and Dong, K and Zhong, Y and Zhao, H and Hu, F and Zheng, H},
title = {Host specificity and cophylogeny in the "animal-gut bacteria-phage" tripartite system.},
journal = {NPJ biofilms and microbiomes},
volume = {10},
number = {1},
pages = {72},
pmid = {39191812},
issn = {2055-5008},
mesh = {Animals ; *Host Specificity ; *Bacteriophages/genetics/physiology ; *Gastrointestinal Microbiome ; Bees/virology/microbiology ; *Bacteria/virology/genetics/classification ; *Phylogeny ; Metagenomics/methods ; Metagenome ; },
abstract = {Cophylogeny has been identified between gut bacteria and their animal host and is highly relevant to host health, but little research has extended to gut bacteriophages. Here we use bee model to investigate host specificity and cophylogeny in the "animal-gut bacteria-phage" tripartite system. Through metagenomic sequencing upon different bee species, the gut phageome revealed a more variable composition than the gut bacteriome. Nevertheless, the bacteriome and the phageome showed a significant association of their dissimilarity matrices, indicating a reciprocal interaction between the two kinds of communities. Most of the gut phages were host generalist at the viral cluster level but host specialist at the viral OTU level. While the dominant gut bacteria Gilliamella and Snodgrassella exhibited matched phylogeny with bee hosts, most of their phages showed a diminished level of cophylogeny. The evolutionary rates of the bee, the gut bacteria and the gut phages showed a remarkably increasing trend, including synonymous and non-synonymous substitution and gene content variation. For all of the three codiversified tripartite members, however, their genes under positive selection and genes involving gain/loss during evolution simultaneously enriched the functions into metabolism of nutrients, therefore highlighting the tripartite coevolution that results in an enhanced ecological fitness for the whole holobiont.},
}

Animals
*Host Specificity
*Bacteriophages/genetics/physiology
*Gastrointestinal Microbiome
Bees/virology/microbiology
*Bacteria/virology/genetics/classification
*Phylogeny
Metagenomics/methods
Metagenome

@article {pmid39191760,
year = {2024},
author = {Hartikainen, AK and Jalanka, J and Lahtinen, P and Ponsero, AJ and Mertsalmi, T and Finnegan, L and Crispie, F and Cotter, PD and Arkkila, P and Satokari, R},
title = {Fecal microbiota transplantation influences microbiota without connection to symptom relief in irritable bowel syndrome patients.},
journal = {NPJ biofilms and microbiomes},
volume = {10},
number = {1},
pages = {73},
pmid = {39191760},
issn = {2055-5008},
support = {316338//Academy of Finland (Suomen Akatemia)/ ; 323156//Academy of Finland (Suomen Akatemia)/ ; },
mesh = {*Irritable Bowel Syndrome/therapy/microbiology ; Humans ; *Fecal Microbiota Transplantation/methods ; *RNA, Ribosomal, 16S/genetics ; Female ; Male ; Adult ; Treatment Outcome ; *Gastrointestinal Microbiome ; Middle Aged ; Feces/microbiology ; Metagenomics/methods ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {Imbalanced microbiota may contribute to the pathophysiology of irritable bowel syndrome (IBS), thus fecal microbiota transplantation (FMT) has been suggested as a potential treatment. Previous studies on the relationship between clinical improvement and microbiota after FMT have been inconclusive. In this study, we used 16S rRNA gene amplicon and shotgun metagenomics data from a randomized, placebo controlled FMT trial on 49 IBS patients to analyze changes after FMT in microbiota composition and its functional potential, and to identify connections between microbiota and patients' clinical outcome. As a result, we found that the successful modulation of microbiota composition and functional profiles by FMT from a healthy donor was not associated with the resolution of symptoms in IBS patients. Notably, a donor derived strain of Prevotella copri dominated the microbiota in those patients in the FMT group who had a low relative abundance of P. copri pre-FMT. The results highlight the multifactorial nature of IBS and the role of recipient's microbiota in the colonization of donor's strains.},
}

*Irritable Bowel Syndrome/therapy/microbiology
Humans
*Fecal Microbiota Transplantation/methods
*RNA, Ribosomal, 16S/genetics
Female
Male
Adult
Treatment Outcome
*Gastrointestinal Microbiome
Middle Aged
Feces/microbiology
Metagenomics/methods
Bacteria/classification/genetics/isolation & purification

@article {pmid39189742,
year = {2024},
author = {Wurzbacher, CE and Hammer, J and Haufschild, T and Wiegand, S and Kallscheuer, N and Jogler, C},
title = {"Candidatus Uabimicrobium helgolandensis"-a planctomycetal bacterium with phagocytosis-like prey cell engulfment, surface-dependent motility, and cell division.},
journal = {mBio},
volume = {},
number = {},
pages = {e0204424},
doi = {10.1128/mbio.02044-24},
pmid = {39189742},
issn = {2150-7511},
abstract = {The unique cell biology presented by members of the phylum Planctomycetota has puzzled researchers ever since their discovery. Initially thought to have eukaryotic-like features, their traits are now recognized as exceptional but distinctly bacterial. However, recently discovered strains again added novel and stunning aspects to the planctomycetal cell biology-shapeshifting by members of the "Saltatorellus" clade to an extent that is unprecedented in any other bacterial phylum, and phagocytosis-like cell engulfment in the bacterium "Candidatus Uabimicrobium amorphum." These recent additions to the phylum Planctomycetota indicate hitherto unexplored members with unique cell biology, which we aimed to make accessible for further investigations. Targeting bacteria with features like "Ca. U. amorphum", we first studied both the morphology and behavior of this microorganism in more detail. While similar to eukaryotic amoeboid organisms at first sight, we found "Ca. U. amorphum" to be rather distinct in many regards. Presenting a detailed description of "Ca. U. amorphum," we furthermore found this organism to divide in a fashion that has never been described in any other organism. Employing the obtained knowledge, we isolated a second "bacterium of prey" from the harbor of Heligoland Island (North Sea, Germany). Our isolate shares key features with "Ca. U. amorphum": phagocytosis-like cell engulfment, surface-dependent motility, and the same novel mode of cell division. Being related to "Ca. U. amorphum" within genus thresholds, we propose the name "Ca. Uabimicrobium helgolandensis" for this strain.IMPORTANCE"Candidatus Uabimicrobium helgolandensis" HlEnr_7 adds to the explored bacterial biodiversity with its phagocytosis-like uptake of prey bacteria. Enrichment of this strain indicates that there might be "impossible" microbes out there, missed by metagenomic analyses. Such organisms have the potential to challenge our understanding of nature. For example, the origin of eukaryotes remains enigmatic, with a contentious debate surrounding both the mitochondrial host entity and the moment of uptake. Currently, favored models involve a proteobacterium as the mitochondrial progenitor and an Asgard archaeon as the fusion partner. Models in which a eukaryotic ancestor engulfed the mitochondrial ancestor via phagocytosis had been largely rejected due to bioenergetic constraints. Thus, the phagocytosis-like abilities of planctomycetal bacteria might influence the debate, demonstrating that prey engulfment is possible in a prokaryotic cellular framework.},
}

@article {pmid39189169,
year = {2024},
author = {Hejazirad, SP and de Abreu, CM and Carneiro, GHF and Gomes, CR and Spinola Filho, PRC and da Costa, MR and Santos, JBD},
title = {The Impact of Metolachlor Applications and Phytoremediation Processes on Soil Microorganisms: Insights from Functional Metagenomics Analysis.},
journal = {Journal of xenobiotics},
volume = {14},
number = {3},
pages = {970-988},
doi = {10.3390/jox14030054},
pmid = {39189169},
issn = {2039-4713},
support = {PQD//National Council for Scientific and Technological Development/ ; 00097-22//Fundação de Amparo à Pesquisa do Estado de Minas Gerais/ ; 001//Coordenação de Aperfeicoamento de Pessoal de Nível Superior/ ; },
abstract = {This study assessed the impact of phytoremediation on reducing the residual concentration of metolachlor in soil treated with doses of 530.7 and 1061.4 g/ha and its effect on microbial biodiversity in contaminated areas. For the plant species Avena sativa and Medicago sativa, a significant efficacy of 54.5 and 36.4% was observed in the dissipation of the herbicide, especially at higher doses. Although metolachlor application reduced soil microbial biodiversity, phytoremediating plants, especially M. sativa, promoted greater richness and distribution of microbial species, mitigating the negative effects of the herbicide. Principal component analysis revealed the influence of these plants and metolachlor on the composition of the microbial community. These results highlight the importance of phytoremediation in promoting soil biodiversity and reducing herbicide contamination, providing crucial insights for remediation strategies in contaminated areas.},
}

@article {pmid39187802,
year = {2024},
author = {Anitua, E and Murias-Freijo, A and Tierno, R and Tejero, R and Alkhraisat, MH},
title = {Assessing peri-implant bacterial community structure: the effect of microbiome sample collection method.},
journal = {BMC oral health},
volume = {24},
number = {1},
pages = {1001},
pmid = {39187802},
issn = {1472-6831},
mesh = {Humans ; *Microbiota ; *Biofilms ; *Gingival Crevicular Fluid/microbiology ; *Dental Implants/microbiology ; Middle Aged ; Specimen Handling/methods ; Female ; Male ; High-Throughput Nucleotide Sequencing ; Bacteria/classification/isolation & purification ; Aged ; },
abstract = {BACKGROUND: Oral microbiota comprises polymicrobial communities shaped by mutualistic coevolution with the host, contributing to homeostasis and regulating immune function. Nevertheless, dysbiosis of oral bacterial communities is associated with a number of clinical symptoms that ranges from infections to oral cancer. Peri-implant diseases are biofilm-associated inflammatory conditions affecting the soft and hard tissues around dental implants. Characterization and identification of the biofilm community are essential for the understanding of the pathophysiology of such diseases. For that sampling methods should be representative of the biofilm communities Therefore, there is a need to know the effect of different sampling strategies on the biofilm characterization by next generation sequencing.

METHODS: With the aim of selecting an appropriate microbiome sampling procedure for periimplant biofilms, next generation sequencing was used for characterizing the bacterial communities obtained by three different sampling strategies two months after transepithelial abutment placement: adjacent periodontal crevicular fluid (ToCF), crevicular fluid from transepithelial abutment (TACF) and transepithelial abutment (TA).

RESULTS: Significant differences in multiple alpha diversity indices were detected at both the OTU and the genus level between different sampling procedures. Differentially abundant taxa were detected between sample collection strategies, including peri-implant health and disease related taxa. At the community level significant differences were also detected between TACF and TA and also between TA and ToCF. Moreover, differential network properties and association patterns were identified.

CONCLUSIONS: The selection of sample collection strategy can significantly affect the community composition and structure.

TRIAL REGISTRATION: This research is part of a randomized clinical trial that was designed to assess the effect of transepithelial abutment surface on the biofilm formation. The trial was registered at Trial Registration ClinicalTrials.gov under the number NCT03554876.},
}

Humans
*Microbiota
*Biofilms
*Gingival Crevicular Fluid/microbiology
*Dental Implants/microbiology
Middle Aged
Specimen Handling/methods
Female
Male
High-Throughput Nucleotide Sequencing
Bacteria/classification/isolation & purification
Aged

@article {pmid39185682,
year = {2024},
author = {Maqsood, R and Holland, LA and Wu, LI and Begnel, ER and Adhiambo, J and Owiti, P and Chohan, BH and Gantt, S and Kinuthia, J and Wamalwa, D and Ojee, E and Richardson, BA and Slyker, J and Lehman, DA and Lim, ES},
title = {Gut virome and microbiome dynamics before and after SARS-CoV-2 infection in women living with HIV and their infants.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2394248},
doi = {10.1080/19490976.2024.2394248},
pmid = {39185682},
issn = {1949-0984},
mesh = {Humans ; Female ; *COVID-19/microbiology/virology ; *HIV Infections/microbiology/virology ; *Virome ; *Gastrointestinal Microbiome ; *SARS-CoV-2/genetics/isolation & purification ; Adult ; Infant, Newborn ; *Feces/microbiology/virology ; Infant ; Bacteria/classification/isolation & purification/genetics ; Longitudinal Studies ; },
abstract = {Microbiome perturbations can have long-term effects on health. The dynamics of the gut microbiome and virome in women living with HIV (WLHIV) and their newborn infants is poorly understood. Here, we performed metagenomic sequencing analyses on longitudinal stool samples including 23 mothers (13 WLHIV, 10 HIV-negative) and 12 infants that experienced SARS-CoV-2 infection with mild disease, as well as 40 mothers (18 WLHIV, 22 HIV-negative) and 60 infants that remained SARS-CoV-2 seronegative throughout the study follow-up. Regardless of HIV or SARS-CoV-2 status, maternal bacterial and viral profiles were distinct from infants. Using linear mixed effects models, we showed that the microbiome alpha diversity trajectory was not significantly different between SARS-CoV-2 seropositive and seronegative women. However, seropositive women's positive trajectory while uninfected was abruptly reversed after SARS-CoV-2 infection (p = 0.015). Gut virome signatures of women were not associated with SARS-CoV-2. Alterations in infant microbiome and virome diversities were generally not impacted by SARS-CoV-2 but were rather driven by development. We did not find statistically significant interactions between HIV and SARS-CoV-2 on the gut microbiome and virome. Overall, our study provides insights into the complex interplay between maternal and infant bacterial microbiome, virome, and the influence of SARS-CoV-2 and HIV status.},
}

Humans
Female
*COVID-19/microbiology/virology
*HIV Infections/microbiology/virology
*Virome
*Gastrointestinal Microbiome
*SARS-CoV-2/genetics/isolation & purification
Adult
Infant, Newborn
*Feces/microbiology/virology
Infant
Bacteria/classification/isolation & purification/genetics
Longitudinal Studies

@article {pmid39120615,
year = {2024},
author = {Li, X and Tao, Q and Hu, Q and Ma, N and Ma, G},
title = {In vitro gastrointestinal digestion and fecal fermentation of Pleurotus eryngii proteins extracted using different methods: insights for the utilization of edible mushroom-based proteins as novel nutritional and functional components.},
journal = {Food & function},
volume = {15},
number = {17},
pages = {8865-8877},
doi = {10.1039/d4fo02604g},
pmid = {39120615},
issn = {2042-650X},
mesh = {*Pleurotus/metabolism/chemistry ; *Digestion ; *Fermentation ; *Feces/microbiology ; *Fungal Proteins/metabolism ; Humans ; Gastrointestinal Tract/metabolism/microbiology ; Gastrointestinal Microbiome ; Hydrolysis ; },
abstract = {Pleurotus eryngii (P. eryngii) protein is considered a high-quality protein because it is rich in essential amino acids and displays multiple significant functional characterizations that vary with its fabrication processes. We aimed to investigate the differences in P. eryngii protein extracted via alkaline extraction and acid precipitation (AA), cellulase complex alkaline extraction and acid precipitation (CAA), ultrasound-assisted alkaline extraction and acid precipitation (UAA), and salt dissolution (S) in terms of gastrointestinal digestion and fecal fermentation consequences. Protein hydrolysis and structural analysis were performed after in vitro gastrointestinal digestion, and it was found that AA showed the highest hydrolysis degree, whereas CAA showed the lowest. The results of fluorescence chromatography and infrared chromatography indicated that the reasons for the digestion difference might be the unfolding degrees of the protein tertiary structure and polysaccharide content, which is the major component of crude proteins and can prevent protein hydrolysis. Metagenomic analysis suggested that compared with other groups, AA had excellent biological functions, including regulating obesity and insulin-related microbiota. This study could provide a new theoretical basis for the P. eryngii protein as a novel type of nutritional and functional component and contributes to the development of a diversified emerging food protein supply system.},
}

*Pleurotus/metabolism/chemistry
*Digestion
*Fermentation
*Feces/microbiology
*Fungal Proteins/metabolism
Humans
Gastrointestinal Tract/metabolism/microbiology
Gastrointestinal Microbiome
Hydrolysis

@article {pmid39117202,
year = {2024},
author = {Tariq, M and Liu, Y and Rizwan, A and Shoukat, CA and Aftab, Q and Lu, J and Zhang, Y},
title = {Impact of elevated CO2 on soil microbiota: A meta-analytical review of carbon and nitrogen metabolism.},
journal = {The Science of the total environment},
volume = {950},
number = {},
pages = {175354},
doi = {10.1016/j.scitotenv.2024.175354},
pmid = {39117202},
issn = {1879-1026},
mesh = {*Soil Microbiology ; *Nitrogen/metabolism ; *Carbon Dioxide/metabolism ; *Microbiota ; *Carbon/metabolism ; Climate Change ; Soil/chemistry ; Carbon Cycle ; },
abstract = {In the face of 21st-century challenges driven by population growth and resource depletion, understanding the intricacies of climate change is crucial for environmental sustainability. This review systematically explores the interaction between rising atmospheric CO2 concentrations and soil microbial populations, with possible feedback effects on climate change and terrestrial carbon (C) cycling through a meta-analytical approach. Furthermore, it investigates the enzymatic activities related to carbon acquisition, gene expression patterns governing carbon and nitrogen metabolism, and metagenomic and meta-transcriptomic dynamics in response to elevated CO2 levels. The study reveals that elevated CO2 levels substantially influence soil microbial communities, increasing microbial biomass C and respiration rate by 15 % and upregulating genes involved in carbon and nitrogen metabolism by 12 %. Despite a 14 % increase in C-acquiring enzyme activity, there is a 5 % decrease in N-acquiring enzyme activity, indicating complex microbial responses to CO2 changes. Additionally, fungal marker ratios increase by 14 % compared to bacterial markers, indicating potential ecosystem changes. However, the current inadequacy of data on metagenomic and meta-transcriptomic processes underscores the need for further research. Understanding soil microbial feedback mechanisms is crucial for elucidating the role of rising CO2 levels in carbon sequestration and climate regulation. Consequently, future research should prioritize a comprehensive elucidation of soil microbial carbon cycling, greenhouse gas emission dynamics, and their underlying drivers.},
}

*Soil Microbiology
*Nitrogen/metabolism
*Carbon Dioxide/metabolism
*Microbiota
*Carbon/metabolism
Climate Change
Soil/chemistry
Carbon Cycle

@article {pmid39111416,
year = {2024},
author = {Wang, HY and Yu, ZG and Zhou, FW and Hernandez, JC and Grandjean, A and Biester, H and Xiao, KQ and Knorr, KH},
title = {Microbial communities and functions are structured by vertical geochemical zones in a northern peatland.},
journal = {The Science of the total environment},
volume = {950},
number = {},
pages = {175273},
doi = {10.1016/j.scitotenv.2024.175273},
pmid = {39111416},
issn = {1879-1026},
mesh = {*Microbiota ; China ; *Soil Microbiology ; *Methane/metabolism/analysis ; RNA, Ribosomal, 16S ; Soil/chemistry ; Wetlands ; Carbon/analysis ; Nitrogen/analysis ; Bacteria/classification ; Sulfur/metabolism/analysis ; Archaea/classification ; },
abstract = {Northern peatlands are important carbon pools; however, differences in the structure and function of microbiomes inhabiting contrasting geochemical zones within these peatlands have rarely been emphasized. Using 16S rRNA gene sequencing, metagenomic profiling, and detailed geochemical analyses, we investigated the taxonomic composition and genetic potential across various geochemical zones of a typical northern peatland profile in the Changbai Mountains region (Northeastern China). Specifically, we focused on elucidating the turnover of organic carbon, sulfur (S), nitrogen (N), and methane (CH4). Three geochemical zones were identified and characterized according to porewater and solid-phase analyses: the redox interface (<10 cm), shallow peat (10-100 cm), and deep peat (>100 cm). The redox interface and upper shallow peat demonstrated a high availability of labile carbon, which decreased toward deeper peat. In deep peat, anaerobic respiration and methanogenesis were likely constrained by thermodynamics, rather than solely driven by available carbon, as the acetate concentrations reached 90 μmol·L[-1]. Both the microbial community composition and metabolic potentials were significantly different (p < 0.05) among the redox interface, shallow peat, and deep peat. The redox interface demonstrated a close interaction between N, S, and CH4 cycling, mainly driven by Thermodesulfovibrionia, Bradyrhizobium, and Syntrophorhabdia metagenome-assembled genomes (MAGs). The archaeal Bathyarchaeia were indicated to play a significant role in the organic carbon, N, and S cycling in shallow peat. Although constrained by anaerobic respiration and methanogenesis, deep peat exhibited a higher metabolic potential for organic carbon degradation, primarily mediated by Acidobacteriota. In terms of CH4 turnover, subsurface peat (10-20 cm) was a CH4 production hotspot, with a net turnover rate of ∼2.9 nmol·cm[-3]·d[-1], while the acetoclastic, hydrogenotrophic, and methylotrophic methanogenic pathways all potentially contributed to CH4 production. The results of this study improve our understanding of biogeochemical cycles and CH4 turnover along peatland profiles.},
}

*Microbiota
China
*Soil Microbiology
*Methane/metabolism/analysis
RNA, Ribosomal, 16S
Soil/chemistry
Wetlands
Carbon/analysis
Nitrogen/analysis
Bacteria/classification
Sulfur/metabolism/analysis
Archaea/classification

@article {pmid39089095,
year = {2024},
author = {Zhuang, M and Yan, W and Xiong, Y and Wu, Z and Cao, Y and Sanganyado, E and Siame, BA and Chen, L and Kashi, Y and Leung, KY},
title = {Horizontal plasmid transfer promotes antibiotic resistance in selected bacteria in Chinese frog farms.},
journal = {Environment international},
volume = {190},
number = {},
pages = {108905},
doi = {10.1016/j.envint.2024.108905},
pmid = {39089095},
issn = {1873-6750},
mesh = {Animals ; *Plasmids/genetics ; China ; *Gene Transfer, Horizontal ; *Bacteria/genetics/drug effects ; Anti-Bacterial Agents/pharmacology ; Farms ; Drug Resistance, Bacterial/genetics ; Rana catesbeiana/microbiology/genetics ; Drug Resistance, Microbial/genetics ; Microbiota/genetics ; },
abstract = {The emergence and dissemination of antibiotic resistance genes (ARGs) in the ecosystem are global public health concerns. One Health emphasizes the interconnectivity between different habitats and seeks to optimize animal, human, and environmental health. However, information on the dissemination of antibiotic resistance genes (ARGs) within complex microbiomes in natural habitats is scarce. We investigated the prevalence of antibiotic resistant bacteria (ARB) and the spread of ARGs in intensive bullfrog (Rana catesbeiana) farms in the Shantou area of China. Antibiotic susceptibilities of 361 strains, combined with microbiome analyses, revealed Escherichia coli, Edwardsiella tarda, Citrobacter and Klebsiella sp. as prevalent multidrug resistant bacteria on these farms. Whole genome sequencing of 95 ARB identified 250 large plasmids that harbored a wide range of ARGs. Plasmid sequences and sediment metagenomes revealed an abundance of tetA, sul1, and aph(3″)-Ib ARGs. Notably, antibiotic resistance (against 15 antibiotics) highly correlated with plasmid-borne rather than chromosome-borne ARGs. Based on sequence similarities, most plasmids (62%) fell into 32 distinct groups, indicating a potential for horizontal plasmid transfer (HPT) within the frog farm microbiome. HPT was confirmed in inter- and intra-species conjugation experiments. Furthermore, identical mobile ARGs, flanked by mobile genetic elements (MGEs), were found in different locations on the same plasmid, or on different plasmids residing in the same or different hosts. Our results suggest a synergy between MGEs and HPT to facilitate ARGs dissemination in frog farms. Mining public databases retrieved similar plasmids from different bacterial species found in other environmental niches globally. Our findings underscore the importance of HPT in mediating the spread of ARGs in frog farms and other microbiomes of the ecosystem.},
}

Animals
*Plasmids/genetics
China
*Gene Transfer, Horizontal
*Bacteria/genetics/drug effects
Anti-Bacterial Agents/pharmacology
Farms
Drug Resistance, Bacterial/genetics
Rana catesbeiana/microbiology/genetics
Drug Resistance, Microbial/genetics
Microbiota/genetics

@article {pmid39082382,
year = {2024},
author = {Vidal-Villarejo, M and Dößelmann, B and Kogler, B and Hammerschmidt, M and Oppliger, B and Oppliger, H and Schmid, K},
title = {Regional diversity and leaf microbiome interactions of the fungal maize pathogen Exserohilum turcicum in Switzerland: A metagenomic analysis.},
journal = {Molecular ecology},
volume = {33},
number = {17},
pages = {e17482},
doi = {10.1111/mec.17482},
pmid = {39082382},
issn = {1365-294X},
support = {SCHM 1354-11/1//Deutsche Forschungsgemeinschaft/ ; 031B0731A//Bundesministerium für Bildung und Forschung/ ; PGRL-NN-0061//Swiss National Action Plan NAP-PGREL/ ; },
mesh = {*Zea mays/microbiology ; Switzerland ; *Ascomycota/genetics ; *Plant Leaves/microbiology ; *Plant Diseases/microbiology ; *Microbiota/genetics ; *Metagenomics ; },
abstract = {The spread and adaptation of fungal plant pathogens in agroecosystems are facilitated by environmental homogeneity. Metagenomic sequencing of infected tissues allowed us to monitor eco-evolutionary dynamics and interactions between host, pathogen and plant microbiome. Exserohilum turcicum, the causal agent of northern corn leaf blight (NCLB) in maize, is distributed in multiple clonal lineages throughout Europe. To characterize regional pathogen diversity, we conducted metagenomic DNA sequencing on 241 infected leaf samples from the highly susceptible Swiss maize landrace Rheintaler Ribelmais, collected over 3 years (2016-2018) from an average of 14 agricultural farms within the Swiss Rhine Valley. All major European clonal lineages of E. turcicum were identified. Lineages differ by their mating types which indicates potential for sexual recombination and rapid evolution of new pathogen strains, although we found no evidence of recent recombination. The associated eukaryotic and prokaryotic leaf microbiome exhibited variation in taxonomic diversity between years and locations and is likely influenced by local weather conditions. A network analysis revealed distinct clusters of eukaryotic and prokaryotic taxa that correlates with the frequency of E. turcicum sequencing reads, suggesting causal interactions. Notably, the yeast genus Metschnikowia exhibited a strongly negative association with E. turcicum, supporting its known potential as biological control agent against fungal pathogens. Our findings show that metagenomic sequencing is a useful tool for analysing the role of environmental factors and potential pathogen-microbiome interactions in shaping pathogen dynamics and evolution, suggesting their potential for effective pathogen management strategies.},
}

*Zea mays/microbiology
Switzerland
*Ascomycota/genetics
*Plant Leaves/microbiology
*Plant Diseases/microbiology
*Microbiota/genetics
*Metagenomics

@article {pmid39056112,
year = {2024},
author = {Dong, J and Zhang, J and Cheng, S and Qin, B and Jin, K and Chen, B and Zhang, Y and Lu, J},
title = {A high-fat diet induced depression-like phenotype via hypocretin-HCRTR1 mediated inflammation activation.},
journal = {Food & function},
volume = {15},
number = {17},
pages = {8661-8673},
doi = {10.1039/d4fo00210e},
pmid = {39056112},
issn = {2042-650X},
mesh = {Animals ; *Diet, High-Fat/adverse effects ; Male ; Mice ; Rats ; *Depression/metabolism ; *Rats, Sprague-Dawley ; *Mice, Inbred C57BL ; *Inflammation/metabolism ; *Orexins/metabolism ; *Gastrointestinal Microbiome/drug effects ; *Orexin Receptors/metabolism/genetics ; Hippocampus/metabolism/drug effects ; 3T3-L1 Cells ; Microglia/metabolism/drug effects ; Phenotype ; Benzoxazoles ; Naphthyridines ; Urea/analogs & derivatives ; },
abstract = {Background: A high-fat diet (HFD) is generally associated with an increased risk of mental disorders that constitute a sizeable worldwide health. A HFD results in the gut microbiota-brain axis being altered and linked to mental disorders. Hypocretin-1, which can promote appetite, has been previously confirmed to be associated with depression. However, no exact relationship has been found for hypocretin between depression and HFDs. Methods: Adult male SD rats were randomly assigned to either a HFD or a normal diet for eight weeks, followed by behavioral tests and plasma biochemical analyses. Then, we investigated the protein and mRNA levels of inflammation-related factors in the hippocampus. We also observed morphological changes in brain microglia and lipid accumulation. Additionally, metagenomic and metabolomic analyses of gut microbiomes were performed. 3T3-L1 cells were utilized in vitro to investigate the impact of hypocretin receptor 1 antagonists (SB334867) on lipid accumulation. To consider the connection between the brain and adipose tissue, we used a conditioned medium (CM) treated with 3T3-L1 cells to observe the activation and phagocytosis of BV2 cells. Following a 12-week period of feeding a HFD to C57BL/6 mice, a three-week intervention period was initiated during which the administration of SB334867 was observed. This was followed by a series of assessments, including monitoring of body weight changes and emotional problems, as well as attention to plasma biochemical levels and microglial cell phenotypes in the brain. Results: The HFD rats displayed anxiety and depressive-like behaviors. HFD rats exhibited increased plasma HDL, LDL, and TC levels. A HFD also causes an increase in hypocretin-1 and hypocretin-2 in the hypothalamus. Metagenomics and metabolomics revealed that the HFD caused an increase in the relative abundance of associated inflammatory bacteria and decreased the abundance of anti-inflammatory and bile acid metabolites. Compared with the CTR group, hippocampal microglia in the HFD group were significantly activated and accompanied by lipid deposition. At the same time, protein and mRNA expression levels of inflammation-related factors were increased. We found that SB334867 could significantly reduce lipid accumulation in 3T3-L1 cells after differentiation. The expression of inflammatory factors decreased in the SB334867 group. The administration of SB334867 was found to reverse the adverse effects of the HFD on body weight, depressive-like behaviour and anxiety-like mood. Furthermore, this treatment was associated with improvements in plasma biochemical levels and a reduction in the number of microglia in the brain. Conclusions: In summary, our results demonstrated that a HFD induced anxiety and depressive-like behaviors, which may be linked to the increased hypocretin-1 level and lipid accumulation. Supplementation with SB334867 improved the above. These observations highlight the possibility of hypocretin-1 inducing the risk of HFD-associated emotional dysfunctions.},
}

Animals
*Diet, High-Fat/adverse effects
Male
Mice
Rats
*Depression/metabolism
*Rats, Sprague-Dawley
*Mice, Inbred C57BL
*Inflammation/metabolism
*Orexins/metabolism
*Gastrointestinal Microbiome/drug effects
*Orexin Receptors/metabolism/genetics
Hippocampus/metabolism/drug effects
3T3-L1 Cells
Microglia/metabolism/drug effects
Phenotype
Benzoxazoles
Naphthyridines
Urea/analogs & derivatives

@article {pmid39042309,
year = {2024},
author = {Hussan, H and Ali, MR and Lyo, V and Webb, A and Pietrzak, M and Zhu, J and Choueiry, F and Li, H and Cummings, BP and Marco, ML and Medici, V and Clinton, SK},
title = {Bariatric Surgery Is Associated with Lower Concentrations of Fecal Secondary Bile Acids and Their Metabolizing Microbial Enzymes: A Pilot Study.},
journal = {Obesity surgery},
volume = {34},
number = {9},
pages = {3420-3433},
pmid = {39042309},
issn = {1708-0428},
support = {R35GM133510/GM/NIGMS NIH HHS/United States ; R35GM133510/GM/NIGMS NIH HHS/United States ; },
mesh = {Humans ; *Feces/microbiology ; Pilot Projects ; Male ; Female ; Cross-Sectional Studies ; Case-Control Studies ; Middle Aged ; *Bariatric Surgery ; *Bile Acids and Salts/metabolism ; Adult ; *Obesity, Morbid/surgery/microbiology ; Gastrointestinal Microbiome/physiology ; Weight Loss ; Lithocholic Acid/metabolism ; },
abstract = {INTRODUCTION: Excess body fat elevates colorectal cancer risk. While bariatric surgery (BRS) induces significant weight loss, its effects on the fecal stream and colon biology are poorly understood. Specifically, limited data exist on the impact of bariatric surgery (BRS) on fecal secondary bile acids (BA), including lithocholic acid (LCA), a putative promotor of colorectal carcinogenesis.

METHODS: This cross-sectional case-control study included 44 patients with obesity; 15 pre-BRS (controls) vs. 29 at a median of 24.1 months post-BRS. We examined the fecal concentrations of 11 BA by liquid chromatography and gene abundance of BA-metabolizing bacterial enzymes through fecal metagenomic sequencing. Differences were quantified using non-parametric tests for BA levels and linear discriminant analysis (LDA) effect size (LEfSe) for genes encoding BA-metabolizing enzymes.

RESULTS: Total fecal secondary BA concentrations trended towards lower levels post- vs. pre-BRS controls (p = 0.07). Individually, fecal LCA concentrations were significantly lower post- vs. pre-BRS (8477.0 vs. 11,914.0 uM/mg, p < 0.008). Consistent with this finding, fecal bacterial genes encoding BA-metabolizing enzymes, specifically 3-betahydroxycholanate-3-dehydrogenase (EC 1.1.1.391) and 3-alpha-hydroxycholanate dehydrogenase (EC 1.1.1.52), were also lower post- vs. pre-BRS controls (LDA of - 3.32 and - 2.64, respectively, adjusted p < 0.0001). Post-BRS fecal BA concentrations showed significant inverse correlations with weight loss, a healthy diet quality, and increased physical activity.

CONCLUSIONS: Concentrations of LCA, a secondary BA, and bacterial genes needed for BA metabolism are lower post-BRS. These changes can impact health and modulate the colorectal cancer cascade. Further research is warranted to examine how surgical alterations and the associated dietary changes impact bile acid metabolism.},
}

Humans
*Feces/microbiology
Pilot Projects
Male
Female
Cross-Sectional Studies
Case-Control Studies
Middle Aged
*Bariatric Surgery
*Bile Acids and Salts/metabolism
Adult
*Obesity, Morbid/surgery/microbiology
Gastrointestinal Microbiome/physiology
Weight Loss
Lithocholic Acid/metabolism

@article {pmid38996003,
year = {2024},
author = {Byndloss, M and Devkota, S and Duca, F and Hendrik Niess, J and Nieuwdorp, M and Orho-Melander, M and Sanz, Y and Tremaroli, V and Zhao, L},
title = {The Gut Microbiota and Diabetes: Research, Translation, and Clinical Applications-2023 Diabetes, Diabetes Care, and Diabetologia Expert Forum.},
journal = {Diabetes care},
volume = {47},
number = {9},
pages = {1491-1508},
doi = {10.2337/dci24-0052},
pmid = {38996003},
issn = {1935-5548},
support = {//Novo Nordisk/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Diabetes Mellitus, Type 2/microbiology ; Diabetes Mellitus/microbiology ; },
abstract = {This article summarizes the state of the science on the role of the gut microbiota (GM) in diabetes from a recent international expert forum organized by Diabetes, Diabetes Care, and Diabetologia, which was held at the European Association for the Study of Diabetes 2023 Annual Meeting in Hamburg, Germany. Forum participants included clinicians and basic scientists who are leading investigators in the field of the intestinal microbiome and metabolism. Their conclusions were as follows: 1) the GM may be involved in the pathophysiology of type 2 diabetes, as microbially produced metabolites associate both positively and negatively with the disease, and mechanistic links of GM functions (e.g., genes for butyrate production) with glucose metabolism have recently emerged through the use of Mendelian randomization in humans; 2) the highly individualized nature of the GM poses a major research obstacle, and large cohorts and a deep-sequencing metagenomic approach are required for robust assessments of associations and causation; 3) because single-time point sampling misses intraindividual GM dynamics, future studies with repeated measures within individuals are needed; and 4) much future research will be required to determine the applicability of this expanding knowledge to diabetes diagnosis and treatment, and novel technologies and improved computational tools will be important to achieve this goal.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Diabetes Mellitus, Type 2/microbiology
Diabetes Mellitus/microbiology

@article {pmid38990271,
year = {2024},
author = {Ulger, Y and Delik, A and Akkız, H},
title = {Gut Microbiome and colorectal cancer: discovery of bacterial changes with metagenomics application in Turkısh population.},
journal = {Genes & genomics},
volume = {46},
number = {9},
pages = {1059-1070},
pmid = {38990271},
issn = {2092-9293},
support = {148-TGD-2022//Turkish Gastroenterology Association/ ; },
mesh = {Humans ; *Colorectal Neoplasms/microbiology/genetics/pathology ; *Gastrointestinal Microbiome/genetics ; Middle Aged ; Female ; Male ; *Metagenomics/methods ; Aged ; Turkey ; Bacteria/genetics/classification/isolation & purification ; RNA, Ribosomal, 16S/genetics ; },
abstract = {BACKGROUND: Colorectal cancer (CRC) is the 3rd most common cancer in the world and colonic carcinogenesis is a multifactorial disease that involves environmental and genetic factors. Gut microbiota plays a critical role in the regulation of intestinal homeostasis. Increasing evidence shows that the gut microbiome plays a role in CRC development and may be a biomarker for early diagnosis.

OBJECTIVE: This study aimed to determine the clinical prognostic significance of gut microbiota in CRC patients in the Turkish population by metagenomic analysis and to determine the microbial composition in tumor tissue biopsy samples.

METHODS: Tissue biopsies were taken from the participants with sterile forceps during colonoscopy and stored at -80 °C. Then, DNA isolation was performed from the tissue samples and the V3-V4 region of the 16 S rRNA gene was sequenced on the Illumina MiSeq platform. Quality control of the obtained sequence data was performed. Operational taxonomic units (OTUs) were classified according to the Greengenes database. Alpha diversity (Shannon index) and beta diversity (Bray-Curtis distance) analyses were performed. The most common bacterial species in CRC patients and healthy controls were determined and whether there were statistically significant differences between the groups was tested.

RESULTS: A total of 40 individuals, 13 CRC patients and 20 healthy control individuals were included in our metagenomic study. The mean age of the patients was 64.83 and BMI was 25.85. In CRC patients, the level of Bacteroidetes at the phylum taxonomy was significantly increased (p = 0.04), the level of Clostridia at the class taxonomy was increased (p = 0.23), and the level of Enterococcus at the genus taxonomy was significantly increased (p = 0.01). When CRC patients were compared with the control group, significant increases were detected in the species of Gemmiger formicilis (p = 0.15), Prevotella copri (p = 0.02) and Ruminococcus bromii (p = 0.001) at the species taxonomy.

CONCLUSIONS: Metagenomic analysis of intestinal microbiota composition in CRC patients provides important data for determining the treatment options for these patients. The results of this study suggest that it may be beneficial in terms of early diagnosis, poor prognosis and survival rates in CRC patients. In addition, this metagenomic study is the first study on the colon microbiome associated with CRC mucosa in the Turkish population.},
}

Humans
*Colorectal Neoplasms/microbiology/genetics/pathology
*Gastrointestinal Microbiome/genetics
Middle Aged
Female
Male
*Metagenomics/methods
Aged
Turkey
Bacteria/genetics/classification/isolation & purification
RNA, Ribosomal, 16S/genetics

@article {pmid39185088,
year = {2024},
author = {Hu, L and Xu, Y and Li, J and Zhang, M and Sun, Z and Ban, Y and Tian, X and Liu, D and Hu, L},
title = {Gut microbiome characteristics of women with hypothyroidism during early pregnancy detected by 16S rRNA amplicon sequencing and shotgun metagenomic.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1369192},
doi = {10.3389/fcimb.2024.1369192},
pmid = {39185088},
issn = {2235-2988},
mesh = {Humans ; Female ; Pregnancy ; *Hypothyroidism/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; Adult ; *Dysbiosis/microbiology ; Bacteria/classification/genetics/isolation & purification ; Pregnancy Complications/microbiology ; Metagenome ; Feces/microbiology ; },
abstract = {OBJECTIVE: This study aimed to explore the correlation between microbiota dysbiosis and hypothyroidism in early pregnancy by 16S rRNA amplicon sequencing combined with metagenomic sequencing.

METHODS: Sixty pregnant women (30 with hypothyroidism and 30 normal controls) were recruited for 16S rRNA amplicon sequencing, and 6 patients from each group were randomly selected for metagenomic sequencing to assess the gut microbiome profile.

RESULTS: The 16S rRNA results showed that beta-diversity in the hypothyroidism group was decreased. The relative abundances of the Prevotella and Paraprevotella genera increased in the hypothyroidism group, and Blautia predominated in the controls. The metagenomics results revealed that Prevotella_stercorea_CAG_629, Prevotella_hominis, Prevotella_sp_AM34_19LB, etc. were enriched in the hypothyroidism group at the species level. Functional analysis revealed that the pyridoxal 5'-phosphate synthase pdxT subunit module was decreased, and the short-chain fatty acid (SCFA) transporter and phospholipase/carboxylesterase modules were strongly enriched in the hypothyroidism group. Hypothyroidism patients had increased C-reactive protein (CRP), interleukin-2 (IL-2), IL-4, IL-10, and tumor necrosis factor (TNF)-α levels. The pyridoxal 5'-phosphate synthase pdxT subunit, the SCFA transporter, and the phospholipase/carboxylesterase module were associated with different Prevotella species.

CONCLUSION: In early pregnancy, women with hypothyroidism exhibit microbiota dysbiosis, and Prevotella may affect the metabolism of glutamate, SCFA, and phospholipases, which could be involved in the development of hypothyroidism during pregnancy.},
}

Humans
Female
Pregnancy
*Hypothyroidism/microbiology
*RNA, Ribosomal, 16S/genetics
*Gastrointestinal Microbiome/genetics
*Metagenomics/methods
Adult
*Dysbiosis/microbiology
Bacteria/classification/genetics/isolation & purification
Pregnancy Complications/microbiology
Metagenome
Feces/microbiology

@article {pmid39185086,
year = {2024},
author = {Wang, X and Xiao, T and Lu, M and Wu, Z and Chen, L and Zhang, Z and Lu, W},
title = {Lower respiratory tract microbiome and lung cancer risk prediction in patients with diffuse lung parenchymal lesions.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1410681},
doi = {10.3389/fcimb.2024.1410681},
pmid = {39185086},
issn = {2235-2988},
mesh = {Humans ; *Lung Neoplasms/microbiology/pathology ; Male ; Female ; *Microbiota ; Middle Aged ; *Bronchoalveolar Lavage Fluid/microbiology ; Retrospective Studies ; Aged ; Lung/microbiology/pathology/diagnostic imaging ; High-Throughput Nucleotide Sequencing ; Adult ; Respiratory System/microbiology ; Metagenomics/methods ; Risk Factors ; },
abstract = {OBJECTIVE: In clinical practice, imaging manifestations of diffuse lung parenchymal lesions are common and indicative of various diseases, making differential diagnosis difficult. Some of these lesions are eventually diagnosed as lung cancer.

METHODS: Because respiratory microorganisms play an important role in lung cancer development, we searched for microbial markers that could predict the risk of lung cancer by retrospectively analyzing the lower respiratory tract (LRT) microbiome of 158 patients who were hospitalized in the First Affiliated Hospital of Guangzhou Medical University (March 2021-March 2023) with diffuse lung parenchymal lesions. The final diagnosis was lung cancer in 21 cases, lung infection in 93 cases, and other conditions (other than malignancy and infections) in 44 cases. The patient's clinical characteristics and the results of metagenomic next-generation sequencing of bronchoalveolar lavage fluid (BALF) were analyzed.

RESULTS: Body mass index (BMI) and LRT microbial diversity (Shannon, Simpson, species richness, and Choa1 index) were significantly lower (P< 0.001, respectively) and Lactobacillus acidophilus relative abundance in the LRT was significantly higher (P< 0.001) in patients with lung cancer. The relative abundance of L. acidophilus in BALF combined with BMI was a good predictor of lung cancer risk (area under the curve = 0.985, accuracy = 98.46%, sensitivity = 95.24%, and specificity = 100.00%; P< 0.001).

CONCLUSION: Our study showed that an imbalance in the component ratio of the microbial community, diminished microbial diversity, and the presence of specific microbial markers in the LRT predicted lung cancer risk in patients with imaging manifestations of diffuse lung parenchymal lesions.},
}

Humans
*Lung Neoplasms/microbiology/pathology
Male
Female
*Microbiota
Middle Aged
*Bronchoalveolar Lavage Fluid/microbiology
Retrospective Studies
Aged
Lung/microbiology/pathology/diagnostic imaging
High-Throughput Nucleotide Sequencing
Adult
Respiratory System/microbiology
Metagenomics/methods
Risk Factors

@article {pmid39182301,
year = {2024},
author = {Peruzzo, A and Petrin, S and Boscolo Anzoletti, A and Mancin, M and Di Cesare, A and Sabatino, R and Lavagnolo, MC and Beggio, G and Baggio, G and Danesi, P and Barco, L and Losasso, C},
title = {The integration of omics and cultivation-dependent methods could effectively determine the biological risks associated with the utilization of soil conditioners in agriculture.},
journal = {Journal of hazardous materials},
volume = {478},
number = {},
pages = {135567},
doi = {10.1016/j.jhazmat.2024.135567},
pmid = {39182301},
issn = {1873-3336},
abstract = {In the circular economy, reusing agricultural residues, treated biowaste, and sewage sludges-commonly referred to as soil conditioners-in agriculture is essential for converting waste into valuable resources. However, these materials can also contribute to the spread of antimicrobial-resistant pathogens in treated soils. In this study, we analyzed different soil conditioners categorized into five groups: compost from source-separated biowaste and green waste, agro-industrial digestate, digestate from anaerobic digestion of source-separated biowaste, compost from biowaste digestate, and sludges from wastewater treatment plants. Under Italian law, only the first two categories are approved for agricultural use, despite Regulation 1009/2019/EU allowing the use of digestate from anaerobic digestion of source-separated biowaste in CE-marked fertilizers. We examined the bacterial community and associated resistome of each sample using metagenomic approaches. Additionally, we detected and isolated various pathogens to provide a comprehensive understanding of the potential risks associated with sludge application in agriculture. The compost samples exhibited higher bacterial diversity and a greater abundance of potentially pathogenic bacteria compared to other samples, except for wastewater treatment plant sludges, which had the highest frequency of Salmonella isolation and resistome diversity. Our findings suggest integrating omics and cultivation-dependent methods to accurately assess the biological risks of using sludge in agriculture.},
}

@article {pmid39182227,
year = {2024},
author = {Chilton, PM and Ghare, SS and Charpentier, BT and Myers, SA and Rao, AV and Petrosino, JF and Hoffman, KL and Greenwell, JC and Tyagi, N and Behera, J and Wang, Y and Sloan, LJ and Zhang, J and Shields, CB and Cooper, GE and Gobejishvili, L and Whittemore, SR and McClain, CJ and Barve, SS},
title = {Age-associated temporal decline in butyrate-producing bacteria plays a key pathogenic role in the onset and progression of neuropathology and memory deficits in 3×Tg-AD mice.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2389319},
doi = {10.1080/19490976.2024.2389319},
pmid = {39182227},
issn = {1949-0984},
mesh = {Animals ; *Butyrates/metabolism ; *Gastrointestinal Microbiome ; Mice ; *Alzheimer Disease/microbiology/pathology/metabolism ; *Memory Disorders/microbiology/metabolism/pathology ; *Bacteria/classification/metabolism/genetics/isolation & purification ; *Disease Models, Animal ; *Dysbiosis/microbiology ; Hippocampus/metabolism/pathology ; Mice, Transgenic ; Male ; Disease Progression ; Brain-Gut Axis/physiology ; Brain/metabolism/pathology ; },
abstract = {Alterations in the gut-microbiome-brain axis are increasingly being recognized to be involved in Alzheimer's disease (AD) pathogenesis. However, the functional consequences of enteric dysbiosis linking gut microbiota and brain pathology in AD progression remain largely undetermined. The present work investigated the causal role of age-associated temporal decline in butyrate-producing bacteria and butyrate in the etiopathogenesis of AD. Longitudinal metagenomics, neuropathological, and memory analyses were performed in the 3×Tg-AD mouse model. Metataxonomic analyses showed a significant temporal decline in the alpha diversity marked by a decrease in butyrate-producing bacterial communities and a concurrent reduction in cecal butyrate production. Inferred metagenomics analysis identified the bacterial acetyl-CoA pathway as the main butyrate synthesis pathway impacted. Concomitantly, there was an age-associated decline in the transcriptionally permissive acetylation of histone 3 at lysines 9 and 14 (H3K9/K14-Ac) in hippocampal neurons. Importantly, these microbiome-gut-brain changes preceded AD-related neuropathology, including oxidative stress, tau hyperphosphorylation, memory deficits, and neuromuscular dysfunction, which manifest by 17-18 months. Initiation of oral administration of tributyrin, a butyrate prodrug, at 6 months of age mitigated the age-related decline in butyrate-producing bacteria, protected the H3K9/K14-Ac status, and attenuated the development of neuropathological and cognitive changes associated with AD pathogenesis. These data causally implicate age-associated decline in butyrate-producing bacteria as a key pathogenic feature of the microbiome-gut-brain axis affecting the onset and progression of AD. Importantly, the regulation of butyrate-producing bacteria and consequent butyrate synthesis could be a significant therapeutic strategy in the prevention and treatment of AD.},
}

Animals
*Butyrates/metabolism
*Gastrointestinal Microbiome
Mice
*Alzheimer Disease/microbiology/pathology/metabolism
*Memory Disorders/microbiology/metabolism/pathology
*Bacteria/classification/metabolism/genetics/isolation & purification
*Disease Models, Animal
*Dysbiosis/microbiology
Hippocampus/metabolism/pathology
Mice, Transgenic
Male
Disease Progression
Brain-Gut Axis/physiology
Brain/metabolism/pathology

@article {pmid39182035,
year = {2024},
author = {Velázquez-Fernández, JB and Aceves Suriano, CE and Thalasso, F and Montoya-Ciriaco, N and Dendooven, L},
title = {Structural and functional bacterial biodiversity in a copper, zinc and nickel amended bioreactor: shotgun metagenomic study.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {313},
pmid = {39182035},
issn = {1471-2180},
mesh = {*Bioreactors/microbiology ; *Zinc/metabolism ; *Nickel/metabolism ; *Bacteria/genetics/classification/metabolism/isolation & purification ; *Metagenomics ; *Copper/metabolism ; *Biodiversity ; Wastewater/microbiology/chemistry ; },
abstract = {BACKGROUND: At lower concentrations copper (Cu), zinc (Zn) and nickel (Ni) are trace metals essential for some bacterial enzymes. At higher concentrations they might alter and inhibit microbial functioning in a bioreactor treating wastewater. We investigated the effect of incremental concentrations of Cu, Zn and Ni on the bacterial community structure and their metabolic functions by shotgun metagenomics. Metal concentrations reported in previous studies to inhibit bacterial metabolism were investigated.

RESULTS: At 31.5 μM Cu, 112.4 μM Ni and 122.3 μM Zn, the most abundant bacteria were Achromobacter and Agrobacterium. When the metal concentration increased 2 or fivefold their abundance decreased and members of Delftia, Stenotrophomonas and Sphingomonas dominated. Although the heterotrophic metabolic functions based on the gene profile was not affected when the metal concentration increased, changes in the sulfur biogeochemical cycle were detected. Despite the large variations in the bacterial community structure when concentrations of Cu, Zn and Ni increased in the bioreactor, functional changes in carbon metabolism were small.

CONCLUSIONS: Community richness and diversity replacement indexes decreased significantly with increased metal concentration. Delftia antagonized Pseudomonas and members of Xanthomonadaceae. The relative abundance of most bacterial genes remained unchanged despite a five-fold increase in the metal concentration, but that of some EPS genes required for exopolysaccharide synthesis, and those related to the reduction of nitrite to nitrous oxide decreased which may alter the bioreactor functioning.},
}

*Bioreactors/microbiology
*Zinc/metabolism
*Nickel/metabolism
*Bacteria/genetics/classification/metabolism/isolation & purification
*Metagenomics
*Copper/metabolism
*Biodiversity
Wastewater/microbiology/chemistry

@article {pmid39180208,
year = {2024},
author = {Wang, YC and Jiang, TM and Mo, L and Lu, HZ and Quan, LH and Zhong, P and Guan, Y},
title = {Distribution of Antibiotic-Resistant Genes in Intestines of Infants and Influencing Factors.},
journal = {Critical reviews in eukaryotic gene expression},
volume = {34},
number = {8},
pages = {59-73},
pmid = {39180208},
issn = {1045-4403},
mesh = {Humans ; Female ; *Feces/microbiology ; *Anti-Bacterial Agents/pharmacology ; *Milk, Human/microbiology ; Infant ; Infant, Newborn ; Intestines/microbiology ; Male ; Drug Resistance, Bacterial/genetics ; Genes, Bacterial ; Gastrointestinal Microbiome/genetics/drug effects ; Bacteria/genetics/drug effects ; Drug Resistance, Microbial/genetics ; },
abstract = {The objective of this study is to assess the prevalence of antibiotic-resistant genes (ARGs) in the intestines of infants and the factors affecting their distribution. Breast milk and infant stool samples were collected from nine full-term, healthy mother-infant pairs. The bacterial distribution and various types of ARGs present in the samples were analyzed using metagenomic next-generation sequencing. Over a period spanning from 2 to 240 d after birth, a total of 273 types of ARGs were identified in both infant feces and breast milk, exhibiting a trend of increasing prevalence over time. High concentrations of representative ARG populations were identified in the intestines of infants, especially at 12-15 d after birth. These populations included APH3-Ib, tetW/N/W, mphA, and Haemophilus influenzae PBP3, and multiple ARG Escherichia coli soxS that were resistant to common clinically used aminoglycoside, tetracycline, macrolide, and beta-lactam antibiotics. Gammaproteobacteria and Bacilli, especially Enterococcus, Staphylococcus, Acinetobacter, Streptococcus, and Escherichia were among the identified ARG carriers. Maternal age and body mass index (present and before pregnancy), infant sex, maternal consumption of probiotic yogurt during pregnancy, and lactation might be substantial factors influencing the occurrence of ARG-carrying bacteria and ARG distribution in the infant feces. These results indicate that environmental factors may influence the distribution of ARG-carrying bacteria and ARGs themselves in infants during early life. Providing appropriate recommendations regarding maternal age, body mass index during pregnancy, and use of probiotic products could potentially mitigate the transmission of antibiotic-resistant microbiota and ARGs, thereby diminishing the risk of antibiotic-resistant infections and safeguarding children's health.},
}

Humans
Female
*Feces/microbiology
*Anti-Bacterial Agents/pharmacology
*Milk, Human/microbiology
Infant
Infant, Newborn
Intestines/microbiology
Male
Drug Resistance, Bacterial/genetics
Genes, Bacterial
Gastrointestinal Microbiome/genetics/drug effects
Bacteria/genetics/drug effects
Drug Resistance, Microbial/genetics

@article {pmid39127363,
year = {2024},
author = {Yun, Y and Lv, T and Gui, Z and Su, T and Cao, W and Tian, X and Chen, Y and Wang, S and Jia, Z and Li, G and Ma, T},
title = {Composition and metabolic flexibility of hydrocarbon-degrading consortia in oil reservoirs.},
journal = {Bioresource technology},
volume = {409},
number = {},
pages = {131244},
doi = {10.1016/j.biortech.2024.131244},
pmid = {39127363},
issn = {1873-2976},
mesh = {*Hydrocarbons/metabolism ; *Biodegradation, Environmental ; *Oil and Gas Fields/microbiology ; Microbial Consortia/physiology ; Bacteria/metabolism ; Petroleum/metabolism ; Phylogeny ; },
abstract = {Hydrocarbon-degrading consortia (HDC) play an important role in petroleum exploitation. However, the real composition and metabolic mechanism of HDC in the microbial enhanced oil recovery (MEOR) process remain unclear. By combining [13]C-DNA stable isotope probing microcosms with metagenomics, some newly reported phyla, including Chloroflexi, Synergistetes, Thermotogae, and Planctomycetes, dominated the HDC in the oil reservoirs. In the field trials, the HDC in the aerobic-facultative-anaerobic stage of oilfields jointly promoted the MEOR process, with monthly oil increments of up to 189 tons. Pseudomonas can improve oil recovery by producing rhamnolipid in the facultative condition. Roseovarius was the novel taxa potentially oxidizing alkane and producing acetate to improve oil porosity and permeability in the aerobic condition. Ca. Bacteroidia were the new members potentially degrading hydrocarbons by fumarate addition in the anaerobic environment. Comprehensive identification of the active HDC in oil reservoirs provides a novel theoretical basis for oilfield regulatory scheme.},
}

*Hydrocarbons/metabolism
*Biodegradation, Environmental
*Oil and Gas Fields/microbiology
Microbial Consortia/physiology
Bacteria/metabolism
Petroleum/metabolism
Phylogeny

@article {pmid39122016,
year = {2024},
author = {Fiorucci, S and Marchianò, S and Urbani, G and Di Giorgio, C and Distrutti, E and Zampella, A and Biagioli, M},
title = {Immunology of bile acids regulated receptors.},
journal = {Progress in lipid research},
volume = {95},
number = {},
pages = {101291},
doi = {10.1016/j.plipres.2024.101291},
pmid = {39122016},
issn = {1873-2194},
mesh = {Humans ; *Bile Acids and Salts/metabolism/immunology ; Animals ; Gastrointestinal Microbiome/immunology ; },
abstract = {Bile acids are steroids formed at the interface of host metabolism and intestinal microbiota. While primary bile acids are generated in the liver from cholesterol metabolism, secondary bile acids represent the products of microbial enzymes. Close to 100 different enzymatic modifications of bile acids structures occur in the human intestine and clinically guided metagenomic and metabolomic analyses have led to the identification of an extraordinary number of novel metabolites. These chemical mediators make an essential contribution to the composition and function of the postbiota, participating to the bidirectional communications of the intestinal microbiota with the host and contributing to the architecture of intestinal-liver and -brain and -endocrine axes. Bile acids exert their function by binding to a group of cell membrane and nuclear receptors collectively known as bile acid-regulated receptors (BARRs), expressed in monocytes, tissue-resident macrophages, CD4+ T effector cells, including Th17, T regulatory cells, dendritic cells and type 3 of intestinal lymphoid cells and NKT cells, highlighting their role in immune regulation. In this review we report on how bile acids and their metabolitesmodulate the immune system in inflammations and cancers and could be exploiting for developing novel therapeutic approaches in these disorders.},
}

Humans
*Bile Acids and Salts/metabolism/immunology
Animals
Gastrointestinal Microbiome/immunology

@article {pmid39098060,
year = {2024},
author = {Cojkic, A and Niazi, A and Morrell, JM},
title = {Metagenomic identification of bull semen microbiota in different seasons.},
journal = {Animal reproduction science},
volume = {268},
number = {},
pages = {107569},
doi = {10.1016/j.anireprosci.2024.107569},
pmid = {39098060},
issn = {1873-2232},
mesh = {Male ; Animals ; *Seasons ; Cattle ; *Semen/microbiology ; *Microbiota ; *Semen Analysis/veterinary ; Bacteria/classification/genetics/isolation & purification ; Metagenomics/methods ; Spermatozoa/microbiology ; RNA, Ribosomal, 16S/genetics/analysis ; },
abstract = {A seasonal effect on sperm quality parameters was observed previously. Although identification of the bull semen microbiota by 16S rRNA sequencing was performed previously, it has not been carried out in commercial semen samples from different seasons, and its connection with sperm quality parameters has not been evaluated yet. The objectives in this study were; (i) to evaluate diversity of bull semen microbiota and sperm quality parameters in different seasons, and (ii) to find if specific bacteria were associated with seasonal differences in specific sperm quality parameters. Bull semen microbiota was identified in 54 commercial bull semen samples from 3 seasons (winter, spring, summer). Sperm quality was analysed by Computer Assisted Sperm Analyses (CASA) and Flow Cytometry (FC). From 28 phyla in all samples, six phyla were identified in samples from all seasons, with observed seasonal differences in their distribution. At genus level, 388 genera were identified, of which 22 genera had a relative abundance over 1 % and showed seasonal differences in bacterial diversity, and 9 bacteria genera were present in all seasons. Differences between spring and summer (P < 0.05) were observed for live hydrogen peroxide positive sperm cells. A trend towards significance (0.10 > P > 0.05) was observed for some CASA kinematics (VCL and LIN) and FC parameters (High respiratory activity, and live hydrogen peroxide positive sperm cells) between seasons. Nevertheless, associations between sperm quality parameters and specific bacteria were observed in spring.},
}

Male
Animals
*Seasons
Cattle
*Semen/microbiology
*Microbiota
*Semen Analysis/veterinary
Bacteria/classification/genetics/isolation & purification
Metagenomics/methods
Spermatozoa/microbiology
RNA, Ribosomal, 16S/genetics/analysis

@article {pmid39024692,
year = {2024},
author = {Chen, L and Bao, Y and Wang, D and Tian, Y and Zeng, T and Gu, T and Xu, W and Lu, L},
title = {Integrated omics analysis reveals the differentiation of intestinal microbiota and metabolites between Pekin ducks and Shaoxing ducks.},
journal = {Poultry science},
volume = {103},
number = {9},
pages = {103976},
pmid = {39024692},
issn = {1525-3171},
mesh = {Animals ; *Ducks ; *Gastrointestinal Microbiome ; Metabolome ; Metabolomics ; Metagenome ; Metagenomics ; Bacteria/classification/genetics/metabolism/isolation & purification ; },
abstract = {Pekin ducks and Shaoxing ducks are 2 Chinese local duck breeds, both domesticated from mallard, but after domestication and long-term artificial selection, the body weight of Pekin ducks is significantly higher than that of Shaoxing ducks. It is no debate that genetic factors are the main factors responsible for this difference, but whether intestinal microbiota contribute to this difference is yet unknown. Thus, we performed comparative intestinal metagenomics and metabolomics analysis between Pekin ducks and Shaoxing ducks. We found obvious differentiation of intestinal metagenome and metabolome between the 2 breeds. Four cecal microbial genera, including Fusobacterium, Methanobrevibacter, Butyricicoccus, and Anaerotignum showed higher abundance in Pekin ducks. Among them, Methanobrevibacter and Butyricicoccus may positively correlate with fat deposition and body weight. A total of 310 metabolites showed difference between the 2 breeds. Functions of these differential metabolites were mainly enriched in amino acid metabolism, including energy metabolism-related histidine metabolism. Integrated omics analysis showed that microbial changes were closely related to altered metabolites. Especially, Butyricicoccus showing higher abundance in Pekin ducks was significantly negatively correlated with D-glucosamine-6-phosphate, which has been reported to prevent body weight gains. These findings may contribute to further understand the difference in body weight between Pekin ducks and Shaoxing ducks.},
}

Animals
*Ducks
*Gastrointestinal Microbiome
Metabolome
Metabolomics
Metagenome
Metagenomics
Bacteria/classification/genetics/metabolism/isolation & purification

@article {pmid38945001,
year = {2024},
author = {Schäfer, L and Grundmann, SM and Rühl, M and Zorn, H and Seel, W and Simon, MC and Schuchardt, S and Most, E and Ringseis, R and Eder, K},
title = {Effects of a biotechnologically produced Pleurotus sapidus mycelium on gut microbiome, liver transcriptome and plasma metabolome of broilers.},
journal = {Poultry science},
volume = {103},
number = {9},
pages = {103975},
pmid = {38945001},
issn = {1525-3171},
mesh = {Animals ; *Chickens ; *Gastrointestinal Microbiome ; *Pleurotus ; *Animal Feed/analysis ; Male ; *Transcriptome ; *Liver/metabolism ; *Diet/veterinary ; *Metabolome ; *Mycelium ; *Dietary Supplements/analysis ; Random Allocation ; },
abstract = {Submerged cultivation using low-value agro-industrial side streams allows large-scale and efficient production of fungal mycelia, which has a high nutritional value. As the dietary properties of fungal mycelia in poultry are largely unknown, the present study aimed to investigate the effect of feeding a Pleurotus sapidus (PSA) mycelium as a feed supplement on growth performance, composition of the cecal microbiota and several physiological traits including gut integrity, nutrient digestibility, liver lipids, liver transcriptome and plasma metabolome in broilers. 72 males, 1-day-old Cobb 500 broilers were randomly assigned to 3 different groups and fed 3 different adequate diets containing either 0% (PSA-0), 2.5% (PSA-2.5) and 5% (PSA-5.0) P. sapidus mycelium in a 3-phase feeding system for 35 d. Each group consisted of 6 cages (replicates) with 4 broilers/cage. Body weight gain, feed intake and feed:gain ratio and apparent ileal digestibility of crude protein, ether extract and amino acids were not different between groups. Metagenomic analysis of the cecal microbiota revealed no differences between groups, except that one α-diversity metric (Shannon index) and the abundance of 2 low-abundance bacterial taxa (Clostridia UCG 014, Eubacteriales) differed between groups (P < 0.05). Concentrations of total and individual short-chain fatty acids in the cecal digesta and concentrations of plasma lipopolysaccharide and mRNA levels of proinflammatory genes, tight-junction proteins, and mucins in the cecum mucosa did not differ between groups. None of the plasma metabolites analyzed using targeted-metabolomics differed across the groups. Hepatic transcript profiling revealed a total of 144 transcripts to be differentially expressed between group PSA-5.0 and group PSA-0 but none of these genes was regulated greater 2-fold. Considering either the lack of effects or the very weak effects of feeding the P. sapidus mycelium in the broilers it can be concluded that inclusion of a sustainably produced fungal mycelium in broiler diets at the expense of other feed components has no negative consequences on broilers´ performance and metabolism.},
}

Animals
*Chickens
*Gastrointestinal Microbiome
*Pleurotus
*Animal Feed/analysis
Male
*Transcriptome
*Liver/metabolism
*Diet/veterinary
*Metabolome
*Mycelium
*Dietary Supplements/analysis
Random Allocation

@article {pmid38755047,
year = {2024},
author = {Wang, Y and Yao, J and Zhu, Y and Yin, Z and Zhao, X},
title = {Combination of Simo Decoction and Golden Bifid alleviates functional dyspepsia through a mechanism involving intestinal microbiota and short-chain fatty acids.},
journal = {Arab journal of gastroenterology : the official publication of the Pan-Arab Association of Gastroenterology},
volume = {25},
number = {3},
pages = {239-249},
doi = {10.1016/j.ajg.2023.12.009},
pmid = {38755047},
issn = {2090-2387},
mesh = {Animals ; *Fatty Acids, Volatile/metabolism ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Drugs, Chinese Herbal/pharmacology ; *Dyspepsia/drug therapy/metabolism/microbiology ; *Disease Models, Animal ; Male ; Duodenum/metabolism/microbiology ; Intestinal Mucosa/metabolism/drug effects ; Colon/metabolism ; Drug Therapy, Combination ; },
abstract = {BACKGROUND AND STUDY AIMS: The integration of traditional Chinese medicine and Western medicine holds promise for the treatment of gastrointestinal disorders, which are influenced by intestinal microbiota and metabolites. This study reports a possible mechanism for the combination of Simo Decoction and Golden Bifid in functional dyspepsia (FD) by regulating intestinal microbiota and short-chain fatty acids (SCFAs).

PATIENTS AND METHODS: A mouse model of food stagnation was constructed and treated with Simo Decoction combined with different concentrations of Golden Bifid. Meta-genomics sequencing was conducted to analyze the cecum contents of the mice. Following analyses of the composition and abundance of intestinal microbiota, gas chromatography-mass spectrometry was performed to measure SCFAs in the colonic content of mice. Finally, ELISA was utilized to determine the levels of pro-inflammatory factors in the duodenal mucosa of mice and the infiltration of eosinophils in the duodenum was observed by immunohistochemical staining.

RESULTS: Combination of Simo Decoction and Golden Bifid more significantly alleviated dyspepsia in mice with food stagnation compared with Simo Decoction alone. The optimal ratio of combined treatment was 0.0075 mL/g (body weight) Simo Decoction and 0.0032 mg/g (body weight) Golden Bifid. The combined treatment increased the abundance of Bifidobacterium and Bacteroides in the intestine. The levels of SCFAs in the colonic contents of mice were increased after the combined treatment, contributing to diminished pro-inflammatory factors in the duodenal mucosa and reduced eosinophil infiltration.

CONCLUSION: Combination of Simo Decoction and Golden Bifid increases the abundance of Bacteroides and Bifidobacterium and promotes the production of SCFAs, which is instrumental for alleviation of FD.},
}

Animals
*Fatty Acids, Volatile/metabolism
*Gastrointestinal Microbiome/drug effects
Mice
*Drugs, Chinese Herbal/pharmacology
*Dyspepsia/drug therapy/metabolism/microbiology
*Disease Models, Animal
Male
Duodenum/metabolism/microbiology
Intestinal Mucosa/metabolism/drug effects
Colon/metabolism
Drug Therapy, Combination

@article {pmid39180123,
year = {2024},
author = {Horigan, S and Kettenburg, G and Kistler, A and Ranaivoson, HC and Andrianiaina, A and Andry, S and Raharinosy, V and Randriambolamanantsoa, TH and Tato, CM and Lacoste, V and Heraud, JM and Dussart, P and Brook, CE},
title = {Detection, characterization, and phylogenetic analysis of novel astroviruses from endemic Malagasy fruit bats.},
journal = {Virology journal},
volume = {21},
number = {1},
pages = {195},
pmid = {39180123},
issn = {1743-422X},
support = {1R01A|129822-01/NH/NIH HHS/United States ; GCE/ID OPP1211841//Bill and Melinda Gates Foundation/ ; PREEMPT Program Cooperative Agreement no D18AC00031//Defense Sciences Office, DARPA/ ; },
mesh = {Animals ; *Chiroptera/virology ; *Phylogeny ; *Astroviridae/genetics/isolation & purification/classification ; *Astroviridae Infections/veterinary/virology/epidemiology ; *Metagenomics ; High-Throughput Nucleotide Sequencing ; Madagascar ; Genome, Viral/genetics ; Sequence Analysis, DNA ; },
abstract = {Bats (order: Chiroptera) are known to host a diverse range of viruses, some of which present a human public health risk. Thorough viral surveillance is therefore essential to predict and potentially mitigate zoonotic spillover. Astroviruses (family: Astroviridae) are an understudied group of viruses with a growing amount of indirect evidence for zoonotic transfer. Astroviruses have been detected in bats with significant prevalence and diversity, suggesting that bats may act as important astrovirus hosts. Most astrovirus surveillance in wild bat hosts has, to date, been restricted to single-gene PCR detection and concomitant Sanger sequencing; additionally, many bat species and many geographic regions have not yet been surveyed for astroviruses at all. Here, we use metagenomic Next Generation Sequencing (mNGS) to detect astroviruses in three species of Madagascar fruit bats, Eidolon dupreanum, Pteropus rufus, and Rousettus madagascariensis. We detect numerous partial sequences from all three species and one near-full length astrovirus sequence from Rousettus madagascariensis, which we use to characterize the evolutionary history of astroviruses both within bats and the broader mammalian clade, Mamastrovirus. Taken together, applications of mNGS implicate bats as important astrovirus hosts and demonstrate novel patterns of bat astrovirus evolutionary history, particularly in the Southwest Indian Ocean region.},
}

Animals
*Chiroptera/virology
*Phylogeny
*Astroviridae/genetics/isolation & purification/classification
*Astroviridae Infections/veterinary/virology/epidemiology
*Metagenomics
High-Throughput Nucleotide Sequencing
Madagascar
Genome, Viral/genetics
Sequence Analysis, DNA

@article {pmid39180058,
year = {2024},
author = {Hua, X and McGoldrick, J and Nakrour, N and Staller, K and Chung, DC and Xavier, RJ and Khalili, H},
title = {Gut microbiome structure and function in asymptomatic diverticulosis.},
journal = {Genome medicine},
volume = {16},
number = {1},
pages = {105},
pmid = {39180058},
issn = {1756-994X},
support = {R01 AG068390/AG/NIA NIH HHS/United States ; DK043351//Center for the study of inflammatory bowel disease/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; Female ; Middle Aged ; Aged ; Metagenomics/methods ; Colonoscopy ; Metagenome ; Bacteria/classification/genetics ; },
abstract = {BACKGROUND: Colonic diverticulosis, the most common lesion found in routine colonoscopy, affects more than 50% of individuals aged ≥ 60 years. Emerging evidence suggest that dysbiosis of gut microbiota may play an important role in the pathophysiology of diverticular disease. However, specific changes in microbial species and metabolic functions in asymptomatic diverticulosis remain unknown.

METHODS: In a cohort of US adults undergoing screening colonoscopy, we analyzed the gut microbiota using shotgun metagenomic sequencing. Demographic factors, lifestyle, and medication use were assessed using a baseline questionnaire administered prior to colonoscopy. Taxonomic structures and metabolic pathway abundances were determined using MetaPhlAn3 and HUMAnN3. We used multivariate association with linear models to identify microbial species and metabolic pathways that were significantly different between asymptomatic diverticulosis and controls, while adjusting for confounders selected a priori including age at colonoscopy, sex, body mass index (BMI), and dietary pattern.

RESULTS: Among 684 individuals undergoing a screening colonoscopy, 284 (42%) had diverticulosis. Gut microbiome composition explained 1.9% variation in the disease status of asymptomatic diverticulosis. We observed no significant differences in the overall diversity of gut microbiome between asymptomatic diverticulosis and controls. However, microbial species Bifidobacterium pseudocatenulatum and Prevotella copri were significantly enriched in controls (q value = 0.19 and 0.14, respectively), whereas Roseburia intestinalis, Dorea sp. CAG:317, and Clostridium sp. CAG: 299 were more abundant in those with diverticulosis (q values = 0.17, 0.24, and 0.10, respectively). We observed that the relationship between BMI and diverticulosis appeared to be limited to carriers of Bifidobacterium pseudocatenulatum and Roseburia intestinalis (Pinteraction = 0.09).

CONCLUSIONS: Our study provides the first large-scale evidence supporting taxonomic and functional shifts of the gut microbiome in individuals with asymptomatic diverticulosis. The suggestive interaction between gut microbiota and BMI on prevalent diverticulosis deserves future investigations.},
}

Humans
*Gastrointestinal Microbiome
Male
Female
Middle Aged
Aged
Metagenomics/methods
Colonoscopy
Metagenome
Bacteria/classification/genetics

@article {pmid39178288,
year = {2024},
author = {Buscaglia, M and Iriarte, JL and Schulz, F and Díez, B},
title = {Adaptation strategies of giant viruses to low-temperature marine ecosystems.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrae162},
pmid = {39178288},
issn = {1751-7370},
abstract = {Microbes in marine ecosystems have evolved their gene content to thrive successfully in the cold. Although this process has been reasonably well studied in bacteria and selected eukaryotes, less is known about the impact of cold environments on the genomes of viruses that infect eukaryotes. Here, we analyzed cold adaptations in giant viruses (Nucleocytoviricota and Mirusviricota) from austral marine environments and compared them with their Arctic and temperate counterparts. We recovered giant virus metagenome-assembled genomes (98 Nucleocytoviricota and 12 Mirusviricota MAGs) from 61 newly sequenced metagenomes and metaviromes from sub-Antarctic Patagonian fjords and Antarctic seawater samples. When analyzing our data set alongside Antarctic and Arctic giant viruses MAGs already deposited in the Global Ocean Eukaryotic Viral (GOEV) database, we found that Antarctic and Arctic giant viruses predominantly inhabit sub-10°C environments, featuring a high proportion of unique phylotypes in each ecosystem. In contrast, giant viruses in Patagonian fjords were subject to broader temperature ranges and showed a lower degree of endemicity. However, despite differences in their distribution, giant viruses inhabiting low-temperature marine ecosystems evolved genomic cold-adaptation strategies that led to changes in genetic functions and amino acid frequencies that ultimately affect both gene content and protein structure. Such changes seem to be absent in their mesophilic counterparts. The uniqueness of these cold-adapted marine giant viruses may now be threatened by climate change, leading to a potential reduction in their biodiversity.},
}

@article {pmid39103543,
year = {2024},
author = {Li, HZ and Peng, J and Yang, K and Zhang, Y and Chen, QL and Zhu, YG and Cui, L},
title = {Single-cell exploration of active phosphate-solubilizing bacteria across diverse soil matrices for sustainable phosphorus management.},
journal = {Nature food},
volume = {5},
number = {8},
pages = {673-683},
pmid = {39103543},
issn = {2662-1355},
support = {42021005//National Natural Science Foundation of China (National Science Foundation of China)/ ; 22241603//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Soil Microbiology ; *Phosphorus/metabolism ; *Bacteria/metabolism/genetics ; *Phosphates/metabolism ; *Soil/chemistry ; *Fertilizers/analysis ; Single-Cell Analysis ; Microbiota/physiology ; Solubility ; },
abstract = {Phosphate-solubilizing bacteria (PSB) are crucial for enhancing phosphorus bioavailability and regulating phosphorus transformation processes. However, the in situ phosphorus-solubilizing activity and the link between phenotypes and genotypes for PSB remain unidentified. Here we employed single-cell Raman spectroscopy combined with heavy water to discern and quantify soil active PSB. Our results reveal that PSB abundance and in situ activity differed significantly between soil types and fertilization treatments. Inorganic fertilizer input was the key driver for active PSB distribution. Targeted single-cell sorting and metagenomic sequencing of active PSB uncovered several low-abundance genera that are easily overlooked within bulk soil microbiota. We elucidate the underlying functional genes and metabolic pathway, and the interplay between phosphorus and carbon cycling involved in high phosphorus solubilization activity. Our study provides a single-cell approach to exploring PSB from native environments, enabling the development of a microbial solution for the efficient agronomic use of phosphorus and mitigating the phosphorus crisis.},
}

*Soil Microbiology
*Phosphorus/metabolism
*Bacteria/metabolism/genetics
*Phosphates/metabolism
*Soil/chemistry
*Fertilizers/analysis
Single-Cell Analysis
Microbiota/physiology
Solubility

@article {pmid39094546,
year = {2024},
author = {Li, Q and Wang, J and Lv, J and Liu, D and Xiao, S and Mo, J and Lu, Z and Qiu, R and Li, C and Tang, L and He, S and Tang, Z and Cheng, Q and Zhan, T},
title = {Total flavonoids of litchi Seed alleviates schistosomiasis liver fibrosis in mice by suppressing hepatic stellate cells activation and modulating the gut microbiomes.},
journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie},
volume = {178},
number = {},
pages = {117240},
doi = {10.1016/j.biopha.2024.117240},
pmid = {39094546},
issn = {1950-6007},
mesh = {Animals ; *Hepatic Stellate Cells/drug effects/metabolism/pathology ; *Liver Cirrhosis/drug therapy/parasitology/pathology ; *Gastrointestinal Microbiome/drug effects ; *Flavonoids/pharmacology ; Mice ; *Litchi/chemistry ; *Seeds/chemistry ; Schistosomiasis japonica/drug therapy/complications ; Cytokines/metabolism ; Schistosoma japonicum/drug effects/pathogenicity ; Male ; Liver/drug effects/pathology/parasitology ; },
abstract = {Infection with Schistosoma japonicum (S. japonicum) is an important zoonotic parasitic disease that causes liver fibrosis in both human and domestic animals. The activation of hepatic stellate cells (HSCs) is a crucial phase in the development of liver fibrosis, and inhibiting their activation can alleviate this progression. Total flavonoids of litchi seed (TFL) is a naturally extracted drug, and modern pharmacological studies have shown its anti-fibrotic and liver-protective effects. However, the role of TFL in schistosomiasis liver fibrosis is still unclear. This study investigated the therapeutic effects of TFL on liver fibrosis in S. japonicum infected mice and explored its potential mechanisms. Animal study results showed that TFL significantly reduced the levels of Interleukin-1β (IL-1β), Tumor Necrosis Factor-α (TNF-α), Interleukin-4 (IL-4), and Interleukin-6 (IL-6) in the serum of S. japonicum infected mice. TFL reduced the spleen index of mice and markedly improved the pathological changes in liver tissues induced by S. japonicum infection, decreasing the expression of alpha-smooth muscle actin (α-SMA), Collagen I and Collagen III protein in liver tissues. In vitro studies indicated that TFL also inhibited the activation of HCSs induced by Transforming Growth Factor-β1 (TGF-β1) and reduced the levels of α-SMA. Gut microbes metagenomics study revealed that the composition, abundance, and functions of the mice gut microbiomes changed significantly after S. japonicum infection, and TLF treatment reversed these changes. Therefore, our study indicated that TFL alleviated granulomatous lesions and improved S. japonicum induced liver fibrosis in mice by inhibiting the activation of HSCs and by improving the gut microbiomes.},
}

Animals
*Hepatic Stellate Cells/drug effects/metabolism/pathology
*Liver Cirrhosis/drug therapy/parasitology/pathology
*Gastrointestinal Microbiome/drug effects
*Flavonoids/pharmacology
Mice
*Litchi/chemistry
*Seeds/chemistry
Schistosomiasis japonica/drug therapy/complications
Cytokines/metabolism
Schistosoma japonicum/drug effects/pathogenicity
Male
Liver/drug effects/pathology/parasitology

@article {pmid38981480,
year = {2024},
author = {Piperni, E and Nguyen, LH and Manghi, P and Kim, H and Pasolli, E and Andreu-Sánchez, S and Arrè, A and Bermingham, KM and Blanco-Míguez, A and Manara, S and Valles-Colomer, M and Bakker, E and Busonero, F and Davies, R and Fiorillo, E and Giordano, F and Hadjigeorgiou, G and Leeming, ER and Lobina, M and Masala, M and Maschio, A and McIver, LJ and Pala, M and Pitzalis, M and Wolf, J and Fu, J and Zhernakova, A and Cacciò, SM and Cucca, F and Berry, SE and Ercolini, D and Chan, AT and Huttenhower, C and Spector, TD and Segata, N and Asnicar, F},
title = {Intestinal Blastocystis is linked to healthier diets and more favorable cardiometabolic outcomes in 56,989 individuals from 32 countries.},
journal = {Cell},
volume = {187},
number = {17},
pages = {4554-4570.e18},
doi = {10.1016/j.cell.2024.06.018},
pmid = {38981480},
issn = {1097-4172},
mesh = {Humans ; *Blastocystis/metabolism ; *Gastrointestinal Microbiome ; *Diet ; Male ; *Obesity ; Female ; Blastocystis Infections ; Adult ; Middle Aged ; Intestines/parasitology/microbiology ; Cardiovascular Diseases/prevention & control ; Metagenome ; },
abstract = {Diet impacts human health, influencing body adiposity and the risk of developing cardiometabolic diseases. The gut microbiome is a key player in the diet-health axis, but while its bacterial fraction is widely studied, the role of micro-eukaryotes, including Blastocystis, is underexplored. We performed a global-scale analysis on 56,989 metagenomes and showed that human Blastocystis exhibits distinct prevalence patterns linked to geography, lifestyle, and dietary habits. Blastocystis presence defined a specific bacterial signature and was positively associated with more favorable cardiometabolic profiles and negatively with obesity (p < 1e-16) and disorders linked to altered gut ecology (p < 1e-8). In a diet intervention study involving 1,124 individuals, improvements in dietary quality were linked to weight loss and increases in Blastocystis prevalence (p = 0.003) and abundance (p < 1e-7). Our findings suggest a potentially beneficial role for Blastocystis, which may help explain personalized host responses to diet and downstream disease etiopathogenesis.},
}

Humans
*Blastocystis/metabolism
*Gastrointestinal Microbiome
*Diet
Male
*Obesity
Female
Blastocystis Infections
Adult
Middle Aged
Intestines/parasitology/microbiology
Cardiovascular Diseases/prevention & control
Metagenome

@article {pmid38945213,
year = {2024},
author = {Si, HR and Wu, K and Su, J and Dong, TY and Zhu, Y and Li, B and Chen, Y and Li, Y and Shi, ZL and Zhou, P},
title = {Individual virome analysis reveals the general co-infection of mammal-associated viruses with SARS-related coronaviruses in bats.},
journal = {Virologica Sinica},
volume = {39},
number = {4},
pages = {565-573},
doi = {10.1016/j.virs.2024.06.008},
pmid = {38945213},
issn = {1995-820X},
mesh = {*Chiroptera/virology ; Animals ; *Virome ; China ; *Coinfection/virology/veterinary/microbiology ; *Metagenomics ; *Severe acute respiratory syndrome-related coronavirus/genetics/isolation & purification/classification ; Phylogeny ; Genome, Viral/genetics ; Disease Reservoirs/virology ; },
abstract = {Bats are the natural reservoir hosts for SARS-related coronavirus (SARSr-CoV) and other highly pathogenic microorganisms. Therefore, it is conceivable that an individual bat may harbor multiple microbes. However, there is limited knowledge on the overall co-circulation of microorganisms in bats. Here, we conducted a 16-year monitoring of bat viruses in south and central China and identified 238 SARSr-CoV positive samples across nine bat species from ten provinces or administrative districts. Among these, 76 individual samples were selected for further metagenomics analysis. We found a complex microenvironment characterized by the general co-circulation of microbes from two different sources: mammal-associated viruses or environment-associated microbes. The later includes commensal bacteria, enterobacteria-related phages, and insect or fungal viruses of food origin. Results showed that 25% (19/76) of the samples contained at least one another mammal-associated virus, notably alphacoronaviruses (13/76) such as AlphaCoV/YN2012, HKU2-related CoV and AlphaCoV/Rf-HuB2013, along with viruses from other families. Notably, we observed three viruses co-circulating within a single bat, comprising two coronavirus species and one picornavirus. Our analysis also revealed the potential presence of pathogenic bacteria or fungi in bats. Furthermore, we obtained 25 viral genomes from the 76 bat SARSr-CoV positive samples, some of which formed new evolutionary lineages. Collectively, our study reveals the complex microenvironment of bat microbiome, facilitating deeper investigations into their pathogenic potential and the likelihood of cross-species transmission.},
}

*Chiroptera/virology
Animals
*Virome
China
*Coinfection/virology/veterinary/microbiology
*Metagenomics
*Severe acute respiratory syndrome-related coronavirus/genetics/isolation & purification/classification
Phylogeny
Genome, Viral/genetics
Disease Reservoirs/virology

@article {pmid38909766,
year = {2024},
author = {Heil, BA and van Heule, M and Thompson, SK and Kearns, TA and Beckers, KF and Oberhaus, EL and King, G and Daels, P and Dini, P and Sones, JL},
title = {Metagenomic characterization of the equine endometrial microbiome during anestrus.},
journal = {Journal of equine veterinary science},
volume = {140},
number = {},
pages = {105134},
doi = {10.1016/j.jevs.2024.105134},
pmid = {38909766},
issn = {0737-0806},
mesh = {Animals ; Horses/microbiology ; Female ; *Endometrium/microbiology ; *Microbiota/genetics ; *Anestrus ; Bacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Estrus/physiology ; RNA, Bacterial/genetics/analysis ; },
abstract = {The equine uterus is highly interrogated during estrus prior to breeding and establishing pregnancy. Many studies in mares have been performed during estrus under the influence of high estrogen concentrations, including the equine estrual microbiome. To date, it is unknown how the uterine microbiome of the mare is influenced by cyclicity; while, the equine vaginal microbiome is stable throughout the estrous cycle. We hypothesized that differences would exist between the equine endometrial microbiome of mares in estrus and anestrus. The aim of this study was two-fold: to characterize the resident endometrial microbiome of healthy mares during anestrus and to compare this with estrus. Double-guarded endometrial swabs were taken from healthy mares during estrus (n = 16) and in the following non-breeding season during anestrus (n = 8). Microbial population was identified using 16S rRNA sequencing. Our results suggest that the equine uterine microbiome in estrus has a low diversity and low richness, while during anestrus, a higher diversity and higher richness were seen compared to estrus. Despite this difference, both the estrus and anestrus endometrial microbiome were dominated by Proteobacteria, Firmicutes, and Bacteroidota. The composition of the microbial community between anestrus and estrus was significantly different. This may be explained by the difference in the composition of the endometrial immune milieu based on the stage of the cycle. Further research investigating the function of the equine endometrial microbiome and dynamics changes within the uterine environment is required.},
}

Animals
Horses/microbiology
Female
*Endometrium/microbiology
*Microbiota/genetics
*Anestrus
Bacteria/classification/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics
Estrus/physiology
RNA, Bacterial/genetics/analysis

@article {pmid38679334,
year = {2024},
author = {Fang, Y and Wang, J and Sun, J and Su, Z and Chen, S and Xiao, J and Ni, J and Hu, Z and He, Y and Shen, S and Deng, F},
title = {RNA viromes of Dermacentor nuttalli ticks reveal a novel uukuvirus in Qīnghăi Province, China.},
journal = {Virologica Sinica},
volume = {39},
number = {4},
pages = {537-545},
doi = {10.1016/j.virs.2024.04.006},
pmid = {38679334},
issn = {1995-820X},
mesh = {Animals ; *Dermacentor/virology ; China ; *Phylogeny ; *Virome/genetics ; *Genome, Viral/genetics ; RNA, Viral/genetics ; High-Throughput Nucleotide Sequencing ; Metagenomics ; RNA Viruses/genetics/classification/isolation & purification ; Bunyaviridae/genetics/classification/isolation & purification ; },
abstract = {Ticks are a major parasite on the Qīnghăi-Tibet Plateau, western China, and represent an economic burden to agriculture and animal husbandry. Despite research on tick-borne pathogens that threaten humans and animals, the viromes of dominant tick species in this area remain unknown. In this study, we collected Dermacentor nuttalli ticks near Qīnghăi Lake and identified 13 viruses belonging to at least six families through metagenomic sequencing. Four viruses were of high abundance in pools, including Xīnjiāng tick-associated virus 1 (XJTAV1), and three novel viruses: Qīnghăi Lake virus 1, Qīnghăi Lake virus 2 (QHLV1, and QHLV2, unclassified), and Qīnghăi Lake virus 3 (QHLV3, genus Uukuvirus of family Phenuiviridae in order Bunyavirales), which lacks the M segment. The minimum infection rates of the four viruses in the tick groups were 8.2%, 49.5%, 6.2%, and 24.7%, respectively, suggesting the prevalence of these viruses in D. nuttalli ticks. A putative M segment of QHLV3 was identified from the next-generation sequencing data and further characterized for its signal peptide cleavage site, N-glycosylation, and transmembrane region. Furthermore, we probed the L, M, and S segments of other viruses from sequencing data of other tick pools by using the putative M segment sequence of QHLV3. By revealing the viromes of D. nuttalli ticks, this study enhances our understanding of tick-borne viral communities in highland regions. The putative M segment identified in a novel uukuvirus suggests that previously identified uukuviruses without M segments should have had the same genome organization as typical bunyaviruses. These findings will facilitate virus discovery and our understanding of the phylogeny of tick-borne uukuviruses.},
}

Animals
*Dermacentor/virology
China
*Phylogeny
*Virome/genetics
*Genome, Viral/genetics
RNA, Viral/genetics
High-Throughput Nucleotide Sequencing
Metagenomics
RNA Viruses/genetics/classification/isolation & purification
Bunyaviridae/genetics/classification/isolation & purification

@article {pmid39177227,
year = {2024},
author = {Deng, Y and Nong, Z and Wei, M and Xu, Y and Luo, Y and Li, X and Zhao, R and Yang, Z and Pan, L},
title = {Characteristics and function of the gut microbiota in patients with IgA nephropathy via metagenomic sequencing technology.},
journal = {Renal failure},
volume = {46},
number = {2},
pages = {2393754},
doi = {10.1080/0886022X.2024.2393754},
pmid = {39177227},
issn = {1525-6049},
mesh = {Humans ; *Glomerulonephritis, IGA/microbiology ; *Gastrointestinal Microbiome/genetics ; Male ; Female ; Adult ; *Feces/microbiology ; *Metagenomics/methods ; Case-Control Studies ; Middle Aged ; Moraxella/isolation & purification/genetics ; Escherichia coli/isolation & purification/genetics ; Acinetobacter/isolation & purification/genetics ; Metagenome ; Young Adult ; },
abstract = {OBJECTIVE: The aim of this study was to investigate the characteristics and related functional pathways of the gut microbiota in patients with IgA nephropathy (IgAN) through metagenomic sequencing technology.

METHODS: We enrolled individuals with primary IgAN, including patients with normal and abnormal renal function. Additionally, we recruited healthy volunteers as the healthy control group. Stool samples were collected, and species and functional annotation were performed through fecal metagenome sequencing. We employed linear discriminant analysis effect size (LEfSe) analysis to identify significantly different bacterial microbiota and functional pathways. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis was used to annotate microbiota functions, and redundancy analysis (RDA) was performed to analyze the factors affecting the composition and distribution of the gut microbiota.

RESULTS: LEfSe analysis revealed differences in the gut microbiota between IgAN patients and healthy controls. The characteristic microorganisms in the IgAN group were classified as Escherichia coli, with a significantly greater abundance than that in the healthy control group (p < 0.05). The characteristic microorganisms in the IgAN group with abnormal renal function were identified as Enterococcaceae, Moraxella, Moraxella, and Acinetobacter. KEGG functional analysis demonstrated that the functional pathways of the microbiota that differed between IgAN patients and healthy controls were related primarily to bile acid metabolism.

CONCLUSIONS: The status of the gut microbiota is closely associated not only with the onset of IgAN but also with the renal function of IgAN patients. The characteristic gut microbiota may serve as a promising diagnostic biomarker and therapeutic target for IgAN.},
}

Humans
*Glomerulonephritis, IGA/microbiology
*Gastrointestinal Microbiome/genetics
Male
Female
Adult
*Feces/microbiology
*Metagenomics/methods
Case-Control Studies
Middle Aged
Moraxella/isolation & purification/genetics
Escherichia coli/isolation & purification/genetics
Acinetobacter/isolation & purification/genetics
Metagenome
Young Adult

@article {pmid39175056,
year = {2024},
author = {Sbardellati, DL and Vannette, RL},
title = {Targeted viromes and total metagenomes capture distinct components of bee gut phage communities.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {155},
pmid = {39175056},
issn = {2049-2618},
support = {2023-67011-40501//U.S. Department of Agriculture/ ; 1929516//National Science Foundation/ ; },
mesh = {Bees/virology/microbiology ; Animals ; *Bacteriophages/genetics/isolation & purification/classification ; *Virome ; *Metagenome ; Gastrointestinal Microbiome/genetics ; Metagenomics/methods ; Gastrointestinal Tract/microbiology/virology ; },
abstract = {BACKGROUND: Despite being among the most abundant biological entities on earth, bacteriophage (phage) remain an understudied component of host-associated systems. One limitation to studying host-associated phage is the lack of consensus on methods for sampling phage communities. Here, we compare paired total metagenomes and viral size fraction metagenomes (viromes) as methods for investigating the dsDNA viral communities associated with the GI tract of two bee species: the European honey bee Apis mellifera and the eastern bumble bee Bombus impatiens.

RESULTS: We find that viromes successfully enriched for phage, thereby increasing phage recovery, but only in honey bees. In contrast, for bumble bees, total metagenomes recovered greater phage diversity. Across both bee species, viromes better sampled low occupancy phage, while total metagenomes were biased towards sampling temperate phage. Additionally, many of the phage captured by total metagenomes were absent altogether from viromes. Comparing between bees, we show that phage communities in commercially reared bumble bees are significantly reduced in diversity compared to honey bees, likely reflecting differences in bacterial titer and diversity. In a broader context, these results highlight the complementary nature of total metagenomes and targeted viromes, especially when applied to host-associated environments.

CONCLUSIONS: Overall, we suggest that studies interested in assessing total communities of host-associated phage should consider using both approaches. However, given the constraints of virome sampling, total metagenomes may serve to sample phage communities with the understanding that they will preferentially sample dominant and temperate phage. Video Abstract.},
}

Bees/virology/microbiology
Animals
*Bacteriophages/genetics/isolation & purification/classification
*Virome
*Metagenome
Gastrointestinal Microbiome/genetics
Metagenomics/methods
Gastrointestinal Tract/microbiology/virology

@article {pmid39174663,
year = {2024},
author = {Jafari, M and Moghimi, H and Tirandaz, H and Ebrahim-Habibi, MB},
title = {Corrosion behavior of predominant Halodesulfovibrio in a marine SRB consortium and its mitigation using ZnO nanoparticles.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {19545},
pmid = {39174663},
issn = {2045-2322},
mesh = {Corrosion ; *Zinc Oxide/chemistry/pharmacology ; *Biofilms/drug effects ; *Bioreactors/microbiology ; Steel/chemistry ; Nanoparticles/chemistry ; Microbial Consortia/drug effects ; },
abstract = {Formation of Sulfate Reducing Bacteria (SRB) biofilm accelerates microbiologically influenced corrosion (MIC). The aim of this study was to investigate both the corrosivity of a marine SRB consortium on carbon steel coupons and its mitigation in the presence of ZnO. Metagenomics analysis revealed that Halodesulfovibrio (78.9%) was predominant and could be related to MIC. The analysis also showed a remarkable shift from a highly corrosive SRB consortium in the control bioreactors to a far less corrosive consortium when ZnO was added to the bioreactors. Further results indicated that the corrosion rate of the SRB consortium was 8.17 mpy on the carbon steel coupons. In the ZnO-treated bioreactors, the count of SRB and MIC in the carbon steel coupons simultaneously reduced. Moreover, Confocal Laser Scanning Microscopy and profilometry analysis determined that ZnO could significantly decrease the amount of biofilm and the corrosion rate. Electrochemical experiments revealed higher corrosion current density (icorr) and lower charge transfer resistance (Rct) in the control bioreactors relative to the ZnO-treated bioreactors. We introduce Halodesulfovibrio as a potentially important corrosive genus in a marine SRB consortium. Additionally, ZnO could be considered a proper candidate to control the corrosion induced by Halodesulfovibrio.},
}

Corrosion
*Zinc Oxide/chemistry/pharmacology
*Biofilms/drug effects
*Bioreactors/microbiology
Steel/chemistry
Nanoparticles/chemistry
Microbial Consortia/drug effects

@article {pmid39173234,
year = {2024},
author = {Jia, P and Liang, JL and Lu, JL and Zhong, SJ and Xiong, T and Feng, SW and Wang, Y and Wu, ZH and Yi, XZ and Gao, SM and Zheng, J and Wen, P and Li, F and Li, Y and Liao, B and Shu, WS and Li, JT},
title = {Soil keystone viruses are regulators of ecosystem multifunctionality.},
journal = {Environment international},
volume = {191},
number = {},
pages = {108964},
doi = {10.1016/j.envint.2024.108964},
pmid = {39173234},
issn = {1873-6750},
abstract = {Ecosystem multifunctionality reflects the capacity of ecosystems to simultaneously maintain multiple functions which are essential bases for human sustainable development. Whereas viruses are a major component of the soil microbiome that drive ecosystem functions across biomes, the relationships between soil viral diversity and ecosystem multifunctionality remain under-studied. To address this critical knowledge gap, we employed a combination of amplicon and metagenomic sequencing to assess prokaryotic, fungal and viral diversity, and to link viruses to putative hosts. We described the features of viruses and their potential hosts in 154 soil samples from 29 farmlands and 25 forests distributed across China. Although 4,460 and 5,207 viral populations (vOTUs) were found in the farmlands and forests respectively, the diversity of specific vOTUs rather than overall soil viral diversity was positively correlated with ecosystem multifunctionality in both ecosystem types. Furthermore, the diversity of these keystone vOTUs, despite being 10-100 times lower than prokaryotic or fungal diversity, was a better predictor of ecosystem multifunctionality and more strongly associated with the relative abundances of prokaryotic genes related to soil nutrient cycling. Gemmatimonadota and Actinobacteria dominated the host community of soil keystone viruses in the farmlands and forests respectively, but were either absent or showed a significantly lower relative abundance in that of soil non-keystone viruses. These findings provide novel insights into the regulators of ecosystem multifunctionality and have important implications for the management of ecosystem functioning.},
}

@article {pmid39167702,
year = {2024},
author = {Prins, FM and Hidding, IJ and Klaassen, MAY and Collij, V and Schultheiss, JPD and Uniken Venema, WTC and Bangma, A and Aardema, JB and Jansen, BH and Mares, WGN and Witteman, BJM and Festen, EAM and Dijkstra, G and Visschedijk, MC and Fidder, HH and Vich Vila, A and Oldenburg, B and Gacesa, R and Weersma, RK},
title = {Limited predictive value of the gut microbiome and metabolome for response to biological therapy in inflammatory bowel disease.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2391505},
doi = {10.1080/19490976.2024.2391505},
pmid = {39167702},
issn = {1949-0984},
mesh = {*Gastrointestinal Microbiome/drug effects ; Humans ; *Inflammatory Bowel Diseases/drug therapy/microbiology/metabolism ; *Metabolome/drug effects ; *Ustekinumab/therapeutic use ; Prospective Studies ; *Antibodies, Monoclonal, Humanized/therapeutic use/pharmacology ; *Feces/microbiology ; Female ; Male ; Adult ; Biological Therapy/methods ; Treatment Outcome ; Middle Aged ; Bacteria/genetics/classification/metabolism/drug effects/isolation & purification ; Biomarkers/analysis/metabolism ; },
abstract = {Emerging evidence suggests the gut microbiome's potential in predicting response to biologic treatments in patients with inflammatory bowel disease (IBD). In this prospective study, we aimed to predict treatment response to vedolizumab and ustekinumab, integrating clinical data, gut microbiome profiles based on metagenomic sequencing, and untargeted fecal metabolomics. We aimed to identify predictive biomarkers and attempted to replicate microbiome-based signals from previous studies. We found that the predictive utility of the gut microbiome and fecal metabolites for treatment response was marginal compared to clinical features alone. Testing our identified microbial ratios in an external cohort reinforced the lack of predictive power of the microbiome. Additionally, we could not confirm previously published predictive signals observed in similar sized cohorts. Overall, these findings highlight the importance of external validation and larger sample sizes, to better understand the microbiome's impact on therapy outcomes in the setting of biologicals in IBD before potential clinical implementation.},
}

*Gastrointestinal Microbiome/drug effects
Humans
*Inflammatory Bowel Diseases/drug therapy/microbiology/metabolism
*Metabolome/drug effects
*Ustekinumab/therapeutic use
Prospective Studies
*Antibodies, Monoclonal, Humanized/therapeutic use/pharmacology
*Feces/microbiology
Female
Male
Adult
Biological Therapy/methods
Treatment Outcome
Middle Aged
Bacteria/genetics/classification/metabolism/drug effects/isolation & purification
Biomarkers/analysis/metabolism

@article {pmid39089548,
year = {2024},
author = {Zeng, X and Tang, S and Dong, X and Dong, M and Shao, R and Liu, R and Li, T and Zhang, X and Wong, YH and Xie, Q},
title = {Analysis of metagenome and metabolome disclosed the mechanisms of Dendrobium officinale polysaccharide on DSS-induced ulcerative colitis-affected mice.},
journal = {International journal of biological macromolecules},
volume = {277},
number = {Pt 2},
pages = {134229},
doi = {10.1016/j.ijbiomac.2024.134229},
pmid = {39089548},
issn = {1879-0003},
mesh = {Animals ; *Dendrobium/chemistry ; *Colitis, Ulcerative/chemically induced/drug therapy/metabolism ; *Polysaccharides/pharmacology/chemistry ; *Dextran Sulfate/adverse effects ; Mice ; *Metabolome/drug effects ; Male ; Gastrointestinal Microbiome/drug effects ; Cytokines/metabolism ; Antioxidants/pharmacology ; Disease Models, Animal ; },
abstract = {Currently, there is no known cause for ulcerative colitis (UC), an inflammatory bowel disease that is difficult to treat. This assay aimed to investigate the protective effects and mechanisms of Dendrobium officinale polysaccharide (DOP) in mice with acute UC induced by dextran sulphate sodium (DSS). We found that DOP could improve weight loss, decrease the disease activity index (DAI), and regulate the release of interleukin 2 (IL-2), IL-4, IL-6, and IL-10 in DSS-induced acute UC mice. Additionally, DOP preserved the integrity of the intestinal barrier in UC mice by increasing goblet cell density and maintaining tight junctions. DOP significantly enhanced total antioxidant capacity (T-AOC), and reduced glutathione (GSH), nitric oxide (NO), and malondialdehyde (MDA) levels in the bloodstream. In terms of serum biochemistry, DOP markedly elevated levels of bilirubin (BIL), alkaline phosphatase (ALP), total bile acid (TBA), creatinine (Crea), and creative kinase isoenzyme (CKMB). Furthermore, DOP increased the relative abundance of Lactobacillales. DOP also improved intestinal health and stimulated the synthesis of potent anti-inflammatory and antiviral substances by regulating the metabolism of purines, prostaglandins, and leukotrienes. Therefore, DOP can be considered a functional dietary supplement for the treatment of UC, as it improves the condition of DSS-induced UC mice.},
}

Animals
*Dendrobium/chemistry
*Colitis, Ulcerative/chemically induced/drug therapy/metabolism
*Polysaccharides/pharmacology/chemistry
*Dextran Sulfate/adverse effects
Mice
*Metabolome/drug effects
Male
Gastrointestinal Microbiome/drug effects
Cytokines/metabolism
Antioxidants/pharmacology
Disease Models, Animal

@article {pmid39033825,
year = {2024},
author = {Dong, Z and Han, K and Xie, Q and Lin, C and Shen, X and Hao, Y and Li, J and Xu, H and He, L and Yu, T and Kuang, W},
title = {Core antibiotic resistance genes mediate gut microbiota to intervene in the treatment of major depressive disorder.},
journal = {Journal of affective disorders},
volume = {363},
number = {},
pages = {507-519},
doi = {10.1016/j.jad.2024.07.106},
pmid = {39033825},
issn = {1573-2517},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/genetics ; *Depressive Disorder, Major/drug therapy/genetics/microbiology ; Female ; Male ; Adult ; Middle Aged ; Drug Resistance, Microbial/genetics ; Case-Control Studies ; },
abstract = {INTRODUCTION: The relationship between depression and gut microbiota remains unclear, but an important role of gut microbiota has been verified. The relationship between gut microbiota and antibiotic resistance genes (ARGs) may be a potential new explanatory pathway.

METHODS: We collected samples from 63 depressed patients and 30 healthy controls for metagenomic sequencing. The two groups' microbiota characteristics, functional characteristics, and ARG differences were analyzed.

RESULTS: We obtained 30 differential KEGG orthologs (KOs) and their producers in 5 genera and 7 species by HUMAnN3. We found 6 KOs from Weissella_cibaria and Lactobacillus_plantaru are potentially coring functional mechanism of gut microbiota. Different metabolites including sphingolipids, pyrans, prenol lipids, and isoflavonoids also showed significance between MDD and HC. We detected 48 significantly different ARGs: 5 ARGs up-regulated and 43 ARGs down-regulated in MDD compared to HC. Based on Cox model results, Three ARGs significantly affected drug efficacy (ARG29, ARG105, and ARG111). Eggerthella, Weissella, and Lactobacillus were correlated with different core ARGs, which indicated different mechanisms in affecting MDD.

LIMITATIONS: The present study needs to be replicated in different ethnic groups. At the same time, a larger Chinese cohort study and detailed experimental verification are also the key to further discussion.

CONCLUSION: Our findings suggest that ARGs play a role in the interplay between major depressive disorder and gut microbiota. The role of ARGs should be taken into account when understanding the relationship between depression and gut microbiota.},
}

Humans
*Gastrointestinal Microbiome/drug effects/genetics
*Depressive Disorder, Major/drug therapy/genetics/microbiology
Female
Male
Adult
Middle Aged
Drug Resistance, Microbial/genetics
Case-Control Studies

@article {pmid39164259,
year = {2024},
author = {Seong, HJ and Kim, JJ and Kim, T and Ahn, SJ and Rho, M and Lee, KJ and Sul, WJ},
title = {Recovery of 240 metagenome-assembled genomes from coastal mariculture environments in South Korea.},
journal = {Scientific data},
volume = {11},
number = {1},
pages = {902},
pmid = {39164259},
issn = {2052-4463},
mesh = {Republic of Korea ; *Metagenome ; *Aquaculture ; Animals ; Bacteria/genetics/classification ; Microbiota ; Ostreidae/microbiology ; Archaea/genetics ; Pectinidae/microbiology/genetics ; Penaeidae/microbiology/genetics ; },
abstract = {The mariculture industry has seen a rapid expansion in recent years due to the increasing global demand for seafood. However, the industry faces challenges from climate change and increased pathogen pressure. Additionally, the chemicals used to enhance mariculture productivity are changing ocean ecosystems. This study analyzed 36 surface-water metagenomes from South Korean mussel, oyster, scallop, and shrimp farms to expand our understanding of aquaculture microbial genetic resources and the potential impacts of these anthropogenic inputs. We recovered 240 non-redundant species-level metagenome-assembled genomes (MAGs), comprising 224 bacteria, 13 archaea, and three eukaryotes. Most MAGs were assigned to Proteobacteria, Bacteroidota, and Actinobacteriota, with 40.7% remaining unclassified at the species level. Among the three eukaryotic MAGs, one was identified as a novel lineage of green algae, highlighting the uncharacterized genetic diversity in mariculture environments. Additionally, 22 prokaryotic MAGs harbored 26 antibiotic and metal resistance genes, with MAGs carrying beta-lactamases being particularly prevalent in most farms. The obtained microbiome data from mariculture environments can be utilized in future studies to foster healthy, sustainable mariculture practices.},
}

Republic of Korea
*Metagenome
*Aquaculture
Animals
Bacteria/genetics/classification
Microbiota
Ostreidae/microbiology
Archaea/genetics
Pectinidae/microbiology/genetics
Penaeidae/microbiology/genetics

@article {pmid39078126,
year = {2024},
author = {Ai, C and Cui, P and Liu, C and Wu, J and Xu, Y and Liang, X and Yang, Q and Tang, X and Zhou, S and Liao, H and Friman, V-P},
title = {Viral and thermal lysis facilitates transmission of antibiotic resistance genes during composting.},
journal = {Applied and environmental microbiology},
volume = {90},
number = {8},
pages = {e0069524},
doi = {10.1128/aem.00695-24},
pmid = {39078126},
issn = {1098-5336},
mesh = {*Composting ; Gene Transfer, Horizontal ; Manure/microbiology/virology ; Soil Microbiology ; Bacteria/genetics/drug effects ; Animals ; Metagenome ; Cattle ; Hot Temperature ; Genes, Bacterial ; Drug Resistance, Microbial/genetics ; Drug Resistance, Bacterial/genetics ; Microbiota ; Bacteriophages/genetics/physiology ; },
abstract = {UNLABELLED: While the distribution of extracellular ARGs (eARGs) in the environment has been widely reported, the factors governing their release remain poorly understood. Here, we combined multi-omics and direct experimentation to test whether the release and transmission of eARGs are associated with viral lysis and heat during cow manure composting. Our results reveal that the proportion of eARGs increased 2.7-fold during composting, despite a significant and concomitant reduction in intracellular ARG abundances. This relative increase of eARGs was driven by composting temperature and viral lysis of ARG-carrying bacteria based on metagenome-assembled genome (MAG) analysis. Notably, thermal lysis of mesophilic bacteria carrying ARGs was a key factor in releasing eARGs at the thermophilic phase, while viral lysis played a relatively stronger role during the non-thermal phase of composting. Furthermore, MAG-based tracking of ARGs in combination with direct transformation experiments demonstrated that eARGs released during composting pose a potential transmission risk. Our study provides bioinformatic and experimental evidence of the undiscovered role of temperature and viral lysis in co-driving the spread of ARGs in compost microbiomes via the horizontal transfer of environmentally released DNA.

IMPORTANCE: The spread of antibiotic resistance genes (ARGs) is a critical global health concern. Understanding the factors influencing the release of extracellular ARGs (eARGs) is essential for developing effective strategies. In this study, we investigated the association between viral lysis, heat, and eARG release during composting. Our findings revealed a substantial increase in eARGs despite reduced intracellular ARG abundance. Composting temperature and viral lysis were identified as key drivers, with thermal lysis predominant during the thermophilic phase and viral lysis during non-thermal phases. Moreover, eARGs released during composting posed a transmission risk through horizontal gene transfer. This study highlights the significance of temperature and phage lysis in ARG spread, providing valuable insights for mitigating antibiotic resistance threats.},
}

*Composting
Gene Transfer, Horizontal
Manure/microbiology/virology
Soil Microbiology
Bacteria/genetics/drug effects
Animals
Metagenome
Cattle
Hot Temperature
Genes, Bacterial
Drug Resistance, Microbial/genetics
Drug Resistance, Bacterial/genetics
Microbiota
Bacteriophages/genetics/physiology

@article {pmid39160620,
year = {2024},
author = {Yu, T and Luo, Y and Tan, X and Zhao, D and Bi, X and Li, C and Zheng, Y and Xiang, H and Hu, S},
title = {Global Marine Cold Seep Metagenomes Reveal Diversity of Taxonomy, Metabolic Function, and Natural Products.},
journal = {Genomics, proteomics & bioinformatics},
volume = {22},
number = {2},
pages = {},
doi = {10.1093/gpbjnl/qzad006},
pmid = {39160620},
issn = {2210-3244},
support = {//Center for Ocean Mega-Science, Chinese Academy of Sciences/ ; 2021QZKK0100//Second Tibetan Plateau Scientific Expedition and Research Program/ ; },
mesh = {*Metagenome/genetics ; *Archaea/genetics/metabolism/classification ; *Microbiota/genetics ; Bacteria/genetics/classification/metabolism ; Biological Products/metabolism ; Cold Temperature ; Phylogeny ; Seawater/microbiology ; Metagenomics/methods ; Biodiversity ; },
abstract = {Cold seeps in the deep sea are closely linked to energy exploration as well as global climate change. The alkane-dominated chemical energy-driven model makes cold seeps an oasis of deep-sea life, showcasing an unparalleled reservoir of microbial genetic diversity. Here, by analyzing 113 metagenomes collected from 14 global sites across 5 cold seep types, we present a comprehensive Cold Seep Microbiomic Database (CSMD) to archive the genomic and functional diversity of cold seep microbiomes. The CSMD includes over 49 million non-redundant genes and 3175 metagenome-assembled genomes, which represent 1895 species spanning 105 phyla. In addition, beta diversity analysis indicates that both the sampling site and cold seep type have a substantial impact on the prokaryotic microbiome community composition. Heterotrophic and anaerobic metabolisms are prevalent in microbial communities, accompanied by considerable mixotrophs and facultative anaerobes, highlighting the versatile metabolic potential in cold seeps. Furthermore, secondary metabolic gene cluster analysis indicates that at least 98.81% of the sequences potentially encode novel natural products, with ribosomally synthesized and post-translationally modified peptides being the predominant type widely distributed in archaea and bacteria. Overall, the CSMD represents a valuable resource that would enhance the understanding and utilization of global cold seep microbiomes.},
}

*Metagenome/genetics
*Archaea/genetics/metabolism/classification
*Microbiota/genetics
Bacteria/genetics/classification/metabolism
Biological Products/metabolism
Cold Temperature
Phylogeny
Seawater/microbiology
Metagenomics/methods
Biodiversity

@article {pmid39094704,
year = {2024},
author = {Dang, S and Fan, W and Meng, F and Li, X and Hao, J and Wang, C},
title = {Decolorization and detoxification of direct blue 5B by a Marinobacter-dominated halo-thermoalkalophilic consortium.},
journal = {Chemosphere},
volume = {363},
number = {},
pages = {142957},
doi = {10.1016/j.chemosphere.2024.142957},
pmid = {39094704},
issn = {1879-1298},
mesh = {*Marinobacter/metabolism/genetics ; *Biodegradation, Environmental ; Azo Compounds/metabolism/chemistry ; Coloring Agents/metabolism/chemistry ; Microbial Consortia ; Salinity ; Sewage/microbiology ; Hydrogen-Ion Concentration ; Temperature ; Water Pollutants, Chemical/metabolism/analysis ; Oryza ; },
abstract = {Azo dye-containing sewage is commonly detected at high salinity, temperature and pH. In this study, a halo-thermoalkalophilic azo dye decolorization consortium was enriched and named "consortium HL". Consortium HL which was dominated by Marinobacter (84.30%), Desulfocurvibacter (1.89%), and Pseudomonas (1.85%), was able to completely decolorize Direct Blue 5B (DB5) during incubation with the material at 5% salinity, 50 °C, and pH 9 for 30 h. The decolorization mechanism was proposed based on combined metagenomic analysis, GC‒MS, and enzymatic activity detection. The action of the consortium HL showed great tolerance to variations in salinity, temperature and pH. A phytotoxicity study indicated that the metabolic intermediates showed no significant toxicity to the generation of Cucumis sativus and Oryza sativa seeds. This study, in which azo dye decolorization and degradation under high-salt, high-temperature and high-alkalinity conditions were investigated and deeply analyzed by metagenomic information, is the first report regarding the ability of Marinobacter to decolorize azo dyes at high temperatures.},
}

*Marinobacter/metabolism/genetics
*Biodegradation, Environmental
Azo Compounds/metabolism/chemistry
Coloring Agents/metabolism/chemistry
Microbial Consortia
Salinity
Sewage/microbiology
Hydrogen-Ion Concentration
Temperature
Water Pollutants, Chemical/metabolism/analysis
Oryza

@article {pmid39082797,
year = {2024},
author = {Roager, L and Kempen, PJ and Bentzon-Tilia, M and Sonnenschein, EC and Gram, L},
title = {Impact of host species on assembly, composition, and functional profiles of phycosphere microbiomes.},
journal = {mSystems},
volume = {9},
number = {8},
pages = {e0058324},
doi = {10.1128/msystems.00583-24},
pmid = {39082797},
issn = {2379-5077},
support = {NNF20OC0064249,NNF19OC0055625//Novo Nordisk Fonden (NNF)/ ; },
mesh = {*Microbiota/physiology ; *Diatoms ; *Microalgae ; *RNA, Ribosomal, 16S/genetics ; *Haptophyta ; Chlorophyta/microbiology ; Seawater/microbiology ; },
abstract = {UNLABELLED: Microalgal microbiomes play vital roles in the growth and health of their host, however, their composition and functions remain only partially characterized, especially across microalgal phyla. In this study, a natural seawater microbiome was introduced to three distinct, axenic species of microalgae, the haptophyte Isochrysis galbana, the chlorophyte Tetraselmis suecica, and the diatom Conticribra weissflogii (previously Thalassiosira), and its divergence and assembly under constant illumination was monitored over 49 days using 16S rRNA amplicon and metagenomic analyses. The microbiomes had a high degree of host specificity in terms of taxonomic composition and potential functions, including CAZymes profiles. Rhodobacteraceae and Flavobacteriaceae families were abundant across all microalgal hosts, but I. galbana microbiomes diverged further from T. suecica and C. weissflogii microbiomes. I. galbana microbiomes had a much higher relative abundance of Flavobacteriaceae, whereas the two other algal microbiomes had higher relative abundances of Rhodobacteraceae. This could be due to the bacterivorous mixotrophic nature of I. galbana affecting the carbohydrate composition available to the microbiomes, which was supported by the CAZymes profile of I. galbana microbiomes diverging further from those of T. suecica and C. weissflogii microbiomes. Finally, the presence of denitrification and other anaerobic pathways was found exclusively in the microbiomes of C. weissflogii, which we speculate could be a result of anoxic microenvironments forming in aggregates formed by this diatom during the experiment. These results underline the significant role of the microalgal host species on microbiome composition and functional profiles along with other factors, such as the trophic mode of the microalgal host.

IMPORTANCE: As the main primary producers of the oceans, microalgae serve as cornerstones of the ecosystems they are part of. Additionally, they are increasingly used for biotechnological purposes such as the production of nutraceuticals, pigments, and antioxidants. Since the bacterial microbiomes of microalgae can affect their hosts in beneficial and detrimental ways, understanding these microbiomes is crucial to both the ecological and applied roles of microalgae. The present study advances the understanding of microalgal microbiome assembly, composition, and functionality across microalgal phyla, which may inform the modeling and engineering of microalgal microbiomes for biotechnological purposes.},
}

*Microbiota/physiology
*Diatoms
*Microalgae
*RNA, Ribosomal, 16S/genetics
*Haptophyta
Chlorophyta/microbiology
Seawater/microbiology

@article {pmid39078158,
year = {2024},
author = {Jin, D-M and Morton, JT and Bonneau, R},
title = {Meta-analysis of the human gut microbiome uncovers shared and distinct microbial signatures between diseases.},
journal = {mSystems},
volume = {9},
number = {8},
pages = {e0029524},
doi = {10.1128/msystems.00295-24},
pmid = {39078158},
issn = {2379-5077},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Diabetes Mellitus, Type 2/microbiology ; Machine Learning ; Crohn Disease/microbiology ; Colorectal Neoplasms/microbiology ; Metagenomics/methods ; Colitis, Ulcerative/microbiology ; Parkinson Disease/microbiology ; Schizophrenia/microbiology ; Alzheimer Disease/microbiology ; },
abstract = {UNLABELLED: Microbiome studies have revealed gut microbiota's potential impact on complex diseases. However, many studies often focus on one disease per cohort. We developed a meta-analysis workflow for gut microbiome profiles and analyzed shotgun metagenomic data covering 11 diseases. Using interpretable machine learning and differential abundance analysis, our findings reinforce the generalization of binary classifiers for Crohn's disease (CD) and colorectal cancer (CRC) to hold-out cohorts and highlight the key microbes driving these classifications. We identified high microbial similarity in disease pairs like CD vs ulcerative colitis (UC), CD vs CRC, Parkinson's disease vs type 2 diabetes (T2D), and schizophrenia vs T2D. We also found strong inverse correlations in Alzheimer's disease vs CD and UC. These findings, detected by our pipeline, provide valuable insights into these diseases.

IMPORTANCE: Assessing disease similarity is an essential initial step preceding a disease-based approach for drug repositioning. Our study provides a modest first step in underscoring the potential of integrating microbiome insights into the disease similarity assessment. Recent microbiome research has predominantly focused on analyzing individual diseases to understand their unique characteristics, which by design excludes comorbidities in individuals. We analyzed shotgun metagenomic data from existing studies and identified previously unknown similarities between diseases. Our research represents a pioneering effort that utilizes both interpretable machine learning and differential abundance analysis to assess microbial similarity between diseases.},
}

Humans
*Gastrointestinal Microbiome/genetics
Diabetes Mellitus, Type 2/microbiology
Machine Learning
Crohn Disease/microbiology
Colorectal Neoplasms/microbiology
Metagenomics/methods
Colitis, Ulcerative/microbiology
Parkinson Disease/microbiology
Schizophrenia/microbiology
Alzheimer Disease/microbiology

@article {pmid39012154,
year = {2024},
author = {Salazar-Jaramillo, L and de la Cuesta-Zuluaga, J and Chica, LA and Cadavid, M and Ley, RE and Reyes, A and Escobar, JS},
title = {Gut microbiome diversity within Clostridia is negatively associated with human obesity.},
journal = {mSystems},
volume = {9},
number = {8},
pages = {e0062724},
doi = {10.1128/msystems.00627-24},
pmid = {39012154},
issn = {2379-5077},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Obesity/microbiology ; Male ; Adult ; Female ; Cross-Sectional Studies ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Metagenomics/methods ; Body Mass Index ; },
abstract = {UNLABELLED: Clostridia are abundant in the human gut and comprise families associated with host health such as Oscillospiraceae, which has been correlated with leanness. However, culturing bacteria within this family is challenging, leading to their detection primarily through 16S rRNA amplicon sequencing, which has a limited ability to unravel diversity at low taxonomic levels, or by shotgun metagenomics, which is hindered by its high costs and complexity. In this cross-sectional study involving 114 Colombian adults, we used an amplicon-based sequencing strategy with alternative markers-gyrase subunit B (gyrB) and DNA K chaperone heat protein 70 (dnaK)-that evolve faster than the 16S rRNA gene. Comparing the diversity and abundance observed with the three markers in our cohort, we found a reduction in the diversity of Clostridia, particularly within Lachnospiraceae and Oscillospiraceae among obese individuals [as measured by the body mass index (BMI)]. Within Lachnospiraceae, the diversity of Ruminococcus_A negatively correlated with BMI. Within Oscillospiraceae, the genera CAG-170 and Vescimonas also exhibited this negative correlation. In addition, the abundance of Vescimonas was negatively correlated with BMI. Leveraging shotgun metagenomic data, we conducted a phylogenetic and genomic characterization of 120 metagenome-assembled genomes from Vescimonas obtained from a larger sample of the same cohort. We identified 17 of the 72 reported species. The functional annotation of these genomes showed the presence of multiple carbohydrate-active enzymes, particularly glycosyl transferases and glycoside hydrolases, suggesting potential beneficial roles in fiber degradation, carbohydrate metabolism, and butyrate production.

IMPORTANCE: The gut microbiota is diverse across various taxonomic levels. At the intra-species level, it comprises multiple strains, some of which may be host-specific. However, our understanding of fine-grained diversity has been hindered by the use of the conserved 16S rRNA gene. While shotgun metagenomics offers higher resolution, it remains costly, may fail to identify specific microbes in complex samples, and requires extensive computational resources and expertise. To address this, we employed a simple and cost-effective analysis of alternative genetic markers to explore diversity within Clostridia, a crucial group within the human gut microbiota whose diversity may be underestimated. We found high intra-species diversity for certain groups and associations with obesity. Notably, we identified Vescimonas, an understudied group. Making use of metagenomic data, we inferred functionality, uncovering potential beneficial roles in dietary fiber and carbohydrate degradation, as well as in short-chain fatty acid production.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Obesity/microbiology
Male
Adult
Female
Cross-Sectional Studies
Middle Aged
RNA, Ribosomal, 16S/genetics
Metagenomics/methods
Body Mass Index

@article {pmid38990071,
year = {2024},
author = {Spirito, CM and Lucas, TN and Patz, S and Jeon, BS and Werner, JJ and Trondsen, LH and Guzman, JJ and Huson, DH and Angenent, LT},
title = {Variability in n-caprylate and n-caproate producing microbiomes in reactors with in-line product extraction.},
journal = {mSystems},
volume = {9},
number = {8},
pages = {e0041624},
doi = {10.1128/msystems.00416-24},
pmid = {38990071},
issn = {2379-5077},
support = {STAR Fellowship//U.S. Environmental Protection Agency (EPA)/ ; Alexander von Humboldt Professorship//Alexander von Humboldt-Stiftung (AvH)/ ; EXC 2124 - 390838134//Deutsche Forschungsgemeinschaft (DFG)/ ; NNF21SA0072700//Novo Nordisk Fonden (NNF)/ ; W911NF-12-1-0555//DOD | USA | AFC | CCDC | Army Research Office (ARO)/ ; Collaboration between the University of Maryland and the University of Tübingen//Reinhard Frank Stiftung/ ; },
mesh = {*Bioreactors/microbiology ; *Microbiota ; Caprylates/metabolism ; Caproates/metabolism ; Bacteria/metabolism/genetics/classification/isolation & purification ; Liquid-Liquid Extraction/methods ; },
abstract = {Medium-chain carboxylates (MCCs) are used in various industrial applications. These chemicals are typically extracted from palm oil, which is deemed not sustainable. Recent research has focused on microbial chain elongation using reactors to produce MCCs, such as n-caproate (C6) and n-caprylate (C8), from organic substrates such as wastes. Even though the production of n-caproate is relatively well-characterized, bacteria and metabolic pathways that are responsible for n-caprylate production are not. Here, three 5 L reactors with continuous membrane-based liquid-liquid extraction (i.e., pertraction) were fed ethanol and acetate and operated for an operating period of 234 days with different operating conditions. Metagenomic and metaproteomic analyses were employed. n-Caprylate production rates and reactor microbiomes differed between reactors even when operated similarly due to differences in H2 and O2 between the reactors. The complete reverse β-oxidation (RBOX) pathway was present and expressed by several bacterial species in the Clostridia class. Several Oscillibacter spp., including Oscillibacter valericigenes, were positively correlated with n-caprylate production rates, while Clostridium kluyveri was positively correlated with n-caproate production. Pseudoclavibacter caeni, which is a strictly aerobic bacterium, was abundant across all the operating periods, regardless of n-caprylate production rates. This study provides insight into microbiota that are associated with n-caprylate production in open-culture reactors and provides ideas for further work.IMPORTANCEMicrobial chain elongation pathways in open-culture biotechnology systems can be utilized to convert organic waste and industrial side streams into valuable industrial chemicals. Here, we investigated the microbiota and metabolic pathways that produce medium-chain carboxylates (MCCs), including n-caproate (C6) and n-caprylate (C8), in reactors with in-line product extraction. Although the reactors in this study were operated similarly, different microbial communities dominated and were responsible for chain elongation. We found that different microbiota were responsible for n-caproate or n-caprylate production, and this can inform engineers on how to operate the systems better. We also observed which changes in operating conditions steered the production toward and away from n-caprylate, but more work is necessary to ascertain a mechanistic understanding that could be predictive. This study provides pertinent research questions for future work.},
}

*Bioreactors/microbiology
*Microbiota
Caprylates/metabolism
Caproates/metabolism
Bacteria/metabolism/genetics/classification/isolation & purification
Liquid-Liquid Extraction/methods

@article {pmid38980054,
year = {2024},
author = {Duller, S and Kumpitsch, C and Moissl-Eichinger, C and Wink, L and Koskinen Mora, K and Mahnert, A},
title = {In-hospital areas with distinct maintenance and staff/patient traffic have specific microbiome profiles, functions, and resistomes.},
journal = {mSystems},
volume = {9},
number = {8},
pages = {e0072624},
doi = {10.1128/msystems.00726-24},
pmid = {38980054},
issn = {2379-5077},
support = {//Medizinische Universität Wien (MediUni Wien)/ ; },
mesh = {Humans ; *Microbiota/drug effects/genetics ; Hospitals ; Cross Infection/microbiology ; Bacteria/genetics/drug effects ; Drug Resistance, Bacterial/genetics ; Drug Resistance, Microbial/genetics ; Plasmids/genetics ; Metagenomics ; Anti-Bacterial Agents/pharmacology ; },
abstract = {UNLABELLED: Hospitals are subject to strict microbial control. Stringent cleaning and confinement measures in hospitals lead to a decrease in microbial diversity, but an increase in resistance genes. Given the rise of antimicrobial resistances and healthcare-associated infections, understanding the hospital microbiome and its resistome is crucial. This study compared the microbiome and resistome at different levels of confinement (CL) within a single hospital. Using amplicon sequencing, shotgun metagenomics, and genome/plasmid reconstruction, we demonstrate that microbial composition differs in a stable way between the CLs and that the most restrictive confinement level CL1 had the lowest microbial but the highest functional diversity. This CL also exhibited a greater abundance of functions related to virulence, disease, defense, and stress response. Comparison of antibiotic resistance also showed differences among CLs in terms of the selection process and specific mechanisms for antimicrobial/antibiotic resistance. The resistances found in the samples of CL1 were mostly mediated via antibiotic efflux pumps and were mainly located on chromosomes, whereas in the other, less restrictive CL antibiotic resistances were more present on plasmids. This could be of particular importance for patient-related areas (CL2), as the potential spread of antibiotic resistances could be a major concern in this area. Our results show that there are differences in the microbiome and resistome even within a single hospital, reflecting room utilization and confinement. Since restrictive confinement selects for resistant microorganisms, strategies are required to deepen our understanding of dynamic processes of microbiome and resistome within hospital environments.

IMPORTANCE: Effective measures to combat antibiotic resistances and healthcare-associated infections are urgently needed, including optimization of microbial control. However, previous studies have indicated that stringent control can lead to an increase in the resistance capacities of microbiomes on surfaces. This study adds to previous knowledge by focusing on the conditions in a single hospital, resolving the microbiomes and their resistomes in three different confinement levels (CL): operating room, patient-related areas, and non-patient-related areas. We were able to identify stable key taxa; profiled the capacities of taxa, functions, and antimicrobial resistances (AMR); and reconstruct genomes and plasmids in each CL. Our results show that the most restrictive CL indeed had the highest functional diversity, but that resistances were mostly encoded on chromosomes, indicating a lower possibility of resistance spread. However, clever strategies are still required to strike a balance between microbial control and selective pressures in environments where patients need protection.},
}

Humans
*Microbiota/drug effects/genetics
Hospitals
Cross Infection/microbiology
Bacteria/genetics/drug effects
Drug Resistance, Bacterial/genetics
Drug Resistance, Microbial/genetics
Plasmids/genetics
Metagenomics
Anti-Bacterial Agents/pharmacology

@article {pmid38980053,
year = {2024},
author = {Sanguineti, D and Zampieri, G and Treu, L and Campanaro, S},
title = {Metapresence: a tool for accurate species detection in metagenomics based on the genome-wide distribution of mapping reads.},
journal = {mSystems},
volume = {9},
number = {8},
pages = {e0021324},
doi = {10.1128/msystems.00213-24},
pmid = {38980053},
issn = {2379-5077},
mesh = {*Metagenomics/methods ; Humans ; *Metagenome/genetics ; Gastrointestinal Microbiome/genetics ; Genome, Bacterial/genetics ; Software ; Bacteria/genetics/classification/isolation & purification ; },
abstract = {Shotgun metagenomics allows comprehensive sampling of the genomic information of microbes in a given environment and is a tool of choice for studying complex microbial systems. Mapping sequencing reads against a set of reference or metagenome-assembled genomes is in principle a simple and powerful approach to define the species-level composition of the microbial community under investigation. However, despite the widespread use of this approach, there is no established way to properly interpret the alignment results, with arbitrary relative abundance thresholds being routinely used to discriminate between present and absent species. Such an approach can be affected by significant biases, especially in the identification of rare species. Therefore, it is important to develop new metrics to overcome these biases. Here, we present Metapresence, a new tool to perform reliable identification of the species in metagenomic samples based on the distribution of mapped reads on the reference genomes. The analysis is based on two metrics describing the breadth of coverage and the genomic distance between consecutive reads. We demonstrate the high precision and wide applicability of the tool using data from various synthetic communities, a real mock community, and the gut microbiome of healthy individuals and antibiotic-associated-diarrhea patients. Overall, our results suggest that the proposed approach has a robust performance in hard-to-analyze microbial communities containing contaminated or closely related genomes in low abundance.IMPORTANCEDespite the prevalent use of genome-centric alignment-based methods to characterize microbial community composition, there lacks a standardized approach for accurately identifying the species within a sample. Currently, arbitrary relative abundance thresholds are commonly employed for this purpose. However, due to the inherent complexity of genome structure and biases associated with genome-centric approaches, this practice tends to be imprecise. Notably, it introduces significant biases, particularly in the identification of rare species. The method presented here addresses these limitations and contributes significantly to overcoming inaccuracies in precisely defining community composition, especially when dealing with rare members.},
}

*Metagenomics/methods
Humans
*Metagenome/genetics
Gastrointestinal Microbiome/genetics
Genome, Bacterial/genetics
Software
Bacteria/genetics/classification/isolation & purification

@article {pmid38980052,
year = {2024},
author = {Flinkstrom, Z and Bryson, S and Candry, P and Winkler, M-KH},
title = {Metagenomic clustering links specific metabolic functions to globally relevant ecosystems.},
journal = {mSystems},
volume = {9},
number = {8},
pages = {e0057324},
doi = {10.1128/msystems.00573-24},
pmid = {38980052},
issn = {2379-5077},
support = {DE-SC0020356//U.S. Department of Energy (DOE)/ ; },
mesh = {*Metagenomics/methods ; *Metagenome/genetics ; Ecosystem ; Cluster Analysis ; Microbiota/genetics ; },
abstract = {UNLABELLED: Metagenomic sequencing has advanced our understanding of biogeochemical processes by providing an unprecedented view into the microbial composition of different ecosystems. While the amount of metagenomic data has grown rapidly, simple-to-use methods to analyze and compare across studies have lagged behind. Thus, tools expressing the metabolic traits of a community are needed to broaden the utility of existing data. Gene abundance profiles are a relatively low-dimensional embedding of a metagenome's functional potential and are, thus, tractable for comparison across many samples. Here, we compare the abundance of KEGG Ortholog Groups (KOs) from 6,539 metagenomes from the Joint Genome Institute's Integrated Microbial Genomes and Metagenomes (JGI IMG/M) database. We find that samples cluster into terrestrial, aquatic, and anaerobic ecosystems with marker KOs reflecting adaptations to these environments. For instance, functional clusters were differentiated by the metabolism of antibiotics, photosynthesis, methanogenesis, and surprisingly GC content. Using this functional gene approach, we reveal the broad-scale patterns shaping microbial communities and demonstrate the utility of ortholog abundance profiles for representing a rapidly expanding body of metagenomic data.

IMPORTANCE: Metagenomics, or the sequencing of DNA from complex microbiomes, provides a view into the microbial composition of different environments. Metagenome databases were created to compile sequencing data across studies, but it remains challenging to compare and gain insight from these large data sets. Consequently, there is a need to develop accessible approaches to extract knowledge across metagenomes. The abundance of different orthologs (i.e., genes that perform a similar function across species) provides a simplified representation of a metagenome's metabolic potential that can easily be compared with others. In this study, we cluster the ortholog abundance profiles of thousands of metagenomes from diverse environments and uncover the traits that distinguish them. This work provides a simple to use framework for functional comparison and advances our understanding of how the environment shapes microbial communities.},
}

*Metagenomics/methods
*Metagenome/genetics
Ecosystem
Cluster Analysis
Microbiota/genetics

@article {pmid38975760,
year = {2024},
author = {Tang-Wing, C and Mohanty, I and Bryant, M and Makowski, K and Melendez, D and Dorrestein, PC and Knight, R and Caraballo-Rodríguez, AM and Allaband, C and Jenné, K},
title = {Impact of diet change on the gut microbiome of common marmosets (Callithrix jacchus).},
journal = {mSystems},
volume = {9},
number = {8},
pages = {e0010824},
doi = {10.1128/msystems.00108-24},
pmid = {38975760},
issn = {2379-5077},
support = {S10 OD026929/CD/ODCDC CDC HHS/United States ; },
mesh = {Animals ; *Callithrix/microbiology ; *Gastrointestinal Microbiome/physiology ; *Diet/veterinary ; Male ; Female ; Feces/microbiology ; Bifidobacterium/isolation & purification ; },
abstract = {UNLABELLED: Gastrointestinal diseases are the most frequently reported clinical problems in captive common marmosets (Callithrix jacchus), often affecting the health and welfare of the animal and ultimately their use as a research subject. The microbiome has been shown to be intimately connected to diet and gastrointestinal health. Here, we use shotgun metagenomics and untargeted metabolomics in fecal samples of common marmosets collected before, during, and after a dietary transition from a biscuit to a gel diet. The overall health of marmosets, measured as weight recovery and reproductive outcome, improved after the diet transition. Moreover, each marmoset pair had significant shifts in the microbiome and metabolome after the diet transition. In general, we saw a decrease in Escherichia coli and Prevotella species and an increase in Bifidobacterium species. Untargeted metabolic profiles indicated that polyamine levels, specifically cadaverine and putrescine, were high after diet transition, suggesting either an increase in excretion or a decrease in intestinal reabsorption at the intestinal level. In conclusion, our data suggest that Bifidobacterium species could potentially be useful as probiotic supplements to the laboratory marmoset diet. Future studies with a larger sample size will be beneficial to show that this is consistent with the diet change.

IMPORTANCE: Appropriate diet and health of the common marmoset in captivity are essential both for the welfare of the animal and to improve experimental outcomes. Our study shows that a gel diet compared to a biscuit diet improves the health of a marmoset colony, is linked to increases in Bifidobacterium species, and increases the removal of molecules associated with disease. The diet transition had an influence on the molecular changes at both the pair and time point group levels, but only at the pair level for the microbial changes. It appears to be more important which genes and functions present changed rather than specific microbes. Further studies are needed to identify specific components that should be considered when choosing an appropriate diet and additional supplementary foods, as well as to validate the benefits of providing probiotics. Probiotics containing Bifidobacterium species appear to be useful as probiotic supplements to the laboratory marmoset diet, but additional work is needed to validate these findings.},
}

Animals
*Callithrix/microbiology
*Gastrointestinal Microbiome/physiology
*Diet/veterinary
Male
Female
Feces/microbiology
Bifidobacterium/isolation & purification

@article {pmid38922379,
year = {2024},
author = {Mikó, E and Sipos, A and Tóth, E and Lehoczki, A and Fekete, M and Sebő, É and Kardos, G and Bai, P},
title = {Guideline for designing microbiome studies in neoplastic diseases.},
journal = {GeroScience},
volume = {46},
number = {5},
pages = {4037-4057},
pmid = {38922379},
issn = {2509-2723},
support = {K142141//NKFIH/ ; FK128387//NKFIH/ ; FK146852//NKFIH/ ; TKP2021-EGA-20//NKFIH/ ; TKP2021-EGA-19//NFKIH/ ; POST-COVID2021-33//Magyar Tudományos Akadémia/ ; NKM2022-30//Magyar Tudományos Akadémia/ ; },
mesh = {Humans ; *Neoplasms/microbiology ; *Microbiota ; Research Design ; },
abstract = {Oncobiosis has emerged as a key contributor to the development, and modulator of the treatment efficacy of cancer. Hereby, we review the modalities through which the oncobiome can support the progression of tumors, and the emerging therapeutic opportunities they present. The review highlights the inherent challenges and limitations faced in sampling and accurately characterizing oncobiome. Additionally, the review underscores the critical need for the standardization of microbial analysis techniques and the consistent reporting of microbiome data. We provide a suggested metadata set that should accompany microbiome datasets from oncological settings so that studies remain comparable and decipherable.},
}

Humans
*Neoplasms/microbiology
*Microbiota
Research Design

@article {pmid38918932,
year = {2024},
author = {Tian, B and Xu, LL and Jiang, LD and Lin, X and Shen, J and Shen, H and Su, KJ and Gong, R and Qiu, C and Luo, Z and Yao, JH and Wang, ZQ and Xiao, HM and Zhang, LS and Deng, HW},
title = {Identification of the serum metabolites associated with cow milk consumption in Chinese Peri-/Postmenopausal women.},
journal = {International journal of food sciences and nutrition},
volume = {75},
number = {6},
pages = {537-549},
doi = {10.1080/09637486.2024.2366223},
pmid = {38918932},
issn = {1465-3478},
mesh = {Humans ; Female ; *Milk ; Animals ; Middle Aged ; *Postmenopause/blood ; China ; *Gastrointestinal Microbiome ; Cattle ; Citrulline/blood ; Aged ; Diet ; Metabolome ; Bacteroides ; East Asian People ; },
abstract = {Cow milk consumption (CMC) and downstream alterations of serum metabolites are commonly considered important factors regulating human health status. Foods may lead to metabolic changes directly or indirectly through remodelling gut microbiota (GM). We sought to identify the metabolic alterations in Chinese Peri-/Postmenopausal women with habitual CMC and explore if the GM mediates the CMC-metabolite associations. 346 Chinese Peri-/Postmenopausal women participants were recruited in this study. Fixed effects regression and partial least squares discriminant analysis (PLS-DA) were applied to reveal alterations of serum metabolic features in different CMC groups. Spearman correlation coefficient was computed to detect metabolome-metagenome association. 36 CMC-associated metabolites including palmitic acid (FA(16:0)), 7alpha-hydroxy-4-cholesterin-3-one (7alphaC4), citrulline were identified by both fixed effects regression (FDR < 0.05) and PLS-DA (VIP score > 2). Some significant metabolite-GM associations were observed, including FA(16:0) with gut species Bacteroides ovatus, Bacteroides sp.D2. These findings would further prompt our understanding of the effect of cow milk on human health.},
}

Humans
Female
*Milk
Animals
Middle Aged
*Postmenopause/blood
China
*Gastrointestinal Microbiome
Cattle
Citrulline/blood
Aged
Diet
Metabolome
Bacteroides
East Asian People

@article {pmid38912690,
year = {2024},
author = {Byndloss, M and Devkota, S and Duca, F and Niess, JH and Nieuwdorp, M and Orho-Melander, M and Sanz, Y and Tremaroli, V and Zhao, L},
title = {The Gut Microbiota and Diabetes: Research, Translation, and Clinical Applications-2023 Diabetes, Diabetes Care, and Diabetologia Expert Forum.},
journal = {Diabetes},
volume = {73},
number = {9},
pages = {1391-1410},
doi = {10.2337/dbi24-0028},
pmid = {38912690},
issn = {1939-327X},
support = {2020 (09150182010020)//ZONMW-VICI/ ; 875534//European Union’s Innovative Medicine Initiative/ ; 310030_219210//Swiss National Science Foundation (SNSF)/ ; CEX2021-001189-S/10.13039/501100011033//Severo Ochoa Center of Excellence/ ; //Novo Nordisk Foundation/ ; 2020 (2020.10.002)//DFN-DON/ ; 1DP1 DK130687/DK/NIDDK NIH HHS/United States ; PID2020-119536RB-I00//Spanish Ministry of Science, Innovation and Universities MICIU/AEI/ ; 1DP1 DK130687/DK/NIDDK NIH HHS/United States ; },
mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; *Diabetes Mellitus, Type 2/microbiology/metabolism/therapy ; Translational Research, Biomedical ; },
abstract = {This article summarizes the state of the science on the role of the gut microbiota (GM) in diabetes from a recent international expert forum organized by Diabetes, Diabetes Care, and Diabetologia, which was held at the European Association for the Study of Diabetes 2023 Annual Meeting in Hamburg, Germany. Forum participants included clinicians and basic scientists who are leading investigators in the field of the intestinal microbiome and metabolism. Their conclusions were as follows: 1) the GM may be involved in the pathophysiology of type 2 diabetes, as microbially produced metabolites associate both positively and negatively with the disease, and mechanistic links of GM functions (e.g., genes for butyrate production) with glucose metabolism have recently emerged through the use of Mendelian randomization in humans; 2) the highly individualized nature of the GM poses a major research obstacle, and large cohorts and a deep-sequencing metagenomic approach are required for robust assessments of associations and causation; 3) because single-time point sampling misses intraindividual GM dynamics, future studies with repeated measures within individuals are needed; and 4) much future research will be required to determine the applicability of this expanding knowledge to diabetes diagnosis and treatment, and novel technologies and improved computational tools will be important to achieve this goal.},
}

*Gastrointestinal Microbiome/physiology
Humans
*Diabetes Mellitus, Type 2/microbiology/metabolism/therapy
Translational Research, Biomedical

@article {pmid39160615,
year = {2024},
author = {Hugerth, LW and Krog, MC and Vomstein, K and Du, J and Bashir, Z and Kaldhusdal, V and Fransson, E and Engstrand, L and Nielsen, HS and Schuppe-Koistinen, I},
title = {Defining Vaginal Community Dynamics: daily microbiome transitions, the role of menstruation, bacteriophages, and bacterial genes.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {153},
pmid = {39160615},
issn = {2049-2618},
support = {KAW 2020.0239//Science for Life Laboratory/ ; E-22614-01, E-22614-02//Rigshospitalet/ ; 2021-01683//Vetenskapsrådet/ ; },
mesh = {Humans ; Female ; *Vagina/microbiology ; *Bacteriophages/genetics/physiology ; *Microbiota/genetics ; *Menstruation ; *Bacteria/classification/genetics ; Adult ; *Dysbiosis/microbiology ; *Menstrual Cycle ; Young Adult ; Genes, Bacterial/genetics ; Metagenomics/methods ; },
abstract = {BACKGROUND: The composition of the vaginal microbiota during the menstrual cycle is dynamic, with some women remaining eu- or dysbiotic and others transitioning between these states. What defines these dynamics, and whether these differences are microbiome-intrinsic or mostly driven by the host is unknown. To address this, we characterized 49 healthy, young women by metagenomic sequencing of daily vaginal swabs during a menstrual cycle. We classified the dynamics of the vaginal microbiome and assessed the impact of host behavior as well as microbiome differences at the species, strain, gene, and phage levels.

RESULTS: Based on the daily shifts in community state types (CSTs) during a menstrual cycle, the vaginal microbiome was classified into four Vaginal Community Dynamics (VCDs) and reported in a classification tool, named VALODY: constant eubiotic, constant dysbiotic, menses-related, and unstable dysbiotic. The abundance of bacteria, phages, and bacterial gene content was compared between the four VCDs. Women with different VCDs showed significant differences in relative phage abundance and bacterial composition even when assigned to the same CST. Women with unstable VCDs had higher phage counts and were more likely dominated by L. iners. Their Gardnerella spp. strains were also more likely to harbor bacteriocin-coding genes.

CONCLUSIONS: The VCDs present a novel time series classification that highlights the complexity of varying degrees of vaginal dysbiosis. Knowing the differences in phage gene abundances and the genomic strains present allows a deeper understanding of the initiation and maintenance of permanent dysbiosis. Applying the VCDs to further characterize the different types of microbiome dynamics qualifies the investigation of disease and enables comparisons at individual and population levels. Based on our data, to be able to classify a dysbiotic sample into the accurate VCD, clinicians would need two to three mid-cycle samples and two samples during menses. In the future, it will be important to address whether transient VCDs pose a similar risk profile to persistent dysbiosis with similar clinical outcomes. This framework may aid interdisciplinary translational teams in deciphering the role of the vaginal microbiome in women's health and reproduction. Video Abstract.},
}

Humans
Female
*Vagina/microbiology
*Bacteriophages/genetics/physiology
*Microbiota/genetics
*Menstruation
*Bacteria/classification/genetics
Adult
*Dysbiosis/microbiology
*Menstrual Cycle
Young Adult
Genes, Bacterial/genetics
Metagenomics/methods

@article {pmid39160043,
year = {2024},
author = {Merino, N and Pagán, E and Berdejo, D and Worby, CJ and Young, M and Manson, AL and Pagán, R and Earl, AM and García-Gonzalo, D},
title = {Dynamics of microbiome and resistome in a poultry burger processing line.},
journal = {Food research international (Ottawa, Ont.)},
volume = {193},
number = {},
pages = {114842},
doi = {10.1016/j.foodres.2024.114842},
pmid = {39160043},
issn = {1873-7145},
mesh = {Animals ; *Microbiota/genetics ; *Food Microbiology ; *Bacteria/genetics/classification/isolation & purification/drug effects ; *Food Handling/methods ; Poultry/microbiology ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing ; Drug Resistance, Bacterial/genetics ; Meat/microbiology ; Poultry Products/microbiology ; },
abstract = {Traditionally, surveillance programs for food products and food processing environments have focused on targeted pathogens and resistance genes. Recent advances in high throughput sequencing allow for more comprehensive and untargeted monitoring. This study assessed the microbiome and resistome in a poultry burger processing line using culturing techniques and whole metagenomic sequencing (WMS). Samples included meat, burgers, and expired burgers, and different work surfaces. Microbiome analysis revealed spoilage microorganisms as the main microbiota, with substantial shifts observed during the shelf-life period. Core microbiota of meat and burgers included Pseudomonas spp., Psychrobacter spp., Shewanella spp. and Brochothrix spp., while expired burgers were dominated by Latilactobacillus spp. and Leuconostoc spp. Cleaning and disinfection (C&D) procedures altered the microbial composition of work surfaces, which still harbored Hafnia spp. and Acinetobacter spp. after C&D. Resistome analysis showed a low overall abundance of resistance genes, suggesting that effective interventions during processing may mitigate their transmission. However, biocide resistance genes were frequently found, indicating potential biofilm formation or inefficient C&D protocols. This study demonstrates the utility of combining culturing techniques and WMS for comprehensive of the microbiome and resistome characterization in food processing lines.},
}

Animals
*Microbiota/genetics
*Food Microbiology
*Bacteria/genetics/classification/isolation & purification/drug effects
*Food Handling/methods
Poultry/microbiology
Metagenomics/methods
High-Throughput Nucleotide Sequencing
Drug Resistance, Bacterial/genetics
Meat/microbiology
Poultry Products/microbiology

@article {pmid39157177,
year = {2024},
author = {Huang, SS and Qiu, JY and Li, SP and Ma, YQ and He, J and Han, LN and Jiao, LL and Xu, C and Mao, YM and Zhang, YM},
title = {Microbial signatures predictive of short-term prognosis in severe pneumonia.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1397717},
pmid = {39157177},
issn = {2235-2988},
mesh = {Humans ; Male ; Female ; Prognosis ; Retrospective Studies ; Middle Aged ; Aged ; *Bronchoalveolar Lavage Fluid/microbiology ; *Microbiota ; Pneumonia/microbiology/mortality ; Bacteria/classification/genetics/isolation & purification ; High-Throughput Nucleotide Sequencing ; Lung/microbiology/pathology ; Metagenomics ; Machine Learning ; },
abstract = {OBJECTIVE: This retrospective cohort study aimed to investigate the composition and diversity of lung microbiota in patients with severe pneumonia and explore its association with short-term prognosis.

METHODS: A total of 301 patients diagnosed with severe pneumonia underwent bronchoalveolar lavage fluid metagenomic next-generation sequencing (mNGS) testing from February 2022 to January 2024. After applying exclusion criteria, 236 patients were included in the study. Baseline demographic and clinical characteristics were compared between survival and non-survival groups. Microbial composition and diversity were analyzed using alpha and beta diversity metrics. Additionally, LEfSe analysis and machine learning methods were employed to identify key pathogenic microorganism associated with short-term mortality. Microbial interaction modes were assessed through network co-occurrence analysis.

RESULTS: The overall 28-day mortality rate was 37.7% in severe pneumonia. Non-survival patients had a higher prevalence of hypertension and exhibited higher APACHE II and SOFA scores, higher procalcitonin (PCT), and shorter hospitalization duration. Microbial α and β diversity analysis showed no significant differences between the two groups. However, distinct species diversity patterns were observed, with the non-survival group showing a higher abundance of Acinetobacter baumannii, Klebsiella pneumoniae, and Enterococcus faecium, while the survival group had a higher prevalence of Corynebacterium striatum and Enterobacter. LEfSe analysis identified 29 distinct terms, with 10 potential markers in the non-survival group, including Pseudomonas sp. and Enterococcus durans. Machine learning models selected 16 key pathogenic bacteria, such as Klebsiella pneumoniae, significantly contributing to predicting short-term mortality. Network co-occurrence analysis revealed greater complexity in the non-survival group compared to the survival group, with differences in central genera.

CONCLUSION: Our study highlights the potential significance of lung microbiota composition in predicting short-term prognosis in severe pneumonia patients. Differences in microbial diversity and composition, along with distinct microbial interaction modes, may contribute to variations in short-term outcomes. Further research is warranted to elucidate the clinical implications and underlying mechanisms of these findings.},
}

Humans
Male
Female
Prognosis
Retrospective Studies
Middle Aged
Aged
*Bronchoalveolar Lavage Fluid/microbiology
*Microbiota
Pneumonia/microbiology/mortality
Bacteria/classification/genetics/isolation & purification
High-Throughput Nucleotide Sequencing
Lung/microbiology/pathology
Metagenomics
Machine Learning

@article {pmid39154041,
year = {2024},
author = {Ma, T and Zhuang, Y and Lu, W and Tu, Y and Diao, Q and Fan, X and Zhang, N},
title = {Seven hundred and ninety-seven metagenome-assembled genomes from the goat rumen during early life.},
journal = {Scientific data},
volume = {11},
number = {1},
pages = {897},
pmid = {39154041},
issn = {2052-4463},
mesh = {Animals ; *Goats/microbiology ; *Rumen/microbiology ; *Metagenome ; Gastrointestinal Microbiome ; },
abstract = {The rumen microbiome plays an important role in providing energy and protein to the host. Manipulation of rumen microbiome during early life may have a long-term beneficial effect on the health, growth performance, and feed efficiency of ruminants. To better understand the profiles and functional potentials of rumen microbiome in young ruminants, metagenomic binning was performed to investigate the rumen microbiome of goat kids from one to 84 days of age. A total of 797 metagenome-assembled genomes (MAGs) were recovered from the rumen of 42 Laiwu black goat kids. Our findings provide fundamental knowledge of the rumen microbiome during early life based on metagenomic binning, which may provide insights into effective strategies to achieve long-term beneficial effects on animal health and production.},
}

Animals
*Goats/microbiology
*Rumen/microbiology
*Metagenome
Gastrointestinal Microbiome

@article {pmid38918632,
year = {2024},
author = {Mei, Z and Wang, F and Bhosle, A and Dong, D and Mehta, R and Ghazi, A and Zhang, Y and Liu, Y and Rinott, E and Ma, S and Rimm, EB and Daviglus, M and Willett, WC and Knight, R and Hu, FB and Qi, Q and Chan, AT and Burk, RD and Stampfer, MJ and Shai, I and Kaplan, RC and Huttenhower, C and Wang, DD},
title = {Strain-specific gut microbial signatures in type 2 diabetes identified in a cross-cohort analysis of 8,117 metagenomes.},
journal = {Nature medicine},
volume = {30},
number = {8},
pages = {2265-2276},
pmid = {38918632},
issn = {1546-170X},
support = {R00DK119412//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R01NR01999//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R01AG077489//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; P30DK046200//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; 897161//American Heart Association (American Heart Association, Inc.)/ ; 209933838//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; R24DK110499//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; },
mesh = {*Diabetes Mellitus, Type 2/microbiology/genetics ; Humans ; *Gastrointestinal Microbiome/genetics ; *Metagenome/genetics ; *Phylogeny ; Cohort Studies ; Male ; Middle Aged ; Female ; China/epidemiology ; Dysbiosis/microbiology ; United States/epidemiology ; Israel/epidemiology ; Europe/epidemiology ; },
abstract = {The association of gut microbial features with type 2 diabetes (T2D) has been inconsistent due in part to the complexity of this disease and variation in study design. Even in cases in which individual microbial species have been associated with T2D, mechanisms have been unable to be attributed to these associations based on specific microbial strains. We conducted a comprehensive study of the T2D microbiome, analyzing 8,117 shotgun metagenomes from 10 cohorts of individuals with T2D, prediabetes, and normoglycemic status in the United States, Europe, Israel and China. Dysbiosis in 19 phylogenetically diverse species was associated with T2D (false discovery rate < 0.10), for example, enriched Clostridium bolteae and depleted Butyrivibrio crossotus. These microorganisms also contributed to community-level functional changes potentially underlying T2D pathogenesis, for example, perturbations in glucose metabolism. Our study identifies within-species phylogenetic diversity for strains of 27 species that explain inter-individual differences in T2D risk, such as Eubacterium rectale. In some cases, these were explained by strain-specific gene carriage, including loci involved in various mechanisms of horizontal gene transfer and novel biological processes underlying metabolic risk, for example, quorum sensing. In summary, our study provides robust cross-cohort microbial signatures in a strain-resolved manner and offers new mechanistic insights into T2D.},
}

*Diabetes Mellitus, Type 2/microbiology/genetics
Humans
*Gastrointestinal Microbiome/genetics
*Metagenome/genetics
*Phylogeny
Cohort Studies
Male
Middle Aged
Female
China/epidemiology
Dysbiosis/microbiology
United States/epidemiology
Israel/epidemiology
Europe/epidemiology

@article {pmid39153763,
year = {2024},
author = {Cleminson, JS and Thomas, J and Stewart, CJ and Campbell, D and Gennery, A and Embleton, ND and Köglmeier, J and Wong, T and Spruce, M and Berrington, JE},
title = {Gut microbiota and intestinal rehabilitation: a prospective childhood cohort longitudinal study of short bowel syndrome (the MIRACLS study): study protocol.},
journal = {BMJ open gastroenterology},
volume = {11},
number = {1},
pages = {},
doi = {10.1136/bmjgast-2024-001450},
pmid = {39153763},
issn = {2054-4774},
mesh = {Humans ; *Short Bowel Syndrome/microbiology/epidemiology ; *Gastrointestinal Microbiome/physiology ; *Quality of Life/psychology ; Prospective Studies ; Child ; Child, Preschool ; Infant ; Longitudinal Studies ; Female ; Adolescent ; *Feces/microbiology ; Male ; *Parenteral Nutrition/methods/statistics & numerical data ; Infant, Newborn ; RNA, Ribosomal, 16S ; Intestines/microbiology ; },
abstract = {INTRODUCTION: Short bowel syndrome (SBS) is the predominant cause of paediatric intestinal failure. Although life-saving, parenteral nutrition (PN) is linked to complications and may impact quality of life (QoL). Most children will experience intestinal rehabilitation (IR), but the mechanisms underpinning this remain to be understood. SBS is characterised by abnormal microbiome patterns, which might serve as predictive indicators for IR. We aim to characterise the microbiome profiles of children with SBS during IR, concurrently exploring how parental perspectives of QoL relate to IR.

METHODS AND ANALYSIS: This study will enrol a minimum of 20 paediatric patients with SBS (0-18 years). Clinical data and biological samples will be collected over a 2-year study period. We will apply 16S rRNA gene sequencing to analyse the microbiome from faecal and gut tissue samples, with additional shotgun metagenomic sequencing specifically on samples obtained around the time of IR. Gas chromatography with flame ionisation detection will profile faecal short-chain fatty acids. Plasma citrulline and urinary intestinal fatty acid binding proteins will be measured annually. We will explore microbiome-clinical covariate interactions. Furthermore, we plan to assess parental perspectives on QoL during PN and post-IR by inviting parents to complete the Paediatric Quality of Life questionnaire at recruitment and after the completion of IR.

ETHICS AND DISSEMINATION: Ethical approval was obtained from the East Midlands-Nottingham 2 Research Ethics Committee (22/EM/0233; 28 November 2022). Recruitment began in February 2023. Outcomes of the study will be published in peer-reviewed scientific journals and presented at scientific meetings. A lay summary of the results will be made available to participants and the public.

TRIAL REGISTRATION NUMBER: ISRCTN90620576.},
}

Humans
*Short Bowel Syndrome/microbiology/epidemiology
*Gastrointestinal Microbiome/physiology
*Quality of Life/psychology
Prospective Studies
Child
Child, Preschool
Infant
Longitudinal Studies
Female
Adolescent
*Feces/microbiology
Male
*Parenteral Nutrition/methods/statistics & numerical data
Infant, Newborn
RNA, Ribosomal, 16S
Intestines/microbiology

@article {pmid39152482,
year = {2024},
author = {Luo, W and Zhao, M and Dwidar, M and Gao, Y and Xiang, L and Wu, X and Medema, MH and Xu, S and Li, X and Schäfer, H and Chen, M and Feng, R and Zhu, Y},
title = {Microbial assimilatory sulfate reduction-mediated H2S: an overlooked role in Crohn's disease development.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {152},
pmid = {39152482},
issn = {2049-2618},
support = {82370551//National Natural Science Foundation of China/ ; 82270579//National Natural Science Foundation of China/ ; 82100577//National Natural Science Foundation of China/ ; 2024GXNSFFA010009//Natural Science Foundation of Guangxi Zhuang Autonomous Region/ ; },
mesh = {*Crohn Disease/microbiology ; Humans ; *Gastrointestinal Microbiome ; *Hydrogen Sulfide/metabolism ; Animals ; Mice ; *Sulfates/metabolism ; Escherichia coli/genetics/metabolism ; Feces/microbiology ; Dysbiosis/microbiology ; Colon/microbiology ; Metagenomics ; Oxidation-Reduction ; Disease Models, Animal ; Female ; },
abstract = {BACKGROUND: H2S imbalances in the intestinal tract trigger Crohn's disease (CD), a chronic inflammatory gastrointestinal disorder characterized by microbiota dysbiosis and barrier dysfunction. However, a comprehensive understanding of H2S generation in the gut, and the contributions of both microbiota and host to systemic H2S levels in CD, remain to be elucidated. This investigation aimed to enhance comprehension regarding the sulfidogenic potential of both the human host and the gut microbiota.

RESULTS: Our analysis of a treatment-naive CD cohorts' fecal metagenomic and biopsy metatranscriptomic data revealed reduced expression of host endogenous H2S generation genes alongside increased abundance of microbial exogenous H2S production genes in correlation with CD. While prior studies focused on microbial H2S production via dissimilatory sulfite reductases, our metagenomic analysis suggests the assimilatory sulfate reduction (ASR) pathway is a more significant contributor in the human gut, given its high prevalence and abundance. Subsequently, we validated our hypothesis experimentally by generating ASR-deficient E. coli mutants ∆cysJ and ∆cysM through the deletion of sulfite reductase and L-cysteine synthase genes. This alteration significantly affected bacterial sulfidogenic capacity, colon epithelial cell viability, and colonic mucin sulfation, ultimately leading to colitis in murine model. Further study revealed that gut microbiota degrade sulfopolysaccharides and assimilate sulfate to produce H2S via the ASR pathway, highlighting the role of sulfopolysaccharides in colitis and cautioning against their use as food additives.

CONCLUSIONS: Our study significantly advances understanding of microbial sulfur metabolism in the human gut, elucidating the complex interplay between diet, gut microbiota, and host sulfur metabolism. We highlight the microbial ASR pathway as an overlooked endogenous H2S producer and a potential therapeutic target for managing CD. Video Abstract.},
}

*Crohn Disease/microbiology
Humans
*Gastrointestinal Microbiome
*Hydrogen Sulfide/metabolism
Animals
Mice
*Sulfates/metabolism
Escherichia coli/genetics/metabolism
Feces/microbiology
Dysbiosis/microbiology
Colon/microbiology
Metagenomics
Oxidation-Reduction
Disease Models, Animal
Female

@article {pmid38977080,
year = {2024},
author = {Lichtenegger, AS and Posadas-Cantera, S and Badr, MT and Häcker, G},
title = {Comparison of the diversity of anaerobic-cultured gut bacterial communities on different culture media using 16S rDNA sequencing.},
journal = {Journal of microbiological methods},
volume = {224},
number = {},
pages = {106988},
doi = {10.1016/j.mimet.2024.106988},
pmid = {38977080},
issn = {1872-8359},
mesh = {Humans ; *Culture Media/chemistry ; *RNA, Ribosomal, 16S/genetics ; *Feces/microbiology ; *Bacteria, Anaerobic/genetics/isolation & purification/classification/growth & development ; *Gastrointestinal Microbiome ; *DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; Biodiversity ; Bacteria/genetics/classification/isolation & purification/drug effects/growth & development ; },
abstract = {The gut microbiome is a dense and diverse community of different microorganisms that deeply influence human physiology and that have important interactions with pathogens. For the correct antibiotic treatment of infections, with its twin goals of effective inhibition of the pathogen and limitation of collateral damage to the microbiome, the identification of infectious organisms is key. Microbiological culturing is still the mainstay of pathogen identification, and anaerobic species are among the most demanding bacterial communities to culture. This study aimed to evaluate the impact of growth media on the culture of an-aerobic bacteria from human stool samples. Stool samples from eight human subjects were cultured each on a yeast extract cysteine blood agar (HCB) and a modified peptone-yeast extract-glucose (MPYG) plate and subjected to Illumina NGS analysis after DNA extraction and amplification. The results showed tight clustering of sequencing samples belonging to the same human subject. Various differences in bacterial richness and evenness could be observed between the two media, with HCB plates supporting the growth of a more diverse microbial community, and MPYG plates improving the growth rates of certain taxa. No statistical significance was observed between the groups. This study highlights the importance of choosing the appropriate growth media for anaerobic bacterial culture and adjusting culture conditions to target specific pathological conditions. HCB plates are suitable for standard microbiological diagnostics, while MPYG plates may be more appropriate for targeting specific conditions. This work emphasizes the role of next-generation sequencing in supporting future research in clinical microbiology.},
}

Humans
*Culture Media/chemistry
*RNA, Ribosomal, 16S/genetics
*Feces/microbiology
*Bacteria, Anaerobic/genetics/isolation & purification/classification/growth & development
*Gastrointestinal Microbiome
*DNA, Bacterial/genetics
DNA, Ribosomal/genetics
High-Throughput Nucleotide Sequencing/methods
Sequence Analysis, DNA/methods
Biodiversity
Bacteria/genetics/classification/isolation & purification/drug effects/growth & development

@article {pmid38750900,
year = {2024},
author = {Lewis, JD and Daniel, SG and Li, H and Hao, F and Patterson, AD and Hecht, AL and Brensinger, CM and Wu, GD and Bittinger, K and , and , },
title = {Surgery for Crohn's Disease Is Associated With a Dysbiotic Microbiome and Metabolome: Results From Two Prospective Cohorts.},
journal = {Cellular and molecular gastroenterology and hepatology},
volume = {18},
number = {3},
pages = {101357},
pmid = {38750900},
issn = {2352-345X},
mesh = {Humans ; *Crohn Disease/microbiology/surgery/pathology/metabolism ; *Gastrointestinal Microbiome ; Female ; Male ; Adult ; *Metabolome ; Prospective Studies ; *Feces/microbiology ; *Dysbiosis/microbiology ; Middle Aged ; Bile Acids and Salts/metabolism ; Butyrates/metabolism ; Metagenomics/methods ; Cholestenones/metabolism ; Ileum/microbiology/surgery/metabolism/pathology ; Young Adult ; Bacteria/isolation & purification/classification/metabolism/genetics ; },
abstract = {BACKGROUND & AIMS: Crohn's disease is associated with alterations in the gut microbiome and metabolome described as dysbiosis. We characterized the microbial and metabolic consequences of ileal resection, the most common Crohn's disease surgery.

METHODS: Patients with and without intestinal resection were identified from the Diet to Induce Remission in Crohn's Disease and Study of a Prospective Adult Research Cohort with Inflammatory Bowel Disease studies. Stool samples were analyzed with shotgun metagenomics sequencing. Fecal butyrate was measured with [1]H nuclear magnetic resonance spectroscopy. Fecal bile acids and plasma 7α-hydroxy-4-cholesten-3-one (C4) was measured with mass spectrometry.

RESULTS: Intestinal resection was associated with reduced alpha diversity and altered beta diversity with increased Proteobacteria and reduced Bacteroidetes and Firmicutes. Surgery was associated with higher representation of genes in the KEGG pathway for ABC transporters and reduction in genes related to bacterial metabolism. Surgery was associated with reduced concentration of the But gene but this did not translate to reduced fecal butyrate concentration. Surgery was associated with decreased abundance of bai operon genes, with increased plasma C4 concentration, increased primary bile acids and reduced secondary bile acids, including isoLCA. Additionally, Egerthella lenta, Adlercreutzia equalofaciens, and Gordonibacter pamelaeae were lower in abundance among patients with prior surgery in both cohorts.

CONCLUSIONS: In 2 different populations, prior surgery in Crohn's disease is associated with altered fecal microbiome. Patients who had undergone ileal resection had reduction in the potentially beneficial bacteria E lenta and related actinobacteria and secondary bile acids, including isoLCA, suggesting that these could be biomarkers of patients at higher risk for disease progression.},
}

Humans
*Crohn Disease/microbiology/surgery/pathology/metabolism
*Gastrointestinal Microbiome
Female
Male
Adult
*Metabolome
Prospective Studies
*Feces/microbiology
*Dysbiosis/microbiology
Middle Aged
Bile Acids and Salts/metabolism
Butyrates/metabolism
Metagenomics/methods
Cholestenones/metabolism
Ileum/microbiology/surgery/metabolism/pathology
Young Adult
Bacteria/isolation & purification/classification/metabolism/genetics

@article {pmid39152146,
year = {2024},
author = {Mizsei, E and Radovics, D and Rák, G and Budai, M and Bancsik, B and Szabolcs, M and Sos, T and Lengyel, S},
title = {Alpine viper in changing climate: thermal ecology and prospects of a cold-adapted reptile in the warming Mediterranean.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {18988},
pmid = {39152146},
issn = {2045-2322},
support = {150510498//Mohamed bin Zayed Species Conservation Fund/ ; 15478-1//Rufford Foundation/ ; PD146621//Nemzeti Kutatási Fejlesztési és Innovációs Hivatal/ ; K106133//Nemzeti Kutatási Fejlesztési és Innovációs Hivatal/ ; K134391//Nemzeti Kutatási Fejlesztési és Innovációs Hivatal,Hungary/ ; },
mesh = {Animals ; *Viperidae/physiology ; *Climate Change ; Male ; Female ; Ecosystem ; Body Temperature Regulation/physiology ; Greece ; Cold Temperature ; Adaptation, Physiological ; Mediterranean Region ; Acclimatization/physiology ; Phylogeny ; Body Temperature/physiology ; },
abstract = {In a rapidly changing thermal environment, reptiles are primarily dependent on in situ adaptation because of their limited ability to disperse and the restricted opportunity to shift their ranges. However, the rapid pace of climate change may surpass these adaptation capabilities or elevate energy expenditures. Therefore, understanding the variability in thermal traits at both individual and population scales is crucial, offering insights into reptiles' vulnerability to climate change. We studied the thermal ecology of the endangered Greek meadow viper (Vipera graeca), an endemic venomous snake of fragmented alpine-subalpine meadows above 1600 m of the Pindos mountain range in Greece and Albania, to assess its susceptibility to anticipated changes in the alpine thermal environment. We measured preferred body temperature in artificial thermal gradient, field body temperatures of 74 individuals in five populations encompassing the entire geographic range of the species, and collected data on the available of temperatures for thermoregulation. We found that the preferred body temperature (Tp) differed only between the northernmost and the southernmost populations and increased with female body size but did not depend on sex or the gravidity status of females. Tp increased with latitude but was unaffected by the phylogenetic position of the populations. We also found high accuracy of thermoregulation in V. graeca populations and variation in the thermal quality of habitats throughout the range. The overall effectiveness of thermoregulation was high, indicating that V. graeca successfully achieves its target temperatures and exploits the thermal landscape. Current climatic conditions limit the activity period by an estimated 1278 h per year, which is expected to increase considerably under future climate scenarios. Restricted time available for thermoregulation, foraging and reproduction will represent a serious threat to the fitness of individuals and the persistence of populations in addition to habitat loss due to mining, tourism or skiing and habitat degradation due to overgrazing in the shrinking mountaintop habitats of V. graeca.},
}

Animals
*Viperidae/physiology
*Climate Change
Male
Female
Ecosystem
Body Temperature Regulation/physiology
Greece
Cold Temperature
Adaptation, Physiological
Mediterranean Region
Acclimatization/physiology
Phylogeny
Body Temperature/physiology

@article {pmid39151620,
year = {2024},
author = {Zheng, Y and Wu, Z and Wang, P and Wei, Y and Jia, K and Zhang, M and Shi, X and Zhang, L and Li, J},
title = {Long-chain fatty acids facilitate acidogenic fermentation of food waste: Attention to the microbial response and the change of core metabolic pathway under saturated and unsaturated fatty acids loading.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {175565},
doi = {10.1016/j.scitotenv.2024.175565},
pmid = {39151620},
issn = {1879-1026},
abstract = {Long-chain fatty acids (LCFAs) are recognized as a significant inhibitory factor in anaerobic digestion of food waste (FW), yet they are inevitably present in FW due to lipid hydrolysis. Given their distinct synthesis mechanism from traditional anaerobic digestion, little is known about the effect of LCFAs on FW acidogenic fermentation. This study reveals that total volatile fatty acids (VFAs) production increased by 9.98 % and 4.03 % under stearic acid and oleic acid loading, respectively. Acetic acid production increased by 20.66 % under stearic acid loading compared to the control group (CK). However, the LCFA stress restricted the degradation of solid organic matter, particularly under oleic acid stress. Analysis of microbial community structure and quorum sensing (QS) indicates that LCFA stress enhanced the relative abundance of Lactobacillus and Klebsiella. In QS system, the relative abundance of luxS declined from 0.157 % to 0.116 % and 0.125 % under oleic acid and stearic acid stress, respectively. LCFA stress limited the Autoinducer-2 (AI-2) biosynthesis, suggesting that microorganisms cannot use QS to resist the LCFA stress. Metagenomic sequencing showed that LCFA stress promoted acetic acid production via the conversion of pyruvate and acetyl-CoA to acetate. Direct conversion of pyruvate to acetic acid increased by 47.23 % compared to the CK group, accounting for the enhanced acetic acid production under stearic acid loading. The abundance of β-oxidation pathway under stearic acid loading was lower than under oleic acid loading. Overall, the stimulating direct conversion of pyruvate plays a pivotal role in enhancing acetic acid biosynthesis under stearic acid loading, providing insights into the effect of LCFA on mechanism of FW acidogenic fermentation.},
}

@article {pmid39147529,
year = {2024},
author = {Xiang, L and Zhuo, S and Luo, W and Tian, C and Xu, S and Li, X and Zhu, Y and Feng, R and Chen, M},
title = {Decoding polyphenol metabolism in patients with Crohn's disease: Insights from diet, gut microbiota, and metabolites.},
journal = {Food research international (Ottawa, Ont.)},
volume = {192},
number = {},
pages = {114852},
doi = {10.1016/j.foodres.2024.114852},
pmid = {39147529},
issn = {1873-7145},
mesh = {Humans ; *Crohn Disease/microbiology/metabolism/drug therapy ; *Gastrointestinal Microbiome/physiology ; *Polyphenols/metabolism ; Female ; Male ; Adult ; *Diet ; Hippurates/metabolism ; Middle Aged ; Young Adult ; Bacteria/classification/metabolism/genetics ; Feces/microbiology ; },
abstract = {Crohn's disease (CD) is a chronic and progressive inflammatory disease that can involve any part of the gastrointestinal tract. The protective role of dietary polyphenols has been documented in preclinical models of CD. Gut microbiota mediates the metabolism of polyphenols and affects their bioactivity and physiological functions. However, it remains elusive the capacity of microbial polyphenol metabolism in CD patients and healthy controls (HCs) along with its correlation with polyphenols intake and polyphenol-derived metabolites. Thus, we aimed to decode polyphenol metabolism in CD patients through aspects of diet, gut microbiota, and metabolites. Dietary intake analysis revealed that CD patients exhibited decreased intake of polyphenols. Using metagenomic data from two independent clinical cohorts (FAH-SYSU and PRISM), we quantified abundance of polyphenol degradation associated bacteria and functional genes in CD and HCs and observed a lower capacity of flavonoids degradation in gut microbiota residing in CD patients. Furthermore, through analysis of serum metabolites and enterotypes in participants of FAH-SYSU cohort, we observed that CD patients exhibited reduced levels of serum hippuric acid (HA), one of polyphenol-derived metabolites. HA level was higher in healthier enterotypes (characterized by dominance of Ruminococcaceae and Prevotellaceae, dominant by HCs) and positively correlated with multiple polyphenols intake and abundance of bacteria engaged in flavonoids degradation as well as short-chain fatty acid production, which could serve as a biomarker for effective polyphenol metabolism by the gut microbiota and a healthier gut microbial community structure. Overall, our findings provide a foundation for future work exploring the polyphenol-based or microbiota-targeted therapeutic strategies in CD.},
}

Humans
*Crohn Disease/microbiology/metabolism/drug therapy
*Gastrointestinal Microbiome/physiology
*Polyphenols/metabolism
Female
Male
Adult
*Diet
Hippurates/metabolism
Middle Aged
Young Adult
Bacteria/classification/metabolism/genetics
Feces/microbiology

@article {pmid39053208,
year = {2024},
author = {Kong, Z and Wang, H and Wang, H and Man, S and Yan, Q},
title = {Magnetite-mediated shifts in denitrifying consortia in bioelectrochemical system: Insights into species selection and metabolic dynamics.},
journal = {Water research},
volume = {262},
number = {},
pages = {122132},
doi = {10.1016/j.watres.2024.122132},
pmid = {39053208},
issn = {1879-2448},
mesh = {*Denitrification ; *Ferrosoferric Oxide/metabolism ; Geobacter/metabolism ; Nitrates/metabolism ; Microbial Consortia ; Bioreactors/microbiology ; },
abstract = {Conductive materials, such as magnetite, are recognized for their ability to enhance electron transfer and stimulate microbial metabolic activities. This study aimed to elucidate the metabolic potential and species interactions of dominant microbial species within complex communities influenced by magnetite. It indicated that the optimal dosage of magnetite at 4.5 mg/cm[2], would significantly improve denitrification efficiency and then reduce the time for removing 50 mg/L nitrate by 24.33 %. This enhancement was attributed to the reduced charge transfer resistance and the promoted formation of extracellular polymeric substances (EPS) facilitated by magnetite. Metagenomic analysis revealed that magnetite addition mitigated the competition among truncated denitrifiers for downstream nitrogen species, diminished the contribution of bacteria with complete nitrogen metabolism pathways to denitrification, and fostered a transition towards co-denitrification through interspecies cooperation, consequently leading to decreased nitrite accumulation and increased tolerance to nitrate shock loads. Furthermore, an in-depth study on a key species, Geobacter anodireducens JN93 within the bioelectrochemical system revealed that while magnetite with varying Fe(II) and Fe(III) ratios improved denitrification performance, the metabolic potential of Geobacter sp. varied for different nitrogen metabolism pathways. Collectively, this research provides insights into the microecological effects of magnetite on denitrifying consortia by shifting interspecific interactions via enhanced electron transfer.},
}

*Denitrification
*Ferrosoferric Oxide/metabolism
Geobacter/metabolism
Nitrates/metabolism
Microbial Consortia
Bioreactors/microbiology

@article {pmid39043054,
year = {2024},
author = {Perdomo, A and Calle, A},
title = {Assessment of microbial communities in a dairy farm from a food safety perspective.},
journal = {International journal of food microbiology},
volume = {423},
number = {},
pages = {110827},
doi = {10.1016/j.ijfoodmicro.2024.110827},
pmid = {39043054},
issn = {1879-3460},
mesh = {Animals ; *Food Safety ; *Dairying ; Cattle ; *Farms ; *Milk/microbiology ; Bacteria/isolation & purification/classification/genetics ; Microbiota ; Food Microbiology ; Feces/microbiology ; Seasons ; Animal Feed/microbiology ; Staphylococcus aureus/isolation & purification/genetics ; },
abstract = {Microbial communities associated with dairy farm operations have a significant influence on food safety, dairy product quality, and animal health. This study aimed to create a microbial mapping at a dairy farm to learn about their bacterial diversity, distribution, and potential dissemination pathways. The investigation included the detection of key zoonotic pathogens, enumeration of Staphylococcus aureus and Escherichia coli as indicators of typical bacterial loads in a dairy production environment, and a microbiome analysis using metagenomics. A total of 160 samples (environmental, udder swabs, feed, feces, raw milk, and water) were collected during winter (N = 80) and spring (N = 80). In winter, Cronobacter spp. were detected in four feed and two water samples; L. monocytogenes was identified in two samples, one from feces and one from a cattle mat; E. coli O157:H7 was found in two feed samples. On the other hand, during spring, Cronobacter spp. were present in four feed samples and one hallway drain, with only one feed sample testing positive for E. coli O157:H7, while L. monocytogenes was absent during the spring season. Regarding microbial counts, there was no significant difference between the two seasons (p = 0.068) for S. aureus; however, a significant difference (p = 0.025) was observed for E. coli. Environmental microbiome analysis showed the presence of Proteobacteria (46.0 %) and Firmicutes (27.2 %) as the dominant phyla during both seasons. Moraxellaceae (11.8 %) and Pseudomonadaceae (10.62 %) were notable during winter, while Lactobacillaceae (13.0 %) and Enterobacteriaceae (12.6 %) were prominent during spring. These findings offer valuable insights into microbial distribution within a dairy farm and potential risks to animal and human health through environmental cross-contamination.},
}

Animals
*Food Safety
*Dairying
Cattle
*Farms
*Milk/microbiology
Bacteria/isolation & purification/classification/genetics
Microbiota
Food Microbiology
Feces/microbiology
Seasons
Animal Feed/microbiology
Staphylococcus aureus/isolation & purification/genetics

@article {pmid39032335,
year = {2024},
author = {Fan, Y and Zhou, Z and Liu, F and Qian, L and Yu, X and Huang, F and Hu, R and Su, H and Gu, H and Yan, Q and He, Z and Wang, C},
title = {The vertical partitioning between denitrification and dissimilatory nitrate reduction to ammonium of coastal mangrove sediment microbiomes.},
journal = {Water research},
volume = {262},
number = {},
pages = {122113},
doi = {10.1016/j.watres.2024.122113},
pmid = {39032335},
issn = {1879-2448},
mesh = {*Denitrification ; *Nitrates/metabolism ; *Geologic Sediments/microbiology ; *Microbiota ; *Ammonium Compounds/metabolism ; Wetlands ; },
abstract = {Mangrove aquatic ecosystems receive substantial nitrogen (N) inputs from both land and sea, playing critical roles in modulating coastal N fluxes. The microbially-mediated competition between denitrification and dissimilatory nitrate reduction to ammonium (DNRA) in mangrove sediments significantly impacts the N fate and transformation processes. Despite their recognized role in N loss or retention in surface sediments, how these two processes vary with sediment depths and their influential factors remain elusive. Here, we employed a comprehensive approach combining [15]N isotope tracer, quantitative PCR (qPCR) and metagenomics to verify the vertical dynamics of denitrification and DNRA across five 100-cm mangrove sediment cores. Our results revealed a clear vertical partitioning, with denitrification dominated in 0-30 cm sediments, while DNRA played a greater role with increasing depths. Quantification of denitrification and DNRA functional genes further explained this phenomenon. Taxonomic analysis identified Pseudomonadota as the primary denitrification group, while Planctomycetota and Pseudomonadota exhibited high proportion in DNRA group. Furthermore, genome-resolved metagenomics revealed multiple salt-tolerance strategies and aromatic compound utilization potential in denitrification assemblages. This allowed denitrification to dominate in oxygen-fluctuating and higher-salinity surface sediments. However, the elevated C/N in anaerobic deep sediments favored DNRA, tending to generate biologically available NH4[+]. Together, our results uncover the depth-related variations in the microbially-mediated competition between denitrification and DNRA, regulating N dynamics in mangrove ecosystems.},
}

*Denitrification
*Nitrates/metabolism
*Geologic Sediments/microbiology
*Microbiota
*Ammonium Compounds/metabolism
Wetlands

@article {pmid39029427,
year = {2024},
author = {Iacovacci, J and Serafini, MS and Avuzzi, B and Badenchini, F and Cicchetti, A and Devecchi, A and Dispinzieri, M and Doldi, V and Giandini, T and Gioscio, E and Mancinelli, E and Noris Chiorda, B and Orlandi, E and Palorini, F and Possenti, L and Reis Ferreira, M and Villa, S and Zaffaroni, N and De Cecco, L and Valdagni, R and Rancati, T},
title = {Intestinal microbiota composition is predictive of radiotherapy-induced acute gastrointestinal toxicity in prostate cancer patients.},
journal = {EBioMedicine},
volume = {106},
number = {},
pages = {105246},
pmid = {39029427},
issn = {2352-3964},
mesh = {Humans ; Male ; *Gastrointestinal Microbiome/radiation effects ; *Prostatic Neoplasms/radiotherapy ; Aged ; *Radiation Injuries/etiology/microbiology/diagnosis ; Middle Aged ; Metagenomics/methods ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; Radiotherapy/adverse effects ; Bacteria/classification/genetics/radiation effects ; Gastrointestinal Diseases/etiology/microbiology ; Metagenome ; },
abstract = {BACKGROUND: The search for factors beyond the radiotherapy dose that could identify patients more at risk of developing radio-induced toxicity is essential to establish personalised treatment protocols for improving the quality-of-life of survivors. To investigate the role of the intestinal microbiota in the development of radiotherapy-induced gastrointestinal toxicity, the MicroLearner observational cohort study characterised the intestinal microbiota of 136 (discovery) and 79 (validation) consecutive prostate cancer patients at baseline radiotherapy.

METHODS: Gastrointestinal toxicity was assessed weekly during RT using CTCAE. An average grade >1.3 over time points was used to identify patients suffering from persistent acute toxicity (endpoint). The microbiota of patients was quantified from the baseline faecal samples using 16S rRNA gene sequencing technology and the Ion Reporter metagenomic pipeline. Statistical techniques and computational and machine learning tools were used to extract, functionally characterise, and predict core features of the bacterial communities of patients who developed acute gastrointestinal toxicity.

FINDINGS: Analysis of the core bacterial composition in the discovery cohort revealed a cluster of patients significantly enriched for toxicity, displaying a toxicity rate of 60%. Based on selected high-risk microbiota compositional features, we developed a clinical decision tree that could effectively predict the risk of toxicity based on the relative abundance of genera Faecalibacterium, Bacteroides, Parabacteroides, Alistipes, Prevotella and Phascolarctobacterium both in internal and external validation cohorts.

INTERPRETATION: We provide evidence showing that intestinal bacteria profiling from baseline faecal samples can be effectively used in the clinic to improve the pre-radiotherapy assessment of gastrointestinal toxicity risk in prostate cancer patients.

FUNDING: Italian Ministry of Health (Promotion of Institutional Research INT-year 2016, 5 × 1000, Ricerca Corrente funds). Fondazione Regionale per la Ricerca Biomedica (ID 2721017). AIRC (IG 21479).},
}

Humans
Male
*Gastrointestinal Microbiome/radiation effects
*Prostatic Neoplasms/radiotherapy
Aged
*Radiation Injuries/etiology/microbiology/diagnosis
Middle Aged
Metagenomics/methods
Feces/microbiology
RNA, Ribosomal, 16S/genetics
Radiotherapy/adverse effects
Bacteria/classification/genetics/radiation effects
Gastrointestinal Diseases/etiology/microbiology
Metagenome

@article {pmid39111271,
year = {2024},
author = {Zhang, Y and Chen, W and Yuan, Y and Liao, X and Mi, J},
title = {Decreasing light exposure increases the abundance of antibiotic resistance genes in the cecum and feces of laying hens.},
journal = {The Science of the total environment},
volume = {949},
number = {},
pages = {175275},
doi = {10.1016/j.scitotenv.2024.175275},
pmid = {39111271},
issn = {1879-1026},
mesh = {Animals ; *Chickens/microbiology ; *Cecum/microbiology ; *Gastrointestinal Microbiome/drug effects ; *Feces/microbiology ; *Drug Resistance, Microbial/genetics ; Light ; Female ; Bacteria/genetics ; Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; },
abstract = {The gut microbiome plays a crucial role in maintaining animal health and is influenced by various factors, including light exposure; however, the response in laying hens of the gut microbiome to intermittent light regimes and the related impact on antibiotic resistance genes (ARGs) remain poorly understood. In this study, we divided 20-week-old laying hens into two groups. These groups were exposed to either continuous normal light or intermittent light for 8 weeks. The feces and cecal contents of laying hens were collected for analysis. Metagenomic analysis of both feces and cecal content samples revealed significant shifts in the microbial composition and abundance of ARGs under intermittent light exposure compared to normal light exposure (P < 0.05). Furthermore, metabolomic analysis of the cecal contents revealed substantial alterations in the abundance and composition of ARGs and mobile genetic elements (MGEs) in response to intermittent light exposure (P < 0.05). Network analysis revealed intricate co-occurrence patterns among bacterial communities, metabolites, and ARGs, highlighting correlations between Bacteroidetes species, ARGs, and metabolites. Although certain bacterial species showed differential associations, the dominant bacteria carrying ARGs or MGEs had relatively low numbers, suggesting that other bacterial communities may have had a greater influence on ARG dissemination. Moreover, our observations highlight the crucial role of metabolites as mediators between bacterial communities and ARGs, providing novel insights into the dynamics of antibiotic resistance development. Our findings underscore the impact of intermittent light exposure on ARG proliferation in poultry farming and emphasize interconnections among ARGs, bacterial communities, and metabolic pathways. The results underscore the importance of considering both microbial communities and metabolic processes to understand antibiotic resistance in agricultural settings.},
}

Animals
*Chickens/microbiology
*Cecum/microbiology
*Gastrointestinal Microbiome/drug effects
*Feces/microbiology
*Drug Resistance, Microbial/genetics
Light
Female
Bacteria/genetics
Genes, Bacterial
Anti-Bacterial Agents/pharmacology

@article {pmid39094311,
year = {2024},
author = {Wang, X and Qian, Y and Wang, Y and Wang, S and Bi, J and Shi, C and Han, Q and Wan-Yan, R and Yu, Q and Li, H},
title = {Metagenomics reveals the potential transmission risk of resistomes from urban park environment to human.},
journal = {Journal of hazardous materials},
volume = {477},
number = {},
pages = {135387},
doi = {10.1016/j.jhazmat.2024.135387},
pmid = {39094311},
issn = {1873-3336},
mesh = {Humans ; *Metagenomics ; Parks, Recreational ; Gastrointestinal Microbiome/drug effects/genetics ; RNA, Ribosomal, 16S/genetics ; China ; Bacteria/genetics/drug effects/classification ; Soil Microbiology ; Cities ; Drug Resistance, Bacterial/genetics ; Water Microbiology ; Genes, Bacterial ; },
abstract = {Urban parks play a significant role in urban ecosystems and are strongly associated with human health. Nevertheless, the biological contamination of urban parks - opportunistic pathogens and antibiotic resistance genes (ARGs) - has been poorly reported. Here, metagenomic and 16 S rRNA sequencing methods were used to study the distribution and assembly of opportunistic pathogens and ARGs in soil and water from nine parks in Lanzhou city, and further compared them with local human gut microbiomes to investigate the potential transmission risk. Our results revealed that the most important type of drug resistance in urban parks was multidrug resistance, with various resistance mechanisms. Approximately half of ARGs were shared between human gut and park environment, and it was noteworthy that cross-species transmission might exist among some high-risk ARGs, such as mepA and mdtE, with a significant enrichment in human gut. Metagenomic binning uncovered several bacterial genomes carrying adjacent ARGs, MGEs, and virulence genes, indicating a possibility that these genes may jointly transfer among different environments, particularly from park environment to human. Our results provided a reference point for the management of environmental pollutants in urban parks.},
}

Humans
*Metagenomics
Parks, Recreational
Gastrointestinal Microbiome/drug effects/genetics
RNA, Ribosomal, 16S/genetics
China
Bacteria/genetics/drug effects/classification
Soil Microbiology
Cities
Drug Resistance, Bacterial/genetics
Water Microbiology
Genes, Bacterial

@article {pmid39084364,
year = {2024},
author = {Kolenc, Ž and Kovač Viršek, M and Klančnik, A and Janecko, N},
title = {Microbial communities on microplastics from seawater and mussels: Insights from the northern Adriatic Sea.},
journal = {The Science of the total environment},
volume = {949},
number = {},
pages = {175130},
doi = {10.1016/j.scitotenv.2024.175130},
pmid = {39084364},
issn = {1879-1026},
mesh = {Animals ; *Seawater/microbiology ; *Microbiota ; *Water Pollutants, Chemical/analysis ; Slovenia ; *Microplastics/analysis ; *Environmental Monitoring ; Mytilus/microbiology ; Bacteria/classification/isolation & purification ; },
abstract = {Microplastics, synthetic solid particles of different sizes (< 5 mm), pose a major challenge to marine ecosystems. Introducing microplastics into the marine environment leads to the formation of complex microbial communities, a topic of growing interest in environmental research. For this study, we selected an area in the northern Adriatic Sea, less affected by human activities, to understand how pristine environmental conditions influence microbial colonization of microplastics. Samples of coastal seawater and Mediterranean mussels (Mytilus galloprovincialis) were collected in a mussel farm near Debeli rtič of the Slovenian coast. Microplastics were isolated, visually and chemically analyzed and DNA was extracted for metagenomics. In the marine water column, 12.7 microplastics per m[3] water column and 0.58 microplastics per individual mussel were found. Sufficient DNA was available to analyze six particles, five originating from seawater, and one from a mussel. This was the first-ever sequenced microplastic particle from a mussel. Genera of Pseudomonas and Serratia were identified in all samples. In one of the samples, the most abundant was a marine genus Pseudoalteromonas, while in another sample Campylobacter was present with >30 % abundance. The microbiomes of the mussel- and seawater-isolated particles were similar, suggesting a common microbial colonization pattern, which may have implications for the transfer of microplastic-associated microbes, including potential pathogens, through the food web to the consumers. Microplastic pollution is a complex issue requiring further research, especially regarding microbial biofilms, pathogen colonization and the potential of pathogen transmission via microplastic particles. Our findings enhance the understanding of microplastic pollution in the Adriatic Sea and stress the necessity for comprehensive strategies to mitigate the impact on marine ecosystems.},
}

Animals
*Seawater/microbiology
*Microbiota
*Water Pollutants, Chemical/analysis
Slovenia
*Microplastics/analysis
*Environmental Monitoring
Mytilus/microbiology
Bacteria/classification/isolation & purification

@article {pmid39069186,
year = {2024},
author = {Zhu, S and Zhao, W and Sun, S and Yang, X and Mao, H and Sheng, L and Chen, Z},
title = {Community metagenomics reveals the processes of cadmium resistance regulated by microbial functions in soils with Oryza sativa root exudate input.},
journal = {The Science of the total environment},
volume = {949},
number = {},
pages = {175015},
doi = {10.1016/j.scitotenv.2024.175015},
pmid = {39069186},
issn = {1879-1026},
mesh = {*Oryza/microbiology/physiology ; *Soil Microbiology ; *Cadmium ; *Soil Pollutants ; *Plant Roots/microbiology ; *Rhizosphere ; *Microbiota/drug effects ; Metagenomics ; Soil/chemistry ; },
abstract = {Plants exert a profound influence on their rhizosphere microbiome through the secretion of root exudates, thereby imparting critical effects on their growth and overall health. The results unveil that japonica rice showcases a remarkable augmentation in its antioxidative stress mechanisms under Cd stress. This augmentation is characterized by the sequestration of heavy metal ions within the root system and the prodigious secretion of a spectrum of flavonoids, including Quercetin, Luteolin, Apigenin, Kaempferide, and Sakuranetin. These flavonoids operate as formidable guardians, shielding the plant from oxidative damage instigated by Cd-induced stress. Furthermore, the metagenomic analyses divulge the transformative potential of flavonoids, as they induce profound alterations in the composition and structural dynamics of plant rhizosphere microbial communities. These alterations manifest through the recruitment of plant growth-promoting bacteria, effectively engineering a conducive milieu for japonica rice. In addition, our symbiotic network analysis discerns that flavonoid compounds significantly improved the positive correlations among dominant species within the rhizosphere of japonica rice. This, in turn, bolsters the stability and intricacy of the microenvironmental ecological network. KEGG functional analyses reveal a notable upregulation in the expression of flavonoid functional genes, specifically cadA, cznA, nccC, and czrB, alongside an array of transporters, encompassing RND, ABC, MIT, and P-ATPase. These molecular orchestrations distinctly demarcated the rhizosphere microbiome of japonica rice, markedly enhancing its tolerance to Cd-induced stress. These findings not only shed light on the establishment of Cd-resistant bacterial consortia in rice but also herald a promising avenue for the precise modulation of plant rhizosphere microbiomes, thereby fortifying the safety and efficiency of crop production.},
}

*Oryza/microbiology/physiology
*Soil Microbiology
*Cadmium
*Soil Pollutants
*Plant Roots/microbiology
*Rhizosphere
*Microbiota/drug effects
Metagenomics
Soil/chemistry

@article {pmid39069174,
year = {2024},
author = {Shu, D and Banerjee, S and Mao, X and Zhang, J and Cui, W and Zhang, W and Zhang, B and Chen, S and Jiao, S and Wei, G},
title = {Conversion of monocropping to intercropping promotes rhizosphere microbiome functionality and soil nitrogen cycling.},
journal = {The Science of the total environment},
volume = {949},
number = {},
pages = {174953},
doi = {10.1016/j.scitotenv.2024.174953},
pmid = {39069174},
issn = {1879-1026},
mesh = {*Rhizosphere ; *Soil Microbiology ; *Microbiota ; *Nitrogen Cycle ; *Soil/chemistry ; *Nitrogen/metabolism ; *Agriculture/methods ; Glycine max/growth & development ; Crop Production/methods ; },
abstract = {Intercropping can increase soil nutrient availability and provide greater crop yields for intensive agroecosystems. Despite its multiple benefits, how intercropping influences rhizosphere microbiome assemblages, functionality, and complex soil nitrogen cycling is not fully understood. Here, a three-year field experiment was carried out on different cropping system with five fertilization treatments at the main soybean production regions. We found that soybean yields in intercropped systems were on average 17 % greater than in monocropping system, regardless of fertilization treatments. We also found that intercropping systems significant increased network modularity (by 46 %) and functional diversity (by 11 %) than monocropping systems. Metagenomics analyses further indicated intercropping promotes microbiome functional adaptation, particularly enriching core functions related to nitrogen metabolism. Cropping patterns had a stronger influence on the functional genes associated with soil nitrogen cycling (R[2] = 0.499). Monocropping systems increased the abundance of functional genes related to organic nitrogen ammonification, nitrogen fixation, and denitrification, while functional guilds of nitrate assimilation (by 28 %), nitrification (by 31 %), and dissimilatory nitrate reduction (by 10.1 %) genes were enriched in intercropping systems. Furthermore, we found that abiotic factors (i.e. AP, pH, and Moisture) are important drivers in shaping soil microbial community assemblage and nitrogen cycling. The functional genes include hzsB, and nrfA, and nxrA that affected by these biotic and abiotic variables were strongly related to crop yield (R[2] = 0.076 ~ R[2] = 0.249), suggesting a key role for maintaining crop production. We demonstrated that land use conversion from maize monocropping to maize-soybean intercropping diversify rhizosphere microbiome and functionality signatures, and intercropping increased key gene abundance related to soil nitrogen cycling to maintain the advantage of crop yield. The results of this study significantly facilitate our understanding of the complex soil nitrogen cycling processes and lay the foundation for manipulating desired specific functional taxa for improved crop productivity under sustainable intensification.},
}

*Rhizosphere
*Soil Microbiology
*Microbiota
*Nitrogen Cycle
*Soil/chemistry
*Nitrogen/metabolism
*Agriculture/methods
Glycine max/growth & development
Crop Production/methods

@article {pmid39068883,
year = {2024},
author = {Zhou, Z and Keiblinger, KM and Huang, Y and Bhople, P and Shi, X and Yang, S and Yu, F and Liu, D},
title = {Virome and metagenomic sequencing reveal the impact of microbial inoculants on suppressions of antibiotic resistome and viruses during co-composting.},
journal = {Journal of hazardous materials},
volume = {477},
number = {},
pages = {135355},
doi = {10.1016/j.jhazmat.2024.135355},
pmid = {39068883},
issn = {1873-3336},
mesh = {*Manure/microbiology/virology ; *Composting ; *Streptomyces/genetics ; *Drug Resistance, Microbial/genetics ; *Metagenomics ; Virome/genetics ; Bacteria/drug effects/genetics ; Viruses/drug effects/genetics ; Soil Microbiology ; Anti-Bacterial Agents/pharmacology ; Metagenome ; },
abstract = {Co-composting with exogenous microbial inoculant, presents an effective approach for the harmless utilization of livestock manure and agroforestry wastes. However, the impact of inoculant application on the variations of viral and antibiotic resistance genes (ARGs) remains poorly understood, particularly under varying manure quantity (low 10 % vs. high 20 % w/w). Thus, employing virome and metagenomic sequencing, we examined the influence of Streptomyces-Bacillus Inoculants (SBI) on viral communities, phytopathogen, ARGs, mobile genetic elements, and their interrelations. Our results indicate that SBI shifted dominant bacterial species from Phenylobacterium to thermotropic Bordetella, and the quantity of manure mediates the effect of SBI on whole bacterial community. Major ARGs and genetic elements experienced substantial changes with SBI addition. There was a higher ARGs elimination rate in the composts with low (∼76 %) than those with high manure (∼70 %) application. Virus emerged as a critical factor influencing ARG dynamics. We observed a significant variation in virus community, transitioning from Gemycircularvirus- (∼95 %) to Chlamydiamicrovirus-dominance. RDA analysis revealed that Gemycircularvirus was the most influential taxon in shaping ARGs, with its abundance decreased approximately 80 % after composting. Collectively, these findings underscore the role of microbial inoculants in modulating virus communities and ARGs during biowaste co-composting.},
}

*Manure/microbiology/virology
*Composting
*Streptomyces/genetics
*Drug Resistance, Microbial/genetics
*Metagenomics
Virome/genetics
Bacteria/drug effects/genetics
Viruses/drug effects/genetics
Soil Microbiology
Anti-Bacterial Agents/pharmacology
Metagenome

@article {pmid39067601,
year = {2024},
author = {Roman, EKB and Ramos, MA and Tomazetto, G and Foltran, BB and Galvão, MH and Ciancaglini, I and Tramontina, R and de Almeida Rodrigues, F and da Silva, LS and Sandano, ALH and Fernandes, DGDS and Almeida, DV and Baldo, DA and de Oliveira Junior, JM and Garcia, W and Damasio, A and Squina, FM},
title = {Plastic-degrading microbial communities reveal novel microorganisms, pathways, and biocatalysts for polymer degradation and bioplastic production.},
journal = {The Science of the total environment},
volume = {949},
number = {},
pages = {174876},
doi = {10.1016/j.scitotenv.2024.174876},
pmid = {39067601},
issn = {1879-1026},
mesh = {*Biodegradation, Environmental ; *Microbiota ; *Plastics/metabolism ; Soil Microbiology ; Polyethylene Terephthalates/metabolism ; Soil Pollutants/metabolism ; Polymers/metabolism ; Bacteria/metabolism/genetics ; Biodegradable Plastics/metabolism ; Microbial Consortia ; Pseudomonas putida/metabolism/genetics ; },
abstract = {Plastics derived from fossil fuels are used ubiquitously owing to their exceptional physicochemical characteristics. However, the extensive and short-term use of plastics has caused environmental challenges. The biotechnological plastic conversion can help address the challenges related to plastic pollution, offering sustainable alternatives that can operate using bioeconomic concepts and promote socioeconomic benefits. In this context, using soil from a plastic-contaminated landfill, two consortia were established (ConsPlastic-A and -B) displaying versatility in developing and consuming polyethylene or polyethylene terephthalate as the carbon source of nutrition. The ConsPlastic-A and -B metagenomic sequencing, taxonomic profiling, and the reconstruction of 79 draft bacterial genomes significantly expanded the knowledge of plastic-degrading microorganisms and enzymes, disclosing novel taxonomic groups associated with polymer degradation. The microbial consortium was utilized to obtain a novel Pseudomonas putida strain (BR4), presenting a striking metabolic arsenal for aromatic compound degradation and assimilation, confirmed by genomic analyses. The BR4 displays the inherent capacity to degrade polyethylene terephthalate (PET) and produce polyhydroxybutyrate (PHB) containing hydroxyvalerate (HV) units that contribute to enhanced copolymer properties, such as increased flexibility and resistance to breakage, compared with pure PHB. Therefore, BR4 is a promising strain for developing a bioconsolidated plastic depolymerization and upcycling process. Collectively, our study provides insights that may extend beyond the artificial ecosystems established during our experiments and supports future strategies for effectively decomposing and valorizing plastic waste. Furthermore, the functional genomic analysis described herein serves as a valuable guide for elucidating the genetic potential of microbial communities and microorganisms in plastic deconstruction and upcycling.},
}

*Biodegradation, Environmental
*Microbiota
*Plastics/metabolism
Soil Microbiology
Polyethylene Terephthalates/metabolism
Soil Pollutants/metabolism
Polymers/metabolism
Bacteria/metabolism/genetics
Biodegradable Plastics/metabolism
Microbial Consortia
Pseudomonas putida/metabolism/genetics

@article {pmid38986687,
year = {2024},
author = {Wang, J and Shen, C and Sun, J and Cheng, L and Zhao, G and Li, MM},
title = {Metagenomic analysis reveals a dynamic rumen microbiome with diversified adaptive functions in response to dietary protein restriction and re-alimentation.},
journal = {The Science of the total environment},
volume = {949},
number = {},
pages = {174618},
doi = {10.1016/j.scitotenv.2024.174618},
pmid = {38986687},
issn = {1879-1026},
mesh = {*Rumen/microbiology/metabolism ; Animals ; *Animal Feed/analysis ; Gastrointestinal Microbiome ; Cattle ; Dietary Proteins/metabolism ; Fermentation ; Metagenomics ; Diet, Protein-Restricted ; Male ; Microbiota ; },
abstract = {Understanding the dynamics of the rumen microbiome is crucial for optimizing ruminal fermentation to improve feed efficiency and addressing concerns regarding antibiotic resistance in the livestock production industry. This study aimed to investigate the adaptive effects of microbiome and the properties of carbohydrate-active enzymes (CAZy) and antibiotic resistance genes (ARGs) in response to dietary protein shifts. Twelve Charolais bulls were randomly divided into two groups based on initial body weight: 1) Treatment (REC), where the animals received a 7 % CP diet in a 4-week restriction period, followed by a 13 % CP diet in a 2-week re-alimentation period; 2) Control (CON), where the animals were fed the 13 % CP diet both in the restriction period and the re-alimentation period. Protein restriction decreased the concentrations of acetate, propionate, isovalerate, glutamine, glutamate, and isoleucine (P < 0.05), while protein re-alimentation increased the concentrations of arginine, methionine sulfoxide, lysine, and glutamate (P < 0.05). Protein restriction decreased the relative abundances of Bacteroidota but increased Proteobacteria, with no difference observed after re-alimentation. Protein restriction decreased relative abundances of the genera Bacteroides, Prevotella, and Bifidobacterium. Following protein recovery, Escherichia was enriched in CON, while Pusillibacter was enriched in REC, indicating that distinct microbial adaptations to protein shifts. Protein restriction increased GH97 while reducing GH94 and GT35 compared to CON. Protein restriction decreased abundances of KO genes involved in VFA production pathways, while they were recovered in the re-alimentation period. Protein restriction reduced tet(W/32/O) abundances but increased those of tet(X), nimJ, and rpoB2. Following protein re-alimentation, there was a decrease in ErmQ and tet(W/N/W), and an increase in Mef(En2) compared to CON, highlighting the impact of dietary protein on the distribution of antibiotic-resistant bacteria. Overall, comprehensive metagenomic analysis reveals the dynamic adaptability of the microbiome in response to dietary shifts, indicating its capacity to modulate carbohydrate metabolism and ARGs in response to protein availability.},
}

*Rumen/microbiology/metabolism
Animals
*Animal Feed/analysis
Gastrointestinal Microbiome
Cattle
Dietary Proteins/metabolism
Fermentation
Metagenomics
Diet, Protein-Restricted
Male
Microbiota

@article {pmid39147499,
year = {2024},
author = {Magliulo, R and Valentino, V and Balivo, A and Esposito, A and Genovese, A and Ercolini, D and De Filippis, F},
title = {Microbiome signatures associated with flavor development differentiate Protected Designation of origin water Buffalo Mozzarella cheese from different production areas.},
journal = {Food research international (Ottawa, Ont.)},
volume = {192},
number = {},
pages = {114798},
doi = {10.1016/j.foodres.2024.114798},
pmid = {39147499},
issn = {1873-7145},
mesh = {*Cheese/microbiology/analysis ; Animals ; *Volatile Organic Compounds/analysis ; *Microbiota ; *Buffaloes ; Italy ; *Gas Chromatography-Mass Spectrometry ; *Taste ; Food Microbiology ; Lactobacillus helveticus ; Streptococcus thermophilus/classification ; },
abstract = {Water Buffalo Mozzarella (BM) is a typical cheese from Southern Italy with unique flavor profile and texture. It is produced following a traditional back-slopping procedure and received the Protected Designation of Origin (PDO) label. To better understand the link between the production area, the microbiome composition and the flavor profile of the products, we performed a multiomic characterization of PDO BM collected from 57 different dairies located in the two main PDO production area, i.e. Caserta (n = 35) and Salerno (n = 22). Thus, we assessed the microbiome by high-throughput shotgun metagenomic sequencing and the Volatile Organic Compounds (VOCs) by gas chromatography/mass spectrometry (GC/MS). Streptococcus thermophilus, Lactobacillus helveticus, and Lactobacillus delbrueckii subsp. delbrueckii were identified as the core microbiome present in all samples. However, the microbiome taxonomic profiles resulted in a clustering of the samples based on their geographical origin, also showing that BM from Caserta had a greater microbial diversity. Consistently, Caserta and Salerno samples also showed different VOC profiles. These results suggest that the microbiome and its specific metabolic activity are part of the terroir that shape BM specific features, linking this traditional product with the area of production, thus opening new clues for improving traceability and fraud protection of traditional products.},
}

*Cheese/microbiology/analysis
Animals
*Volatile Organic Compounds/analysis
*Microbiota
*Buffaloes
Italy
*Gas Chromatography-Mass Spectrometry
*Taste
Food Microbiology
Lactobacillus helveticus
Streptococcus thermophilus/classification

@article {pmid39143364,
year = {2024},
author = {Akhlaghi, E and Salari, E and Mansouri, M and Shafiei, M and Kalantar-Neyestanaki, D and Aghassi, H and Fasihi Harandi, M},
title = {Identification and comparison of intestinal microbial diversity in patients at different stages of hepatic cystic echinococcosis.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {18912},
pmid = {39143364},
issn = {2045-2322},
support = {400000473//Kerman University of Medical Sciences/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Echinococcosis, Hepatic/microbiology/parasitology ; Male ; Female ; *RNA, Ribosomal, 16S/genetics ; Adult ; Middle Aged ; Feces/microbiology/parasitology ; Bacteria/classification/genetics/isolation & purification ; Biodiversity ; High-Throughput Nucleotide Sequencing ; },
abstract = {There is a significant focus on the role of the host microbiome in different outcomes of human parasitic diseases, including cystic echinococcosis (CE). This study was conducted to identify the intestinal microbiome of patients with CE at different stages of hydatid cyst compared to healthy individuals. Stool samples from CE patients as well as healthy individuals were collected. The samples were divided into three groups representing various stages of hepatic hydatid cyst: active (CE1 and CE2), transitional (CE3), and inactive (CE4 and CE5). One family member from each group was selected to serve as a control. The gut microbiome of patients with different stages of hydatid cysts was investigated using metagenomic next-generation amplicon sequencing of the V3-V4 region of the 16S rRNA gene. In this study, we identified 4862 Operational Taxonomic Units from three stages of hydatid cysts in CE patients and healthy individuals with a combined frequency of 2,955,291. The most abundant genera observed in all the subjects were Blautia, Agathobacter, Faecalibacterium, Bacteroides, Bifidobacterium, and Prevotella. The highest microbial frequency was related to inactive forms of CE, and the lowest frequency was observed in the group with active forms. However, the lowest OTU diversity was found in patients with inactive cysts compared with those with active and transitional cyst stages. The genus Agatobacter had the highest OTU frequency. Pseudomonas, Gemella, and Ligilactobacillus showed significant differences among the patients with different stages of hydatid cysts. Additionally, Anaerostipes and Candidatus showed significantly different reads in CE patients compared to healthy individuals. Our findings indicate that several bacterial genera can play a role in the fate of hydatid cysts in patients at different stages of the disease.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Echinococcosis, Hepatic/microbiology/parasitology
Male
Female
*RNA, Ribosomal, 16S/genetics
Adult
Middle Aged
Feces/microbiology/parasitology
Bacteria/classification/genetics/isolation & purification
Biodiversity
High-Throughput Nucleotide Sequencing

@article {pmid39059396,
year = {2024},
author = {Kim, Y and Kim, G and Kim, S and Cho, B and Kim, SY and Do, EJ and Bae, DJ and Kim, S and Kweon, MN and Song, JS and Park, SH and Hwang, SW and Kim, MN and Kim, Y and Min, K and Kim, SH and Adams, MD and Lee, C and Park, H and Park, SR},
title = {Fecal microbiota transplantation improves anti-PD-1 inhibitor efficacy in unresectable or metastatic solid cancers refractory to anti-PD-1 inhibitor.},
journal = {Cell host & microbe},
volume = {32},
number = {8},
pages = {1380-1393.e9},
doi = {10.1016/j.chom.2024.06.010},
pmid = {39059396},
issn = {1934-6069},
mesh = {*Fecal Microbiota Transplantation ; Humans ; Animals ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; Female ; Male ; Middle Aged ; *Neoplasms/immunology/therapy/microbiology ; *Programmed Cell Death 1 Receptor/antagonists & inhibitors ; Aged ; Feces/microbiology ; Adult ; Cytokines/metabolism ; },
abstract = {The gut microbiome significantly influences immune responses and the efficacy of immune checkpoint inhibitors. We conducted a clinical trial (NCT04264975) combining an anti-programmed death-1 (PD-1) inhibitor with fecal microbiota transplantation (FMT) from anti-PD-1 responder in 13 patients with anti-PD-1-refractory advanced solid cancers. FMT induced sustained microbiota changes and clinical benefits in 6 of 13 patients, with 1 partial response and 5 stable diseases, achieving an objective response rate of 7.7% and a disease control rate of 46.2%. The clinical response correlates with increased cytotoxic T cells and immune cytokines in blood and tumors. We isolated Prevotella merdae Immunoactis from a responder to FMT, which stimulates T cell activity and suppresses tumor growth in mice by enhancing cytotoxic T cell infiltration. Additionally, we found Lactobacillus salivarius and Bacteroides plebeius may inhibit anti-tumor immunity. Our findings suggest that FMT with beneficial microbiota can overcome resistance to anti-PD-1 inhibitors in advanced solid cancers, especially gastrointestinal cancers.},
}

*Fecal Microbiota Transplantation
Humans
Animals
*Gastrointestinal Microbiome/drug effects
Mice
*Immune Checkpoint Inhibitors/therapeutic use/pharmacology
Female
Male
Middle Aged
*Neoplasms/immunology/therapy/microbiology
*Programmed Cell Death 1 Receptor/antagonists & inhibitors
Aged
Feces/microbiology
Adult
Cytokines/metabolism

@article {pmid38996548,
year = {2024},
author = {Wu, C and Yang, F and Zhong, H and Hong, J and Lin, H and Zong, M and Ren, H and Zhao, S and Chen, Y and Shi, Z and Wang, X and Shen, J and Wang, Q and Ni, M and Chen, B and Cai, Z and Zhang, M and Cao, Z and Wu, K and Gao, A and Li, J and Liu, C and Xiao, M and Li, Y and Shi, J and Zhang, Y and Xu, X and Gu, W and Bi, Y and Ning, G and Wang, W and Wang, J and Liu, R},
title = {Obesity-enriched gut microbe degrades myo-inositol and promotes lipid absorption.},
journal = {Cell host & microbe},
volume = {32},
number = {8},
pages = {1301-1314.e9},
doi = {10.1016/j.chom.2024.06.012},
pmid = {38996548},
issn = {1934-6069},
mesh = {*Inositol/metabolism ; *Obesity/microbiology/metabolism ; *Gastrointestinal Microbiome ; Animals ; Humans ; Mice ; Male ; Lipid Metabolism ; Female ; Intestinal Absorption ; Mice, Inbred C57BL ; Metagenomics ; Middle Aged ; Adult ; Fatty Acids/metabolism ; Escherichia coli/genetics/metabolism ; },
abstract = {Numerous studies have reported critical roles for the gut microbiota in obesity. However, the specific microbes that causally contribute to obesity and the underlying mechanisms remain undetermined. Here, we conducted shotgun metagenomic sequencing in a Chinese cohort of 631 obese subjects and 374 normal-weight controls and identified a Megamonas-dominated, enterotype-like cluster enriched in obese subjects. Among this cohort, the presence of Megamonas and polygenic risk exhibited an additive impact on obesity. Megamonas rupellensis possessed genes for myo-inositol degradation, as demonstrated in vitro and in vivo, and the addition of myo-inositol effectively inhibited fatty acid absorption in intestinal organoids. Furthermore, mice colonized with M. rupellensis or E. coli heterologously expressing the myo-inositol-degrading iolG gene exhibited enhanced intestinal lipid absorption, thereby leading to obesity. Altogether, our findings uncover roles for M. rupellensis as a myo-inositol degrader that enhances lipid absorption and obesity, suggesting potential strategies for future obesity management.},
}

*Inositol/metabolism
*Obesity/microbiology/metabolism
*Gastrointestinal Microbiome
Animals
Humans
Mice
Male
Lipid Metabolism
Female
Intestinal Absorption
Mice, Inbred C57BL
Metagenomics
Middle Aged
Adult
Fatty Acids/metabolism
Escherichia coli/genetics/metabolism