@article {pmid39356745,
year = {2024},
author = {Hartman, SJ and Hibberd, MC and Mostafa, I and Naila, NN and Islam, MM and Zaman, MU and Huq, S and Mahfuz, M and Islam, MT and Mukherji, K and Moghaddam, VA and Chen, RY and Province, MA and Webber, DM and Henrissat, S and Henrissat, B and Terrapon, N and Rodionov, DA and Osterman, AL and Barratt, MJ and Ahmed, T and Gordon, JI},
title = {A microbiome-directed therapeutic food for children recovering from severe acute malnutrition.},
journal = {Science translational medicine},
volume = {16},
number = {767},
pages = {eadn2366},
doi = {10.1126/scitranslmed.adn2366},
pmid = {39356745},
issn = {1946-6242},
mesh = {Humans ; *Severe Acute Malnutrition/diet therapy/therapy ; Infant ; Microbiota ; Male ; Female ; Bangladesh ; Gastrointestinal Microbiome ; },
abstract = {Globally, severe acute malnutrition (SAM), defined as a weight-for-length z-score more than three SDs below a reference mean (WLZ < -3), affects 14 million children under 5 years of age. Complete anthropometric recovery after standard, short-term interventions is rare, with children often left with moderate acute malnutrition (MAM; WLZ -2 to -3). We conducted a randomized controlled trial (RCT) involving 12- to 18-month-old Bangladeshi children from urban and rural sites, who, after initial hospital-based treatment for SAM, received a 3-month intervention with a microbiome-directed complementary food (MDCF-2) or a calorically more dense, standard ready-to-use supplementary food (RUSF). The rate of WLZ improvement was significantly greater in MDCF-2-treated children (P = 8.73 × 10[-3]), similar to our previous RCT of Bangladeshi children with MAM without antecedent SAM (P = 0.032). A correlated meta-analysis of plasma levels of 4520 proteins in both RCTs revealed 215 positively associated with WLZ (largely representing musculoskeletal and central nervous system development) and 44 negatively associated (primarily related to immune activation). Moreover, the positively associated proteins were significantly enriched by MDCF-2 (q = 1.1 × 10[-6]). Characterizing the abundances of 754 bacterial metagenome-assembled genomes in serially collected fecal samples disclosed the effects of acute rehabilitation for SAM on the microbiome and how, during treatment for MAM, specific strains of Prevotella copri function at the intersection between MDCF-2 glycan metabolism and anthropometric recovery. These results provide a rationale for further testing the generalizability of MDCF efficacy and for identifying biomarkers to define treatment responses.},
}

Humans
*Severe Acute Malnutrition/diet therapy/therapy
Infant
Microbiota
Male
Female
Bangladesh
Gastrointestinal Microbiome

@article {pmid39354019,
year = {2024},
author = {Oaikhena, AO and Coker, ME and Cyril-Okoh, D and Wicaksono, WA and Olimi, E and Berg, G and Okeke, IN},
title = {The phyllosphere of Nigerian medicinal plants, Euphorbia lateriflora and Ficus thonningii is inhabited by a specific microbiota.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {22806},
pmid = {39354019},
issn = {2045-2322},
mesh = {*Euphorbia ; *Ficus/microbiology ; *Microbiota/genetics ; *Plants, Medicinal/microbiology ; *Bacteria/genetics/classification/isolation & purification ; *RNA, Ribosomal, 16S/genetics ; *Plant Leaves/microbiology ; *Fungi/genetics/classification/isolation & purification ; Nigeria ; Phylogeny ; },
abstract = {The microbiota of medicinal plants is known to be highly specific and can contribute to medicinal activity. However, the majority of plant species have not yet been studied. Here, we investigated the phyllosphere composition of two common Nigerian medicinal plants, Euphorbia lateriflora and Ficus thonningii, by a polyphasic approach combining analyses of metagenomic DNA and isolates. Microbial abundance estimated via qPCR using specific marker gene primers showed that all leaf samples were densely colonized, with up to 10[8] per gram of leaf, with higher bacterial and fungal abundance than Archaea. While no statistically significant differences between both plant species were found for abundance, amplicon sequencing of 16S rRNA and ITS genes revealed distinct microbiota compositions. Only seven of the 27 genera isolated were represented on both plants, e.g. dominant Sphingomonas spp., and numerous members of Xanthomonadaceae and Enterobacteriaceae. The most dominant fungal families on both plants were Cladosporiaceae, Mycosphaerellaceae and Trichosphaeriaceae. In addition, 225 plant-specific isolates were identified, with Pseudomonadota and Enterobacteriaceae being dominant. Interestingly, 29 isolates are likely species previously unknown, and 14 of these belong to Burkholderiales. However, a high proportion, 56% and 40% of the isolates from E. lateriflora and F. thonningii, respectively, were characterized as various Escherichia coli. The growth of most of the bacterial isolates was not influenced by extractable secondary metabolites of plants. Our results suggest that a specific and diverse microbial community inhabits the leaves of both E. lateriflora and F. thonningii, including potentially new species and producers of antimicrobials.},
}

*Euphorbia
*Ficus/microbiology
*Microbiota/genetics
*Plants, Medicinal/microbiology
*Bacteria/genetics/classification/isolation & purification
*RNA, Ribosomal, 16S/genetics
*Plant Leaves/microbiology
*Fungi/genetics/classification/isolation & purification
Nigeria
Phylogeny

@article {pmid39354003,
year = {2024},
author = {Li, Y and Liu, H and Xiao, Y and Jing, H},
title = {Metagenome sequencing and 982 microbial genomes from Kermadec and Diamantina Trenches sediments.},
journal = {Scientific data},
volume = {11},
number = {1},
pages = {1067},
pmid = {39354003},
issn = {2052-4463},
mesh = {*Geologic Sediments/microbiology ; *Metagenome ; *Archaea/genetics ; *Phylogeny ; *Bacteria/genetics/classification ; Genome, Microbial ; Microbiota ; Genome, Archaeal ; },
abstract = {Deep-sea trenches representing an intriguing ecosystem for exploring the survival and evolutionary strategies of microbial communities in the highly specialized deep-sea environments. Here, 29 metagenomes were obtained from sediment samples collected from Kermadec and Diamantina trenches. Notably, those samples covered a varying sampling depths (from 5321 m to 9415 m) and distinct layers within the sediment itself (from 0~40 cm in Kermadec trench and 0~24 cm in Diamantina trench). Through metagenomic binning process, we reconstructed 982 metagenome assembled genomes (MAGs) with completeness >60% and contamination <5%. Within them, completeness of 351 MAGs were >90%, while an additional 331 were >80%. Phylogenomic analysis for the MAGs revealed nearly all of them were distantly related to known cultivated isolates. The abundant bacterial MAGs affiliated to phyla of Proteobacteria, Planctomycetota, Nitrospirota, Acidobacteriota, Actinobacteriota, and Chlorofexota, while the abundant archaeal phyla affiliated with Nanoarchaeota and Thermoproteota. These results provide a dataset available for further interrogation of diversity, distribution and ecological function of deep-sea microbes existed in the trenches.},
}

*Geologic Sediments/microbiology
*Metagenome
*Archaea/genetics
*Phylogeny
*Bacteria/genetics/classification
Genome, Microbial
Microbiota
Genome, Archaeal

@article {pmid39242817,
year = {2024},
author = {Shao, Y and Garcia-Mauriño, C and Clare, S and Dawson, NJR and Mu, A and Adoum, A and Harcourt, K and Liu, J and Browne, HP and Stares, MD and Rodger, A and Brocklehurst, P and Field, N and Lawley, TD},
title = {Primary succession of Bifidobacteria drives pathogen resistance in neonatal microbiota assembly.},
journal = {Nature microbiology},
volume = {9},
number = {10},
pages = {2570-2582},
pmid = {39242817},
issn = {2058-5276},
support = {WT101169MA, 206194 and 108413/A/15/D//Wellcome Trust (Wellcome)/ ; },
mesh = {Humans ; *Feces/microbiology ; Animals ; Infant, Newborn ; *Gastrointestinal Microbiome ; *Bifidobacterium/genetics/isolation & purification ; Mice ; Female ; United Kingdom ; Metagenomics ; Enterococcus faecalis/genetics/isolation & purification ; Milk, Human/microbiology ; Male ; },
abstract = {Human microbiota assembly commences at birth, seeded by both maternal and environmental microorganisms. Ecological theory postulates that primary colonizers dictate microbial community assembly outcomes, yet such microbial priority effects in the human gut remain underexplored. Here using longitudinal faecal metagenomics, we characterized neonatal microbiota assembly for a cohort of 1,288 neonates from the UK. We show that the pioneering neonatal gut microbiota can be stratified into one of three distinct community states, each dominated by a single microbial species and influenced by clinical and host factors, such as maternal age, ethnicity and parity. A community state dominated by Enterococcus faecalis displayed stochastic microbiota assembly with persistent high pathogen loads into infancy. In contrast, community states dominated by Bifidobacterium, specifically B. longum and particularly B. breve, exhibited a stable assembly trajectory and long-term pathogen colonization resistance, probably due to strain-specific functional adaptions to a breast milk-rich neonatal diet. Consistent with our human cohort observation, B. breve demonstrated priority effects and conferred pathogen colonization resistance in a germ-free mouse model. Our findings solidify the crucial role of Bifidobacteria as primary colonizers in shaping the microbiota assembly and functions in early life.},
}

Humans
*Feces/microbiology
Animals
Infant, Newborn
*Gastrointestinal Microbiome
*Bifidobacterium/genetics/isolation & purification
Mice
Female
United Kingdom
Metagenomics
Enterococcus faecalis/genetics/isolation & purification
Milk, Human/microbiology
Male

@article {pmid39152661,
year = {2024},
author = {Leugger, F and Schmidlin, M and Lüthi, M and Kontarakis, Z and Pellissier, L},
title = {Scanning amplicons with CRISPR-Dx detects endangered amphibians in environmental DNA.},
journal = {Molecular ecology resources},
volume = {24},
number = {8},
pages = {e14009},
doi = {10.1111/1755-0998.14009},
pmid = {39152661},
issn = {1755-0998},
support = {//Swiss Federal Institute for Forest, Snow and Landscape Research/ ; 40B2-0_203550//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; },
mesh = {Animals ; *Amphibians/genetics/classification ; *DNA, Environmental/genetics ; *Endangered Species ; Switzerland ; *Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; DNA Barcoding, Taxonomic/methods ; Ponds ; Biodiversity ; Metagenomics/methods ; },
abstract = {More efficient methods for extensive biodiversity monitoring are required to support rapid measures to address the biodiversity crisis. While environmental DNA (eDNA) metabarcoding and quantitative PCR (qPCR) methods offer advantages over traditional monitoring approaches, their large-scale application is limited by the time and labour required for developing assays and/or for analysis. CRISPR (clustered regularly interspaced short palindromic repeats) diagnostic technologies (Dx) may overcome some of these limitations, but they have been used solely with species-specific primers, restricting their versatility for biodiversity monitoring. Here, we demonstrate the feasibility of designing species-specific CRISPR-Dx assays in silico within a short metabarcoding fragment using a general primer set, a methodology we term 'ampliscanning', for 18 of the 22 amphibian species in Switzerland. We sub-selected nine species, including three classified as regionally endangered, to test the methodology using eDNA sampled from ponds at nine sites. We compared the ampliscanning detections to data from traditional monitoring at these sites. Ampliscanning was successful at detecting target species with different prevalences across the landscape. With only one visit, we detected more species per site than three traditional monitoring visits (visual and acoustic detections by trained experts), in particular more elusive species and previously undocumented but expected populations. Ampliscanning detected 25 species/site combinations compared to 12 with traditional monitoring. Sensitivity analyses showed that larger numbers of field visits and PCR replicates are more important for reliable detection than many technical replicates at the CRISPR-Dx assay level. Given the reduced sampling and analysis effort, our results highlight the benefits of eDNA and CRISPR-Dx combined with universal primers for large-scale monitoring of multiple endangered species across landscapes to inform conservation measures.},
}

Animals
*Amphibians/genetics/classification
*DNA, Environmental/genetics
*Endangered Species
Switzerland
*Clustered Regularly Interspaced Short Palindromic Repeats/genetics
DNA Barcoding, Taxonomic/methods
Ponds
Biodiversity
Metagenomics/methods

@article {pmid39084575,
year = {2024},
author = {Yadav, A and Shinde, PB and Mohan, H and Dhar, MS and Ponnusamy, K and Marwal, R and Radhakrishnan, VS and Goyal, S and Kedia, S and Ahuja, V and Sharma, KK},
title = {Gut colonization with antibiotic-resistant Escherichia coli pathobionts leads to disease severity in ulcerative colitis.},
journal = {International journal of antimicrobial agents},
volume = {64},
number = {4},
pages = {107289},
doi = {10.1016/j.ijantimicag.2024.107289},
pmid = {39084575},
issn = {1872-7913},
mesh = {Humans ; *Colitis, Ulcerative/microbiology ; *Gastrointestinal Microbiome/drug effects/genetics ; *Escherichia coli/genetics/drug effects/pathogenicity ; *Anti-Bacterial Agents/pharmacology ; Drug Resistance, Multiple, Bacterial/genetics ; Male ; Escherichia coli Infections/microbiology ; Adult ; Female ; Virulence Factors/genetics ; Microbial Sensitivity Tests ; Middle Aged ; Severity of Illness Index ; Metagenomics ; },
abstract = {BACKGROUND: Escherichia coli is a Gram-negative commensal of human gut. Surprisingly, the role of E. coli in the pathogenesis of ulcerative colitis (UC) has not been explored until now.

METHODS: Human gut microbiota composition and meta-gut resistome were evaluated using metagenomics. Antibiotic susceptibility of E. coli isolates against different class of antibiotics was investigated. Further, the genome sequence analysis of E. coli isolates was performed to gain insight into the antimicrobial resistance (AMR) mechanism and virulence factors. Gut proteome of UC and non-UC was examined to understand the effect of resistant bacteria on host physiology.

RESULTS: In UC patients, meta-gut resistome was found to be dominated by AMR genes (829) compared to healthy controls (HC) [518]. The metagenome study revealed a higher prevalence of AMR genes in the rural population (378 in HC; 607 in UC) compared to the urban (340 in HC; 578 in UC). Approximately, 40% of all E. coli isolates were multi-drug resistant (MDR), with higher prevalence in UC (43.75%) compared to HC (33.33%). Up-regulated expression of antimicrobial human proteins (lactotransferrin, azurocidin, cathepsin G, neutrophil elastase, and neutrophil defensin 3) and inflammatory mediator (Protein S100-A9 and Protein S100-A8) suggest microbial infection in UC gut.

CONCLUSIONS: In addition to the conventional culturomics method, a multi-omics strategy provides deeper insights into the disease etiology, emergence of MDR pathobionts, and their roles in the disruption of the healthy gut environment in UC patients.},
}

Humans
*Colitis, Ulcerative/microbiology
*Gastrointestinal Microbiome/drug effects/genetics
*Escherichia coli/genetics/drug effects/pathogenicity
*Anti-Bacterial Agents/pharmacology
Drug Resistance, Multiple, Bacterial/genetics
Male
Escherichia coli Infections/microbiology
Adult
Female
Virulence Factors/genetics
Microbial Sensitivity Tests
Middle Aged
Severity of Illness Index
Metagenomics

@article {pmid38977240,
year = {2024},
author = {Chac, D and Slater, DM and Guillaume, Y and Dunmire, CN and Ternier, R and Vissières, K and Juin, S and Lucien, MAB and Boncy, J and Sanchez, VM and Dumayas, MG and Augustin, GC and Bhuiyan, TR and Qadri, F and Chowdhury, F and Khan, AI and Weil, AA and Ivers, LC and Harris, JB},
title = {Association between chlorine-treated drinking water, the gut microbiome, and enteric pathogen burden in young children in Haiti: An observational study.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {147},
number = {},
pages = {107165},
doi = {10.1016/j.ijid.2024.107165},
pmid = {38977240},
issn = {1878-3511},
mesh = {Humans ; Haiti/epidemiology ; *Chlorine/pharmacology ; *Drinking Water/microbiology ; Infant ; Child, Preschool ; *Gastrointestinal Microbiome/drug effects ; *Feces/microbiology ; Male ; Female ; Water Purification ; },
abstract = {OBJECTIVE: The effects of sanitation and hygiene interventions on the gut microbiome and enteric pathogen burden are not well understood. We measured the association between free chlorine residue (FCR) levels in drinking water, microbiome composition, and stool enteric pathogens in infants and young children in Haiti.

METHODS: FCR levels were measured in household drinking water and enteric pathogen burden was evaluated using multiplex RT-PCR of stool among 131 children from one month to five years of age living in Mirebalais, Haiti. Microbiome profiling was performed using metagenomic sequencing.

RESULTS: Most individuals lived in households with undetectable FCR measured in the drinking water (112/131, 86%). Detection of enteric pathogen DNA in stool was common and did not correlate with household water FCR. The infant microbiome in households with detectable FCR demonstrated reduced richness (fewer total number of species, P = 0.04 Kruskall-Wallis test) and less diversity by Inverse Simpson measures (P = 0.05) than households with undetectable FCR. Infants in households with a detectable FCR were more likely to have abundant Bifidobacterium. Using in vitro susceptibility testing, we found that some Bifidobacterium species were resistant to chlorine.

CONCLUSIONS: FCR in household drinking water did not correlate with enteric pathogen burden in our study.},
}

Humans
Haiti/epidemiology
*Chlorine/pharmacology
*Drinking Water/microbiology
Infant
Child, Preschool
*Gastrointestinal Microbiome/drug effects
*Feces/microbiology
Male
Female
Water Purification

@article {pmid38952337,
year = {2024},
author = {Sardar, P and Almeida, A and Pedicord, VA},
title = {Integrating functional metagenomics to decipher microbiome-immune interactions.},
journal = {Immunology and cell biology},
volume = {102},
number = {8},
pages = {680-691},
doi = {10.1111/imcb.12798},
pmid = {38952337},
issn = {1440-1711},
support = {MR/W016184/1//Career Development Award by the Medical Research Council/ ; 206245/Z/17/Z//Sir Henry Dale Fellowship jointly funded by the Wellcome Trust and the Royal Society/ ; PGS22/100116//Rosetrees Trust/ ; },
mesh = {*Metagenomics/methods ; Humans ; Animals ; *Gastrointestinal Microbiome/immunology/genetics ; Microbiota/immunology/genetics ; Metagenome ; Bacteria/genetics/immunology/classification ; },
abstract = {Microbial metabolites can be viewed as the cytokines of the microbiome, transmitting information about the microbial and metabolic environment of the gut to orchestrate and modulate local and systemic immune responses. Still, many immunology studies focus solely on the taxonomy and community structure of the gut microbiota rather than its functions. Early sequencing-based microbiota profiling approaches relied on PCR amplification of small regions of bacterial and fungal genomes to facilitate identification of the microbes present. However, recent microbiome analysis methods, particularly shotgun metagenomic sequencing, now enable culture-independent profiling of microbiome functions and metabolites in addition to taxonomic characterization. In this review, we showcase recent advances in functional metagenomics methods and applications and discuss the current limitations and potential avenues for future development. Importantly, we highlight a few examples of key areas of opportunity in immunology research where integrating functional metagenomic analyses of the microbiome can substantially enhance a mechanistic understanding of microbiome-immune interactions and their contributions to health and disease states.},
}

*Metagenomics/methods
Humans
Animals
*Gastrointestinal Microbiome/immunology/genetics
Microbiota/immunology/genetics
Metagenome
Bacteria/genetics/immunology/classification

@article {pmid39351905,
year = {2024},
author = {Feng, M and Robinson, S and Qi, W and Edwards, A and Stierli, B and van der Heijden, M and Frey, B and Varliero, G},
title = {Microbial genetic potential differs among cryospheric habitats of the Damma glacier.},
journal = {Microbial genomics},
volume = {10},
number = {10},
pages = {},
doi = {10.1099/mgen.0.001301},
pmid = {39351905},
issn = {2057-5858},
mesh = {*Ice Cover/microbiology ; *Ecosystem ; Soil Microbiology ; Nitrogen Fixation/genetics ; Microbiota/genetics ; Metagenomics ; Geologic Sediments/microbiology ; Bacteria/genetics/classification/isolation & purification ; Metagenome ; Nitrogen Cycle/genetics ; },
abstract = {Climate warming has led to glacier retreat worldwide. Studies on the taxonomy and functions of glacier microbiomes help us better predict their response to glacier melting. Here, we used shotgun metagenomic sequencing to study the microbial functional potential in different cryospheric habitats, i.e. surface snow, supraglacial and subglacial sediments, subglacial ice, proglacial stream water and recently deglaciated soils. The functional gene structure varied greatly among habitats, especially for snow, which differed significantly from all other habitats. Differential abundance analysis revealed that genes related to stress responses (e.g. chaperones) were enriched in ice habitat, supporting the fact that glaciers are a harsh environment for microbes. The microbial metabolic capabilities related to carbon and nitrogen cycling vary among cryospheric habitats. Genes related to auxiliary activities were overrepresented in the subglacial sediment, suggesting a higher genetic potential for the degradation of recalcitrant carbon (e.g., lignin). As for nitrogen cycling, genes related to nitrogen fixation were more abundant in barren proglacial soils, possibly due to the presence of Cyanobacteriota in this habitat. Our results deepen our understanding of microbial processes in glacial ecosystems, which are vulnerable to ongoing global warming, and they have implications for downstream ecosystems.},
}

*Ice Cover/microbiology
*Ecosystem
Soil Microbiology
Nitrogen Fixation/genetics
Microbiota/genetics
Metagenomics
Geologic Sediments/microbiology
Bacteria/genetics/classification/isolation & purification
Metagenome
Nitrogen Cycle/genetics

@article {pmid39351368,
year = {2024},
author = {Tolstoganov, I and Chen, Z and Pevzner, P and Korobeynikov, A},
title = {SpLitteR: diploid genome assembly using TELL-Seq linked-reads and assembly graphs.},
journal = {PeerJ},
volume = {12},
number = {},
pages = {e18050},
pmid = {39351368},
issn = {2167-8359},
mesh = {*Diploidy ; Animals ; Humans ; Genome, Human/genetics ; Sheep/genetics ; Software ; Sequence Analysis, DNA/methods ; Gastrointestinal Microbiome/genetics ; High-Throughput Nucleotide Sequencing/methods ; Genome/genetics ; },
abstract = {BACKGROUND: Recent advances in long-read sequencing technologies enabled accurate and contiguous de novo assemblies of large genomes and metagenomes. However, even long and accurate high-fidelity (HiFi) reads do not resolve repeats that are longer than the read lengths. This limitation negatively affects the contiguity of diploid genome assemblies since two haplomes share many long identical regions. To generate the telomere-to-telomere assemblies of diploid genomes, biologists now construct their HiFi-based phased assemblies and use additional experimental technologies to transform them into more contiguous diploid assemblies. The barcoded linked-reads, generated using an inexpensive TELL-Seq technology, provide an attractive way to bridge unresolved repeats in phased assemblies of diploid genomes.

RESULTS: We developed the SpLitteR tool for diploid genome assembly using linked-reads and assembly graphs and benchmarked it against state-of-the-art linked-read scaffolders ARKS and SLR-superscaffolder using human HG002 genome and sheep gut microbiome datasets. The benchmark showed that SpLitteR scaffolding results in 1.5-fold increase in NGA50 compared to the baseline LJA assembly and other scaffolders while introducing no additional misassemblies on the human dataset.

CONCLUSION: We developed the SpLitteR tool for assembly graph phasing and scaffolding using barcoded linked-reads. We benchmarked SpLitteR on assembly graphs produced by various long-read assemblers and have demonstrated that TELL-Seq reads facilitate phasing and scaffolding in these graphs. This benchmarking demonstrates that SpLitteR improves upon the state-of-the-art linked-read scaffolders in the accuracy and contiguity metrics. SpLitteR is implemented in C++ as a part of the freely available SPAdes package and is available at https://github.com/ablab/spades/releases/tag/splitter-preprint.},
}

*Diploidy
Animals
Humans
Genome, Human/genetics
Sheep/genetics
Software
Sequence Analysis, DNA/methods
Gastrointestinal Microbiome/genetics
High-Throughput Nucleotide Sequencing/methods
Genome/genetics

@article {pmid38546675,
year = {2024},
author = {Pötgens, SA and Havelange, V and Lecop, S and Li, F and Neyrinck, AM and Bindels, F and Neveux, N and Demoulin, JB and Moors, I and Kerre, T and Maertens, J and Walter, J and Schoemans, H and Delzenne, NM and Bindels, LB},
title = {Gut microbiome alterations at acute myeloid leukemia diagnosis are associated with muscle weakness and anorexia.},
journal = {Haematologica},
volume = {109},
number = {10},
pages = {3194-3208},
doi = {10.3324/haematol.2023.284138},
pmid = {38546675},
issn = {1592-8721},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Leukemia, Myeloid, Acute/microbiology/diagnosis/complications ; Male ; *Muscle Weakness/diagnosis/microbiology/etiology ; Female ; Middle Aged ; *Anorexia/microbiology/etiology/diagnosis ; Aged ; Adult ; Prospective Studies ; Feces/microbiology ; Cross-Sectional Studies ; Metabolomics/methods ; Metabolome ; },
abstract = {The gut microbiota makes critical contributions to host homeostasis, and its role in the treatment of acute myeloid leukemia (AML) has attracted attention. We investigated whether the gut microbiome is affected by AML, and whether such changes are associated with hallmarks of cachexia. Biological samples and clinical data were collected from 30 antibiotic- free AML patients at diagnosis and matched volunteers (1:1) in a multicenter, cross-sectional, prospective study. The composition and functional potential of the fecal microbiota were analyzed using shotgun metagenomics. Fecal, blood, and urinary metabolomics analyses were performed. AML patients displayed muscle weakness, anorexia, signs of altered gut function, and glycemic disorders. The composition of the fecal microbiota differed between patients with AML and control subjects, with an increase in oral bacteria. Alterations in bacterial functions and fecal metabolome support an altered redox status in the gut microbiota, which may contribute to the altered redox status observed in patients with AML. Eubacterium eligens, reduced 3-fold in AML patients, was strongly correlated with muscle strength and citrulline, a marker of enterocyte mass and function. Blautia and Parabacteroides, increased in patients with AML, were correlated with anorexia. Several bacterial taxa and metabolites (e.g., Blautia, Prevotella, phenylacetate, and hippurate) previously associated with glycemic disorders were altered. Our work revealed important perturbations in the gut microbiome of AML patients at diagnosis, which are associated with muscle strength, altered redox status, and anorexia. These findings pave the way for future mechanistic work to explore the function and therapeutic potential of the bacteria identified in this study.},
}

Humans
*Gastrointestinal Microbiome
*Leukemia, Myeloid, Acute/microbiology/diagnosis/complications
Male
*Muscle Weakness/diagnosis/microbiology/etiology
Female
Middle Aged
*Anorexia/microbiology/etiology/diagnosis
Aged
Adult
Prospective Studies
Feces/microbiology
Cross-Sectional Studies
Metabolomics/methods
Metabolome

@article {pmid37548643,
year = {2023},
author = {Li, Z and Ju, Y and Xia, J and Zhang, Z and Zhen, H and Tong, X and Sun, Y and Lu, H and Zong, Y and Chen, P and Cai, K and Wang, Z and Yang, H and Wang, J and Wang, J and Hou, Y and Jin, X and Zhang, T and Zhang, W and Xu, X and Xiao, L and Guo, R and Nie, C},
title = {Integrated Human Skin Bacteria Genome Catalog Reveals Extensive Unexplored Habitat-Specific Microbiome Diversity and Function.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {10},
number = {28},
pages = {e2300050},
pmid = {37548643},
issn = {2198-3844},
support = {2022ZD0211600//STI2030-Major Projects/ ; 2019-I2M-5-066//CAMS Innovation Fund for Medical Sciences/ ; },
mesh = {Humans ; *Skin/microbiology/metabolism ; *Microbiota/genetics ; *Genome, Bacterial/genetics ; *Bacteria/genetics/classification ; Metagenome/genetics ; Ecosystem ; Metagenomics/methods ; },
abstract = {The skin is the largest organ in the human body. Various skin environments on its surface constitutes a complex ecosystem. One of the characteristics of the skin micro-ecosystem is low biomass, which greatly limits a comprehensive identification of the microbial species through sequencing. In this study, deep-shotgun sequencing (average 21.5 Gigabyte (Gb)) from 450 facial samples and publicly available skin metagenomic datasets of 2069 samples to assemble a Unified Human Skin Genome (UHSG) catalog is integrated. The UHSG encompasses 813 prokaryotic species derived from 5779 metagenome-assembled genomes, among which 470 are novel species covering 20 phyla with 1385 novel assembled genomes. Based on the UHSG, the core functions of the skin microbiome are described and the differences in amino acid metabolism, carbohydrate metabolism, and drug resistance functions among different phyla are identified. Furthermore, analysis of secondary metabolites of the near-complete genomes further find 1220 putative novel secondary metabolites, several of which are found in previously unknown genomes. Single nucleotide variant (SNV) reveals a possible skin protection mechanism: the negative selection process of the skin environment to conditional pathogens. UHSG offers a convenient reference database that will facilitate a more in-depth understanding of the role of skin microorganisms in the skin.},
}

Humans
*Skin/microbiology/metabolism
*Microbiota/genetics
*Genome, Bacterial/genetics
*Bacteria/genetics/classification
Metagenome/genetics
Ecosystem
Metagenomics/methods

@article {pmid39349486,
year = {2024},
author = {Sun, W and Zhang, Y and Guo, R and Sha, S and Chen, C and Ullah, H and Zhang, Y and Ma, J and You, W and Meng, J and Lv, Q and Cheng, L and Fan, S and Li, R and Mu, X and Li, S and Yan, Q},
title = {A population-scale analysis of 36 gut microbiome studies reveals universal species signatures for common diseases.},
journal = {NPJ biofilms and microbiomes},
volume = {10},
number = {1},
pages = {96},
pmid = {39349486},
issn = {2055-5008},
support = {5050071720001//Beijing University of Chinese Medicine (BUCM)/ ; 2180072120049//Beijing University of Chinese Medicine (BUCM)/ ; 81503455//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Feces/microbiology ; Case-Control Studies ; *Bacteria/classification/genetics/isolation & purification ; Metagenome ; Metagenomics/methods ; China ; Biodiversity ; },
abstract = {The gut microbiome has been implicated in various human diseases, though findings across studies have shown considerable variability. In this study, we reanalyzed 6314 publicly available fecal metagenomes from 36 case-control studies on different diseases to investigate microbial diversity and disease-shared signatures. Using a unified analysis pipeline, we observed reduced microbial diversity in many diseases, while some exhibited increased diversity. Significant alterations in microbial communities were detected across most diseases. A meta-analysis identified 277 disease-associated gut species, including numerous opportunistic pathogens enriched in patients and a depletion of beneficial microbes. A random forest classifier based on these signatures achieved high accuracy in distinguishing diseased individuals from controls (AUC = 0.776) and high-risk patients from controls (AUC = 0.825), and it also performed well in external cohorts. These results offer insights into the gut microbiome's role in common diseases in the Chinese population and will guide personalized disease management strategies.},
}

Humans
*Gastrointestinal Microbiome
*Feces/microbiology
Case-Control Studies
*Bacteria/classification/genetics/isolation & purification
Metagenome
Metagenomics/methods
China
Biodiversity

@article {pmid39347539,
year = {2024},
author = {Yuan, Y and Hu, H and Sun, Z and Wang, W and Wang, Z and Zheng, M and Xing, Y and Zhang, W and Wang, M and Lu, X and Li, Y and Liang, C and Lin, Z and Xie, C and Li, J and Mao, T},
title = {Combining Metagenomics, Network Pharmacology and RNA-Seq Strategies to Reveal the Therapeutic Effects and Mechanisms of Qingchang Wenzhong Decoction on Inflammatory Bowel Disease in Mice.},
journal = {Drug design, development and therapy},
volume = {18},
number = {},
pages = {4273-4289},
pmid = {39347539},
issn = {1177-8881},
mesh = {Animals ; Mice ; *Drugs, Chinese Herbal/pharmacology/chemistry ; *Inflammatory Bowel Diseases/drug therapy ; *Metagenomics ; *Gastrointestinal Microbiome/drug effects ; *Network Pharmacology ; *Dextran Sulfate ; *Mice, Inbred C57BL ; Disease Models, Animal ; Male ; RNA-Seq ; },
abstract = {BACKGROUND: Inflammatory bowel disease (IBD) is a chronic and recurrent inflammatory disease that lacks effective treatments. Qingchang Wenzhong Decoction (QCWZD) is a clinically effective herbal prescription that has been proven to attenuate intestinal inflammation in IBD. However, its molecular mechanism of action has not been clearly elucidated.

PURPOSE: We aimed to probe the mechanism of QCWZD for the treatment of IBD.

METHODS: The dextran sulfate sodium (DSS)-induced mouse model of IBD was used to identify the molecular targets involved in the mechanism of action of QCWZD. Metagenomics sequencing was utilized to analyze the differences in gut microbiota and the functional consequences of these changes. Network pharmacology combined with RNA sequencing (RNA-seq) were employed to predict the molecular targets and mechanism of action of QCWZD, and were validated through in vivo experiments.

RESULTS: Our results demonstrated that QCWZD treatment alleviated intestinal inflammation and accelerated intestinal mucosal healing that involved restoration of microbial homeostasis. This hypothesis was supported by the results of bacterial metagenomics sequencing that showed attenuation of gut dysbiosis by QCWZD treatment, especially the depletion of the pathogenic bacterial genus Bacteroides, while increasing the beneficial microorganism Akkermansia muciniphila that led to altered bacterial gene functions, such as metabolic regulation. Network pharmacology and RNA-seq analyses showed that Th17 cell differentiation plays an important role in QCWZD-based treatment of IBD. This was confirmed by in vivo experiments showing a marked decrease in the percentage of CD3[+]CD4[+]IL-17[+] (Th17) cells. Furthermore, our results also showed that the key factors associated with Th17 cell differentiation (IL-17, NF-κB, TNF-α and IL-6) in the colon were significantly reduced in QCWZD-treated colitis mice.

CONCLUSION: QCWZD exerted beneficial effects in the treatment of IBD by modulating microbial homeostasis while inhibiting Th17 cell differentiation and its associated pathways, providing a novel and promising therapeutic strategy for the treatment of IBD.},
}

Animals
Mice
*Drugs, Chinese Herbal/pharmacology/chemistry
*Inflammatory Bowel Diseases/drug therapy
*Metagenomics
*Gastrointestinal Microbiome/drug effects
*Network Pharmacology
*Dextran Sulfate
*Mice, Inbred C57BL
Disease Models, Animal
Male
RNA-Seq

@article {pmid39346055,
year = {2024},
author = {Knobloch, S and Salimi, F and Buaya, A and Ploch, S and Thines, M},
title = {RAPiD: a rapid and accurate plant pathogen identification pipeline for on-site nanopore sequencing.},
journal = {PeerJ},
volume = {12},
number = {},
pages = {e17893},
pmid = {39346055},
issn = {2167-8359},
mesh = {*Nanopore Sequencing/methods ; Metagenomics/methods ; Plant Diseases/microbiology ; Bacteria/genetics/isolation & purification/classification ; Sequence Analysis, DNA/methods ; Fungi/genetics/isolation & purification/classification ; Plants/microbiology ; Computational Biology/methods ; },
abstract = {Nanopore sequencing technology has enabled the rapid, on-site taxonomic identification of samples from anything and anywhere. However, sequencing errors, inadequate databases, as well as the need for bioinformatic expertise and powerful computing resources, have hampered the widespread use of the technology for pathogen identification in the agricultural sector. Here we present RAPiD, a lightweight and accurate real-time taxonomic profiling pipeline. Compared to other metagenomic profilers, RAPiD had a higher classification precision achieved through the use of a curated, non-redundant database of common agricultural pathogens and extensive quality filtering of alignments. On a fungal, bacterial and mixed mock community RAPiD was the only pipeline to detect all members of the communities. We also present a protocol for in-field sample processing enabling pathogen identification from plant sample to sequence within 3 h using low-cost equipment. With sequencing costs continuing to decrease and more high-quality reference genomes becoming available, nanopore sequencing provides a viable method for rapid and accurate pathogen identification in the field. A web implementation of the RAPiD pipeline for real-time analysis is available at https://agrifuture.senckenberg.de.},
}

*Nanopore Sequencing/methods
Metagenomics/methods
Plant Diseases/microbiology
Bacteria/genetics/isolation & purification/classification
Sequence Analysis, DNA/methods
Fungi/genetics/isolation & purification/classification
Plants/microbiology
Computational Biology/methods

@article {pmid39343535,
year = {2024},
author = {Masuda, N and Kato, S and Ohkuma, M and Endo, K},
title = {Metagenomic Insights into Ecophysiology of Zetaproteobacteria and Gammaproteobacteria in Shallow Zones within Deep-sea Massive Sulfide Deposits.},
journal = {Microbes and environments},
volume = {39},
number = {3},
pages = {},
doi = {10.1264/jsme2.ME23104},
pmid = {39343535},
issn = {1347-4405},
mesh = {*Sulfides/metabolism ; *Gammaproteobacteria/genetics/classification/isolation & purification ; *Metagenomics ; *Seawater/microbiology ; *Metagenome ; Geologic Sediments/microbiology/chemistry ; Phylogeny ; Ecosystem ; Pacific Ocean ; Oxidation-Reduction ; Microbiota/genetics ; Carbon Cycle ; },
abstract = {Deep-sea massive sulfide deposits serve as energy sources for chemosynthetic ecosystems in dark, cold environments even after hydrothermal activity ceases. However, the vertical distribution of microbial communities within sulfide deposits along their depth from the seafloor as well as their ecological roles remain unclear. We herein conducted a culture-independent metagenomic ana-lysis of a core sample of massive sulfide deposits collected in a hydrothermally inactive field of the Southern Mariana Trough, Western Pacific, by drilling (sample depth: 0.52‍ ‍m below the seafloor). Based on the gene context of the metagenome-assembled genomes (MAGs) obtained, we showed the metabolic potential of as-yet-uncultivated microorganisms, particularly those unique to the shallow zone rich in iron hydroxides. Some members of Gammaproteobacteria have potential for the oxidation of reduced sulfur species (such as sulfide and thiosulfate) to sulfate coupled to nitrate reduction to ammonia and carbon fixation via the Calvin-Benson-Bassham (CBB) cycle, as the primary producers. The Zetaproteobacteria member has potential for iron oxidation coupled with microaerobic respiration. A comparative ana-lysis with previously reported metagenomes from deeper zones (~2‍ ‍m below the seafloor) of massive sulfide deposits revealed a difference in the relative abundance of each putative primary producer between the shallow and deep zones. Our results expand knowledge on the ecological potential of uncultivated microorganisms in deep-sea massive sulfide deposits and provide insights into the vertical distribution patterns of chemosynthetic ecosystems.},
}

*Sulfides/metabolism
*Gammaproteobacteria/genetics/classification/isolation & purification
*Metagenomics
*Seawater/microbiology
*Metagenome
Geologic Sediments/microbiology/chemistry
Phylogeny
Ecosystem
Pacific Ocean
Oxidation-Reduction
Microbiota/genetics
Carbon Cycle

@article {pmid39342083,
year = {2024},
author = {Wang, X and Yao, S and Yang, X and Li, Y and Yu, Z and Huang, J and Wang, J},
title = {Peritoneal dialysis promotes microbial-driven biosynthesis pathways of sesquiterpenes and triterpenes compounds in end-stage renal disease patients.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {377},
pmid = {39342083},
issn = {1471-2180},
support = {32170071//National Natural Science Foundation of China/ ; 32300051//National Natural Science Foundation of China/ ; 2022JJ40663//Natural Science Foundation of Hunan Province/ ; C2023045//Hunan Province Traditional Chinese Medicine Research Program Project/ ; },
mesh = {Humans ; *Kidney Failure, Chronic/therapy/metabolism/microbiology ; *Gastrointestinal Microbiome ; *Peritoneal Dialysis ; *Sesquiterpenes/metabolism ; Male ; Female ; *Feces/microbiology ; Middle Aged ; *Triterpenes/metabolism ; Bacteria/metabolism/classification/genetics/isolation & purification ; Biosynthetic Pathways ; Adult ; Metagenomics ; Aged ; },
abstract = {The concept of the gut-kidney axis is gaining significant attention due to the close relationship between gut microbiota and kidney disease. Peritoneal dialysis is recognized as a crucial renal replacement therapy for end-stage renal disease (ESRD). The alterations in gut microbiota and related mechanisms after receiving this dialysis method are not fully understood. This study conducted shotgun metagenomic sequencing on fecal samples from 11 end-stage renal disease patients who did not receive dialysis (ESRD_N) and 7 patients who received peritoneal dialysis (ESRD_P). After quality control and correlation analysis of the data, our study is aimed at exploring the impact of peritoneal dialysis on the gut microbiota and health of ESRD patients. Our research findings indicate that the complexity and aggregation characteristics of gut microbiota interactions increase in ESRD_P. In addition, the gut microbiota drives the biosynthesis pathways of sesquiterpenes and triterpenes in ESRD_P patients, which may contribute to blood purification and improve circulation. Therefore, our research will lay the foundation for the prevention and treatment of ESRD.},
}

Humans
*Kidney Failure, Chronic/therapy/metabolism/microbiology
*Gastrointestinal Microbiome
*Peritoneal Dialysis
*Sesquiterpenes/metabolism
Male
Female
*Feces/microbiology
Middle Aged
*Triterpenes/metabolism
Bacteria/metabolism/classification/genetics/isolation & purification
Biosynthetic Pathways
Adult
Metagenomics
Aged

@article {pmid39342284,
year = {2024},
author = {Seitz, VA and McGivern, BB and Borton, MA and Chaparro, JM and Schipanski, ME and Prenni, JE and Wrighton, KC},
title = {Cover crop root exudates impact soil microbiome functional trajectories in agricultural soils.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {183},
pmid = {39342284},
issn = {2049-2618},
support = {2021-67019-34814//U.S. Department of Agriculture/ ; 2021-67019-34814//U.S. Department of Agriculture/ ; 2021-67019-34814//U.S. Department of Agriculture/ ; 2021-67019-34814//U.S. Department of Agriculture/ ; 2021-67019-34814//U.S. Department of Agriculture/ ; 2021-67019-34814//U.S. Department of Agriculture/ ; 2021-67019-34814//U.S. Department of Agriculture/ ; P30CA046934//Cancer Center Support Grant/ ; P30CA046934//Cancer Center Support Grant/ ; P30CA046934//Cancer Center Support Grant/ ; 507580//Facilities Integrating Collaborations for User Science/ ; 507580//Facilities Integrating Collaborations for User Science/ ; 507580//Facilities Integrating Collaborations for User Science/ ; },
abstract = {BACKGROUND: Cover cropping is an agricultural practice that uses secondary crops to support the growth of primary crops through various mechanisms including erosion control, weed suppression, nutrient management, and enhanced biodiversity. Cover crops may elicit some of these ecosystem services through chemical interactions with the soil microbiome via root exudation, or the release of plant metabolites from roots. Phytohormones are one metabolite type exuded by plants that activate the rhizosphere microbiome, yet managing this chemical interaction remains an untapped mechanism for optimizing plant-soil-microbiome interactions. Currently, there is limited understanding on the diversity of cover crop phytohormone root exudation patterns and our aim was to understand how phytochemical signals selectively enrich specific microbial taxa and functionalities in agricultural soils.

RESULTS: Here, we link variability in cover crop root exudate composition to changes in soil microbiome functionality. Exudate chemical profiles from 4 cover crop species (Sorghum bicolor, Vicia villosa, Brassica napus, and Secale cereal) were used as the chemical inputs to decipher microbial responses. These distinct exudate profiles, along with a no exudate control, were amended to agricultural soil microcosms with microbial responses tracked over time using metabolomes and genome-resolved metatranscriptomes. Our findings illustrated microbial metabolic patterns were unique in response to cover crop exudate inputs over time, particularly by sorghum and cereal rye amended microcosms. In these microcosms, we identify novel microbial members (at the genera and family level) who produced IAA and GA4 over time. Additionally, we identified cover crop exudates exclusively enriched for bacterial nitrite oxidizers, while control microcosms were discriminated for nitrogen transport, mineralization, and assimilation, highlighting distinct changes in microbial nitrogen cycling in response to chemical inputs.

CONCLUSIONS: We highlight that root exudate amendments alter microbial community function (i.e., N cycling) and microbial phytohormone metabolisms, particularly in response to root exudates isolated from cereal rye and sorghum plants. Additionally, we constructed a soil microbial genomic catalog of microorganisms responding to commonly used cover crops, a public resource for agriculturally relevant microbes. Many of our exudate-stimulated microorganisms are representatives from poorly characterized or novel taxa, revealing the yet to be discovered metabolic reservoir harbored in agricultural soils. Our findings emphasize the tractability of high-resolution multi-omics approaches to investigate processes relevant for agricultural soils, opening the possibility of targeting specific soil biogeochemical outcomes through biological precision agricultural practices that use cover crops and the microbiome as levers for enhanced crop production. Video Abstract.},
}

@article {pmid39342129,
year = {2024},
author = {García-Estrada, DA and Selem-Mojica, N and Martínez-Hernández, A and Lara-Reyna, J and Dávila-Ramos, S and Verdel-Aranda, K},
title = {Diversity of bacterial communities in wetlands of Calakmul Biosphere Reserve: a comparative analysis between conserved and semi-urbanized zones in pre-Mayan Train era.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {376},
pmid = {39342129},
issn = {1471-2180},
support = {No. 320237//Consejo Nacional de Humanidades, Ciencias y Tecnologías, México/ ; },
abstract = {BACKGROUND: The Calakmul Biosphere Reserve (CBR) is known for its rich animal and plant biodiversity, yet its microbial communities remain largely unknown. The reserve does not possess permanent bodies of water; nevertheless, seasonal depressions associated with fractures create wetlands, known locally as aguadas. Given the recent construction of the Maya train that crosses the CRB, it is essential to assess the biodiversity of its microorganisms and recognize their potential as a valuable source of goods. This evaluation is pivotal in mitigating potential mismanagement of the forest ecosystem. To enhance comprehension of microbial communities, we characterized the microbiota in three different wetlands. Ag-UD1 and Ag-UD2 wetlands are located in a zone without human disturbances, while the third, Ag-SU3, is in a semi-urbanized zone. Sampling was carried out over three years (2017, 2018, and 2019), enabling the monitoring of spatiotemporal variations in bacterial community diversity. The characterization of microbiome composition was conducted using 16S rRNA metabarcoding. Concurrently, the genomic potential of select samples was examined through shotgun metagenomics.

RESULTS: Statistical analysis of alpha and beta diversity indices showed significant differences among the bacterial communities found in undisturbed sites Ag-UD1 and Ag-UD2 compared to Ag-SU3. However, no significant differences were observed among sites belonging to the undisturbed area. Furthermore, a comparative analysis at the zone level reveals substantial divergence among the communities, indicating that the geographic location of the samples significantly influences these patterns. The bacterial communities in the CBR wetlands predominantly consist of genera from phyla Actinobacteria, Acidobacteria, and Proteobacteria.

CONCLUSION: This characterization has identified the composition of microbial communities and provided the initial overview of the metabolic capacities of the microbiomes inhabiting the aguadas across diverse conservation zones. The three sites exhibit distinct microbial compositions, suggesting that variables such as chemical composition, natural and anthropogenic disturbances, vegetation, and fauna may play a pivotal role in determining the microbial structure of the aguadas. This study establishes a foundational baseline for evaluating the impact of climatic factors and human interventions on critical environments such as wetlands.},
}

@article {pmid39341403,
year = {2024},
author = {Chen, X and Balliew, J and Bauer, CX and Deegan, J and Gitter, A and Hanson, BM and Maresso, AW and Tisza, MJ and Troisi, CL and Rios, J and Mena, KD and Boerwinkle, E and Wu, F},
title = {Revealing patterns of SARS-CoV-2 variant emergence and evolution using RBD amplicon sequencing of wastewater.},
journal = {The Journal of infection},
volume = {},
number = {},
pages = {106284},
doi = {10.1016/j.jinf.2024.106284},
pmid = {39341403},
issn = {1532-2742},
abstract = {OBJECTIVES: Rapid evolution of SARS-CoV-2 has resulted in the emergence of numerous variants, posing significant challenges to public health surveillance. Clinical genome sequencing, while valuable, has limitations in capturing the full epidemiological dynamics of circulating variants in the general population. This study aimed to monitor the SARS-CoV-2 variant community dynamics and evolution using receptor-binding domain (RBD) amplicon sequencing of wastewater samples.

METHODS: We sequenced wastewater from El Paso, Texas over 17 months, compared the sequencing data with clinical genome data, and performed biodiversity analysis to reveal SARS-CoV-2 variant dynamics and evolution.

RESULTS: We identified 91 variants and observed waves of dominant variants transitioning from BA.2 to BA.2.12.1, BA.4&5, BQ.1, and XBB.1.5. Comparison with clinical genome sequencing data revealed earlier detection of variants and identification of unreported outbreaks. Our results also showed strong consistency with clinical data for dominant variants at the local, state, and national levels. Alpha diversity analyses revealed significant seasonal variations, with the highest diversity observed in winter. By segmenting the outbreak into lag, growth, stationary, and decline phases, we found higher variant diversity during the lag phase, likely due to lower inter-variant competition preceding outbreak growth.

CONCLUSIONS: Our findings underscore the importance of low transmission periods in facilitating rapid mutation and variant evolution. Our approach, integrating RBD amplicon sequencing with wastewater surveillance, demonstrates effectiveness in tracking viral evolution and understanding variant emergence, thus enhancing public health preparedness.},
}

@article {pmid39340684,
year = {2024},
author = {Vinothini, K and Nakkeeran, S and Saranya, N and Jothi, P and Richard, JI and Perveen, K and Bukhari, NA and Glick, BR and Sayyed, RZ and Mastinu, A},
title = {Rhizosphere Engineering of Biocontrol Agents Enriches Soil Microbial Diversity and Effectively Controls Root-Knot Nematodes.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {120},
pmid = {39340684},
issn = {1432-184X},
mesh = {Animals ; *Solanum lycopersicum/microbiology/parasitology ; *Soil Microbiology ; *Rhizosphere ; *Bacillus/genetics/physiology ; *Plant Roots/microbiology/parasitology ; *Pest Control, Biological ; Plant Diseases/parasitology/prevention & control/microbiology ; Trichoderma/physiology/genetics ; Tylenchoidea/physiology ; Microbiota ; Antinematodal Agents/pharmacology ; Biological Control Agents/pharmacology ; Bacteria/genetics/classification ; },
abstract = {The root-knot nematode (RKN) causes significant yield loss in tomatoes. Understanding the interaction of biocontrol agents (BCAs)-nematicides-soil microbiomes and RKNs is essential for enhancing the efficacy of biocontrol agents and nematicides to curb RKN damage to crops. The present study aimed to evaluate the in vitro effectiveness of BACa and nematicide against RKN and to apply the amplicon sequencing to assess the interaction of Bacillus velezensis (VB7) and Trichoderma koningiopsis (TK) against RKNs. Metagenomic analysis revealed the relative abundance of three phyla such as Proteobacteria (42.16%), Firmicutes (19.57%), and Actinobacteria (17.69%) in tomato rhizospheres. Those tomato rhizospheres treated with the combined application of B. velezensis VB7 + T. koningiopsis TK and RKN had a greater frequency of diversity and richness than the control. RKN-infested tomato rhizosphere drenched with bacterial and fungal antagonists had the maximum diversity index of bacterial communities. A strong correlation with a maximum number of interconnection edges in the phyla Proteobacteria, Firmicutes, and Actinobacteria was evident in soils treated with both B. velezensis VB7 and T. koningiopsis TK challenged against RKN in infected soil. The present study determined a much greater diversity of bacterial taxa observed in tomato rhizosphere soils treated with B. velezensis VB7 and T. koningiopsis TK than in untreated soil. It is suggested that the increased diversity and abundance of bacterial communities might be responsible for increased nematicidal properties in tomato plants. Hence, the combined applications of B. velezensis VB7 and T. koningiopsis TK can enhance the nematicidal action to curb RKN infecting tomatoes.},
}

Animals
*Solanum lycopersicum/microbiology/parasitology
*Soil Microbiology
*Rhizosphere
*Bacillus/genetics/physiology
*Plant Roots/microbiology/parasitology
*Pest Control, Biological
Plant Diseases/parasitology/prevention & control/microbiology
Trichoderma/physiology/genetics
Tylenchoidea/physiology
Microbiota
Antinematodal Agents/pharmacology
Biological Control Agents/pharmacology
Bacteria/genetics/classification

@article {pmid39340212,
year = {2024},
author = {Avellaneda-Franco, L and Xie, L and Nakai, M and Barr, JJ and Marques, FZ},
title = {Dietary fiber intake impacts gut bacterial and viral populations in a hypertensive mouse model.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2407047},
doi = {10.1080/19490976.2024.2407047},
pmid = {39340212},
issn = {1949-0984},
mesh = {Animals ; *Gastrointestinal Microbiome ; *Dietary Fiber/administration & dosage ; Mice ; Male ; *Hypertension/virology ; *Mice, Inbred C57BL ; *Bacteria/classification/genetics/isolation & purification ; *Bacteriophages/physiology/genetics ; *Disease Models, Animal ; Angiotensin II/metabolism ; Genome, Viral ; },
abstract = {The gut microbiome is an emerging factor in preventing hypertension, yet the influence of gut bacteriophages, viruses infecting bacteria, on this condition remains unclear. Bacteriophage-bacteria interactions, which impact the gut microbiome, are influenced differentially by temperate and virulent bacteriophages. However, the standard technique for studying viral populations, viral-like particles (VLPs)-metagenomes, often overlook prophages, the intracellular stage of temperate bacteriophages, creating a knowledge gap. To address this, we investigated alterations in extracellular and intracellular bacteriophages, alongside bacterial populations, in the angiotensin II-hypertension model. We sequenced VLPs and bulk DNA from cecal-colonic samples collected from male C57BL/6J mice implanted with minipumps containing saline or angiotensin II. We assembled 106 bacterial and 816 viral genomes and found that gut viral and bacterial populations remained stable between hypertensive and normotensive mice. A higher number of temperate viruses were observed across all treatments. Although temperate viruses outnumbered virulent viruses, sequencing of both VLPs and bulk revealed that virions from virulent viruses were more abundant in the murine gut. We then evaluated the impact of low- and high-fiber intake on gut microbiome composition in the angiotensin II model. Fiber intake significantly influenced the gut microbiome composition and hypertension development. Mice receiving high-fiber had lower blood pressure, a higher bacterial-encoded carbohydrate-associated enzyme, and a higher total relative abundance of temperate viruses than those receiving low-fiber. Our findings suggest that phages are not associated with hypertension development in the angiotensin II model. However, they support a complex diet-bacteria/phage interaction that may be involved in blood pressure regulation.},
}

Animals
*Gastrointestinal Microbiome
*Dietary Fiber/administration & dosage
Mice
Male
*Hypertension/virology
*Mice, Inbred C57BL
*Bacteria/classification/genetics/isolation & purification
*Bacteriophages/physiology/genetics
*Disease Models, Animal
Angiotensin II/metabolism
Genome, Viral

@article {pmid39338979,
year = {2024},
author = {Opitz-Ríos, C and Burgos-Pacheco, A and Paredes-Cárcamo, F and Campanini-Salinas, J and Medina, DA},
title = {Metagenomics Insight into Veterinary and Zoonotic Pathogens Identified in Urban Wetlands of Los Lagos, Chile.},
journal = {Pathogens (Basel, Switzerland)},
volume = {13},
number = {9},
pages = {},
doi = {10.3390/pathogens13090788},
pmid = {39338979},
issn = {2076-0817},
support = {11230295//Agencia Nacional de Investigación y Desarrollo/ ; VRID_FAPPE21-07//Universidad San Sebastián/ ; VRID_INTER23/02//Universidad San Sebastián/ ; VRID_DocI22/06//Universidad San Sebastián/ ; },
abstract = {Wetlands are ecosystems that are essential to ecological balance and biodiversity; nevertheless, human activity is a constant threat to them. Excess nutrients are caused by intensive livestock and agricultural operations, pollution, and population growth, which in turn leads to uncontrolled microbiological development. This impairment in water quality can constitute a risk to animal, human, and environmental health. To thoroughly characterize the microbial communities, shotgun metagenomics was used to characterize the taxonomic and functional pattern of microorganisms that inhabit urban wetlands in the Los Lagos Region of Chile. The main objective was to identify microorganisms of veterinary relevance, assess their potential antibiotic resistance, and characterize the main virulence mechanism. As expected, a high diversity of microorganisms was identified, including bacteria described as animal or human pathogens, such as Pasteurella multocida, Pseudomonas aeruginosa, Staphylococcus aureus, and Escherichia coli. Also, a diverse repertory of antimicrobial-resistant genes (ARGs) was detected in metagenomic assembled sequences and inside the sequence of mobile genetic elements, genes that confer mainly resistance to beta-lactams, consistent with the families of antibiotics most used in Chile. In addition, a diverse collection of virulence mechanisms was also identified. Given the significance of the relationship between environmental, animal, and human health-a concept known as One Health-there is a need to establish molecular surveillance programs that monitor the environmental biohazard elements using molecular tools. This work is the first report of the presence of these harmful biological elements in urban wetlands subjected to anthropogenic pressure, located in the south of Chile.},
}

@article {pmid39338129,
year = {2024},
author = {Mayer, MH and Woldemariam, S and Gisinger, C and Dorner, TE},
title = {Association of Gut Microbiome with Muscle Mass, Muscle Strength, and Muscle Performance in Older Adults: A Systematic Review.},
journal = {International journal of environmental research and public health},
volume = {21},
number = {9},
pages = {},
doi = {10.3390/ijerph21091246},
pmid = {39338129},
issn = {1660-4601},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Sarcopenia/microbiology/physiopathology ; *Muscle Strength ; Aged ; *Muscle, Skeletal/microbiology/physiology ; Middle Aged ; Aged, 80 and over ; },
abstract = {Sarcopenia, characterized by reduced muscle mass, strength, or performance, is a common condition in older adults. The association between the gut microbiome and sarcopenia remains poorly understood. This systematic review aims to evaluate the relationship between muscle parameters and the intestinal microbiome. A systematic search was conducted in PubMed, EMBASE, Cochrane Library, and Google Scholar for studies published between 2002 and 2022 involving participants aged 50+. Studies were included if they assessed sarcopenia using at least one measure of muscle mass (skeletal muscle mass, bioelectrical impedance analysis, MRI), muscle strength, or muscle performance (SARC-F questionnaire, Timed-Up-and-Go Test, Chair Stand Test, grip strength, gait speed, Short Physical Performance Battery, 400 m Walk Test). The microbiome was measured using at least RNA/DNA sequencing or shotgun metagenomic sequencing. Twelve studies were analyzed. Findings revealed that a higher abundance of bacterial species such as Desulfovibrio piger, and Clostridium symbiosum and reduced diversity of butyrate-producing bacteria was associated with sarcopenia severity, as indicated by decreased grip strength, muscle mass, or physical performance. The gut microbiome plays a significant role in age-related muscle loss. Probiotics, prebiotics, and bacterial products could be potential interventions to improve muscle health in older adults.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Sarcopenia/microbiology/physiopathology
*Muscle Strength
Aged
*Muscle, Skeletal/microbiology/physiology
Middle Aged
Aged, 80 and over

@article {pmid39334245,
year = {2024},
author = {Van Herzele, C and Coppens, S and Vereecke, N and Theuns, S and de Graaf, DC and Nauwynck, H},
title = {New insights into honey bee viral and bacterial seasonal infection patterns using third-generation nanopore sequencing on honey bee haemolymph.},
journal = {Veterinary research},
volume = {55},
number = {1},
pages = {118},
pmid = {39334245},
issn = {1297-9716},
support = {1SB3123N//Fonds Wetenschappelijk Onderzoek/ ; Baekeland mandate HBC.2020.2889//Agentschap Innoveren en Ondernemen/ ; },
mesh = {Animals ; Bees/virology/microbiology ; *Seasons ; *Hemolymph/virology/microbiology ; Nanopore Sequencing/methods/veterinary ; Bacteria/genetics/isolation & purification/classification ; Virome ; },
abstract = {Honey bees are rapidly declining, which poses a significant threat to our environment and agriculture industry. These vital insects face a disease complex believed to be caused by a combination of parasites, viruses, pesticides, and nutritional deficiencies. However, the real aetiology is still enigmatic. Due to the conventional analysis methods, we still lack complete insights into the honey bee virome and the presence of pathogenic bacteria. To fill this knowledge gap, we employed third-generation nanopore metagenomic sequencing on honey bee haemolymph to monitor the presence of pathogens over almost a year. This study provides valuable insights into the changes in bacterial and viral loads within honey bee colonies. We identified different pathogens in the honey bee haemolymph, which are not included in honey bee screenings. These pathogens comprise the Apis mellifera filamentous virus, Apis rhabdoviruses, and various bacteria such as Frischella sp. and Arsenophonus sp. Furthermore, a sharp contrast was observed between young and old bees. Our research proposes that transgenerational immune priming may play a role in shaping infection patterns in honey bees. We observed a significant increase in pathogen loads in the spring, followed by a notable decrease in pathogen presence during the summer and autumn months. However, certain pathogens seem to be able to evade this priming effect, making them particularly intriguing as potential factors contributing to mortality. In the future, we aim to expand our research on honey bee transgenerational immune priming and investigate its potential in natural settings. This knowledge will ultimately enhance honey bee health and decrease colony mortality.},
}

Animals
Bees/virology/microbiology
*Seasons
*Hemolymph/virology/microbiology
Nanopore Sequencing/methods/veterinary
Bacteria/genetics/isolation & purification/classification
Virome

@article {pmid39333778,
year = {2024},
author = {Msango, K and Gouda, MNR and Ramakrishnan, B and Kumar, A and Subramanian, S},
title = {Variation and functional profile of gut bacteria in the scarab beetle, Anomala dimidiata, under a cellulose-enriched microenvironment.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {22400},
pmid = {39333778},
issn = {2045-2322},
mesh = {Animals ; *Coleoptera/microbiology ; *Cellulose/metabolism ; *Gastrointestinal Microbiome ; *Bacteria/genetics/metabolism/classification/isolation & purification ; Larva/microbiology ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; Symbiosis ; },
abstract = {This study utilized cultivable methods and 16 S amplicon sequencing to compare taxonomic profiles and functional potential of gut bacteria in the scarab beetle, Anomola dimidiata, under cellulose-enriched conditions. Eight culturable cellulolytic gut bacteria were isolated from the midgut and hindgut of the scarab larvae, respectively. 16 S amplicon sequencing evinced that the most represented taxonomic profiles at phylum level in the fermentation chamber and midgut were Bacillota (71.62 and 56.76%), Pseudomonadota (22.66 and 36.89%) and Bacteroidota (2.7 and 2.81%). Bacillota (56.74 and 91.39%) were significantly enriched in the midgut with the addition of cellulose. In contrast, Bacillota and Psedomonadota were significantly enriched in the fermentation chamber. Carbohydrate metabolism was up-regulated in the midgut, while nitrogen and phosphorus metabolism were up-regulated in the fermentation chamber, suggesting these symbionts' possible metabolic roles to the host. An analysis of total cellulases as well as amplicon sequence variants indicated that the gut bacteria belonging to Acinetobacter, Bacillus, Brucella, Brevibacillus, Enterobacter, Lysinibacillus and Paenibacillus are involved in nutrition provisioning. These results have provided additional insights into the gut bacteria associated with cellulose digestion in A. dimidiata and created a platform for bioprospecting novel isolates to produce biomolecules for biotechnological use, besides identifying eco-friendly targets for its management.},
}

Animals
*Coleoptera/microbiology
*Cellulose/metabolism
*Gastrointestinal Microbiome
*Bacteria/genetics/metabolism/classification/isolation & purification
Larva/microbiology
RNA, Ribosomal, 16S/genetics
Phylogeny
Symbiosis

@article {pmid39333734,
year = {2024},
author = {Ishak, S and Rondeau-Leclaire, J and Faticov, M and Roy, S and Laforest-Lapointe, I},
title = {Boreal moss-microbe interactions are revealed through metagenome assembly of novel bacterial species.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {22168},
pmid = {39333734},
issn = {2045-2322},
mesh = {*Bryophyta/microbiology ; *Bacteria/genetics/metabolism/classification ; *Metagenome ; Taiga ; Metagenomics/methods ; Microbiota ; Quebec ; Nitrogen Fixation ; Photosynthesis ; },
abstract = {Moss-microbe interactions contribute to ecosystem processes in boreal forests. Yet, how host-specific characteristics and the environment drive the composition and metabolic potential of moss microbiomes is still poorly understood. In this study, we use shotgun metagenomics to identify the taxonomy and metabolic potential of the bacteria of four moss species of the boreal forests of Northern Québec, Canada. To characterize moss bacterial community composition and diversity, we assembled the genomes of 110 potentially novel bacterial species. Our results highlight that moss genus, species, gametophyte section, and to a lesser extent soil pH and soil temperature, drive moss-associated bacterial community composition and diversity. In the brown gametophyte section, two Stigonema spp. showed partial pathway completeness for photosynthesis and nitrogen fixation, while all brown-associated Hyphomicrobiales had complete assimilatory nitrate reduction pathways and many nearly complete carbon fixation pathways. Several brown-associated species showed partial to complete pathways for coenzyme M and F420 biosynthesis, important for methane metabolism. In addition, green-associated Hyphomicrobiales (Methylobacteria spp.) displayed potential for the anoxygenic photosystem II pathway. Overall, our findings demonstrate how host-specific characteristics and environmental factors shape the composition and metabolic potential of moss bacteria, highlighting their roles in carbon fixation, nitrogen cycling, and methane metabolism in boreal forests.},
}

*Bryophyta/microbiology
*Bacteria/genetics/metabolism/classification
*Metagenome
Taiga
Metagenomics/methods
Microbiota
Quebec
Nitrogen Fixation
Photosynthesis

@article {pmid39333577,
year = {2024},
author = {Zhao, B and Zi, M and Zhang, X and Wang, Y},
title = {Microbial communities and metagenomes in methane-rich deep coastal sediments.},
journal = {Scientific data},
volume = {11},
number = {1},
pages = {1043},
pmid = {39333577},
issn = {2052-4463},
support = {U22B2012//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Methane/metabolism ; *Geologic Sediments/microbiology ; *Microbiota ; *Metagenome ; *Archaea/genetics ; *RNA, Ribosomal, 16S/genetics ; Phylogeny ; },
abstract = {Coastal sediments are rich in embedded recalcitrant organic carbons that are biotransformed into methane. In this study, gas composition (carbon dioxide, methane and nitrogen) and chemical indicators (total nitrogen, total carbon, and total sulfate) were examined in five deep sediment cores (up to 130 m in length) obtained from the Hangzhou Bay. The V3-V4 region of the 16S rRNA gene amplicons was amplified and sequenced for the prokaryotic community analysis. The species composition, along with the physicochemical factors of the sediments, revealed a strong correlation with methane content in one of the sediment cores. We then obtained metagenomes of the two sediment samples selected for their high methane content and enrichment of methanogenic Bathyarchaeota with phylogenetic evidence. A total of 27 draft genomes were retrieved through metagenomic binning methodologies and were classified into Bathyarchaeota, Asgard archaea, Planctomycetes, and other microbial groups. The data provided are valuable for understanding the relationship between methane generation and microbial community composition in deep sediment core samples from coastal to marine environments.},
}

*Methane/metabolism
*Geologic Sediments/microbiology
*Microbiota
*Metagenome
*Archaea/genetics
*RNA, Ribosomal, 16S/genetics
Phylogeny

@article {pmid39333527,
year = {2024},
author = {Cheng, M and Xu, Y and Cui, X and Wei, X and Chang, Y and Xu, J and Lei, C and Xue, L and Zheng, Y and Wang, Z and Huang, L and Zheng, M and Luo, H and Leng, Y and Jiang, C},
title = {Deep longitudinal lower respiratory tract microbiome profiling reveals genome-resolved functional and evolutionary dynamics in critical illness.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {8361},
pmid = {39333527},
issn = {2041-1723},
mesh = {Humans ; *Critical Illness ; *Microbiota/genetics ; *Intensive Care Units ; *Metagenome/genetics ; Metagenomics/methods ; Longitudinal Studies ; Male ; Female ; Plasmids/genetics ; Genome, Bacterial/genetics ; Respiratory System/microbiology ; Aged ; Middle Aged ; Bacteria/genetics/classification/isolation & purification ; Pneumonia/microbiology ; Evolution, Molecular ; },
abstract = {The lower respiratory tract (LRT) microbiome impacts human health, especially among critically ill patients. However, comprehensive characterizations of the LRT microbiome remain challenging due to low microbial mass and host contamination. We develop a chelex100-based low-biomass microbial-enrichment method (CMEM) that enables deep metagenomic profiling of LRT samples to recover near-complete microbial genomes. We apply the method to 453 longitudinal LRT samples from 157 intensive care unit (ICU) patients in three geographically distant hospitals. We recover 120 high-quality metagenome-assembled genomes (MAGs) and associated plasmids without culturing. We detect divergent longitudinal microbiome dynamics and hospital-specific dominant opportunistic pathogens and resistomes in pneumonia patients. Diagnosed pneumonia and the ICU stay duration were associated with the abundance of specific antibiotic-resistance genes (ARGs). Moreover, CMEM can serve as a robust tool for genome-resolved analyses. MAG-based analyses reveal strain-specific resistome and virulome among opportunistic pathogen strains. Evolutionary analyses discover increased mobilome in prevailing opportunistic pathogens, highly conserved plasmids, and new recombination hotspots associated with conjugative elements and prophages. Integrative analysis with epidemiological data reveals frequent putative inter-patient strain transmissions in ICUs. In summary, we present a genome-resolved functional, transmission, and evolutionary landscape of the LRT microbiota in critically ill patients.},
}

Humans
*Critical Illness
*Microbiota/genetics
*Intensive Care Units
*Metagenome/genetics
Metagenomics/methods
Longitudinal Studies
Male
Female
Plasmids/genetics
Genome, Bacterial/genetics
Respiratory System/microbiology
Aged
Middle Aged
Bacteria/genetics/classification/isolation & purification
Pneumonia/microbiology
Evolution, Molecular

@article {pmid39333204,
year = {2024},
author = {Martin Říhová, J and Gupta, S and Nováková, E and Hypša, V},
title = {Fur microbiome as a putative source of symbiotic bacteria in sucking lice.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {22326},
pmid = {39333204},
issn = {2045-2322},
support = {GA20-07674S//Grantová Agentura České Republiky/ ; },
mesh = {Animals ; *Symbiosis ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Phthiraptera/microbiology ; Bacteria/genetics/classification/isolation & purification ; },
abstract = {Symbiosis between insects and bacteria has been established countless times. While it is well known that the symbionts originated from a variety of different bacterial taxa, it is usually difficult to determine their environmental source and a route of their acquisition by the host. In this study, we address this question using a model of Neisseriaceae symbionts in rodent lice. These bacteria established their symbiosis independently with different louse taxa (Polyplax, Hoplopleura, Neohaematopinus), most likely from the same environmental source. We first applied amplicon analysis to screen for candidate source bacterium in the louse environment. Since lice are permanent ectoparasites, often specific to the particular host, we screened various microbiomes associated with three rodent species (Microtus arvalis, Clethrionomys glareolus, and Apodemus flavicollis). The analyzed samples included fur, skin, spleen, and other ectoparasites sampled from these rodents. The fur microbiome data revealed a Neisseriaceae bacterium, closely related to the known louse symbionts. The draft genomes of the environmental Neisseriaceae, assembled from all three rodent hosts, converged to a remarkably small size of approximately 1.4 Mbp, being even smaller than the genomes of the related symbionts. Our results suggest that the rodent fur microbiome can serve as a source for independent establishment of bacterial symbiosis in associated louse species. We further propose a hypothetical scenario of the genome evolution during the transition of a free-living bacterium to the member of the rodent fur-associated microbiome and subsequently to the facultative and obligate louse symbionts.},
}

Animals
*Symbiosis
*Microbiota
Phylogeny
RNA, Ribosomal, 16S/genetics
Phthiraptera/microbiology
Bacteria/genetics/classification/isolation & purification

@article {pmid39333145,
year = {2024},
author = {Boie, W and Schemmel, M and Ye, W and Hasler, M and Goll, M and Verreet, JA and Cai, D},
title = {An assessment of the species diversity and disease potential of Pythium communities in Europe.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {8369},
pmid = {39333145},
issn = {2041-1723},
support = {031B0910-A//Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research)/ ; 221NR-058B//Fachagentur Nachwachsende Rohstoffe (Agency for Renewable Resources)/ ; },
mesh = {*Pythium/genetics/isolation & purification ; Europe ; *Plant Diseases/microbiology ; *Zea mays/microbiology ; Soil Microbiology ; Biodiversity ; Metagenomics/methods ; },
abstract = {Pythium sensu lato (s.l.) is a genus of parasitic oomycetes that poses a serious threat to agricultural production worldwide, but their severity is often neglected because little knowledge about them is available. Using an internal transcribed spacer (ITS) amplicon-based-metagenomics approach, we investigate the occurrence, abundance, and diversity of Pythium spp. s.l. in 127 corn fields of 11 European countries from the years 2019 to 2021. We also identify 73 species, with up to 20 species in a single soil sample, and the prevalent species, which show high species diversity, varying disease potential, and are widespread in most countries. Further, we show species-species co-occurrence patterns considering all detected species and link species abundance to soil parameter using the LUCAS topsoil dataset. Infection experiments with recovered isolates show that Pythium s.l. differ in disease potential, and that effective interference with plant hormone networks suppressing JA (jasmonate)-mediated defenses is an essential component of the virulence mechanism of Pythium s.l. species. This study provides a valuable dataset that enables deep insights into the structure and species diversity of Pythium s.l. communities in European corn fields and knowledge for better understanding plant-Pythium interactions, facilitating the development of an effective strategy to cope with this pathogen.},
}

*Pythium/genetics/isolation & purification
Europe
*Plant Diseases/microbiology
*Zea mays/microbiology
Soil Microbiology
Biodiversity
Metagenomics/methods

@article {pmid39327429,
year = {2024},
author = {Schmartz, GP and Rehner, J and Schuff, MJ and Molano, LG and Becker, SL and Krawczyk, M and Tagirdzhanov, A and Gurevich, A and Francke, R and Müller, R and Keller, V and Keller, A},
title = {Exploring microbial diversity and biosynthetic potential in zoo and wildlife animal microbiomes.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {8263},
pmid = {39327429},
issn = {2041-1723},
support = {469073465//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
mesh = {Animals ; *Animals, Wild/microbiology ; *Animals, Zoo/microbiology ; *Gastrointestinal Microbiome/genetics ; *Anti-Bacterial Agents/pharmacology ; *Microbiota/genetics/drug effects ; Bacteria/genetics/metabolism/classification/drug effects ; Multigene Family ; Humans ; Biodiversity ; Drug Resistance, Bacterial/genetics ; Vancomycin/pharmacology ; Biosynthetic Pathways/genetics ; },
abstract = {Understanding human, animal, and environmental microbiota is essential for advancing global health and combating antimicrobial resistance (AMR). We investigate the oral and gut microbiota of 48 animal species in captivity, comparing them to those of wildlife animals. Specifically, we characterize the microbiota composition, metabolic pathways, AMR genes, and biosynthetic gene clusters (BGCs) encoding the production of specialized metabolites. Our results reveal a high diversity of microbiota, with 585 novel species-level genome bins (SGBs) and 484 complete BGCs identified. Functional gene analysis of microbiomes shows diet-dependent variations. Furthermore, by comparing our findings to wildlife-derived microbiomes, we observe the impact of captivity on the animal microbiome, including examples of converging microbiome compositions. Importantly, our study identifies AMR genes against commonly used veterinary antibiotics, as well as resistance to vancomycin, a critical antibiotic in human medicine. These findings underscore the importance of the 'One Health' approach and the potential for zoonotic transmission of pathogenic bacteria and AMR. Overall, our study contributes to a better understanding of the complexity of the animal microbiome and highlights its BGC diversity relevant to the discovery of novel antimicrobial compounds.},
}

Animals
*Animals, Wild/microbiology
*Animals, Zoo/microbiology
*Gastrointestinal Microbiome/genetics
*Anti-Bacterial Agents/pharmacology
*Microbiota/genetics/drug effects
Bacteria/genetics/metabolism/classification/drug effects
Multigene Family
Humans
Biodiversity
Drug Resistance, Bacterial/genetics
Vancomycin/pharmacology
Biosynthetic Pathways/genetics

@article {pmid39217664,
year = {2024},
author = {Yu, Y and Wei, R and Yi, S and Teng, Y and Ning, R and Wei, S and Bai, L and Liu, H and Li, L and Xu, H and Han, C},
title = {Research Note: Integrative analysis of transcriptome and gut microbiome reveals foie gras capacity difference between cage and floor rearing systems.},
journal = {Poultry science},
volume = {103},
number = {11},
pages = {104248},
pmid = {39217664},
issn = {1525-3171},
mesh = {Animals ; *Gastrointestinal Microbiome ; *Geese ; *Transcriptome ; *Animal Husbandry/methods ; Housing, Animal ; Liver/metabolism ; Lipid Metabolism ; Male ; Gene Expression Profiling/veterinary ; },
abstract = {To explore the differences in foie gras performance between geese raised in cages and on the ground, we conducted an integrative analysis of liver transcriptome and gut microbial metagenomes. The results showed extremely significant differences in the liver weight (P < 0.01) and liver lipid accumulation of FRS and CRS groups. The levels of triglyceride (TG), high-density lipoprotein cholesterol (HDL-C) and low-density lipoprotein cholesterol (LDL-C) of CRS were significantly higher than those of FRS (P < 0.05). Transcriptome analysis showed that 3,917 upregulated and 1,395 downregulated genes were identified, and lipid metabolism pathway and fatty acid metabolism were significantly enriched. Analysis of cecum microbiota revealed that several inflammation-related bacteria (including Gallibacterium, Escherichia-Shigella, Desulfovibrio, Alistipes, and Fournierella) were enriched in CRS, while beneficial bacteria (including Lactobacillus, Limosilactobacillus, and Ligilactobacillus) were significantly enriched in FRS. In conclusion, CRS was better than FRS in foie gras production, which was more conducive to lipid deposition in the goose liver.},
}

Animals
*Gastrointestinal Microbiome
*Geese
*Transcriptome
*Animal Husbandry/methods
Housing, Animal
Liver/metabolism
Lipid Metabolism
Male
Gene Expression Profiling/veterinary

@article {pmid39331712,
year = {2024},
author = {Fellows, RC and Chun, SK and Larson, N and Fortin, BM and Mahieu, AL and Song, WA and Seldin, MM and Pannunzio, NR and Masri, S},
title = {Disruption of the intestinal clock drives dysbiosis and impaired barrier function in colorectal cancer.},
journal = {Science advances},
volume = {10},
number = {39},
pages = {eado1458},
doi = {10.1126/sciadv.ado1458},
pmid = {39331712},
issn = {2375-2548},
mesh = {Animals ; *Colorectal Neoplasms/microbiology/metabolism/pathology ; *Gastrointestinal Microbiome ; *Dysbiosis/microbiology ; Mice ; *Circadian Clocks/genetics ; Intestinal Mucosa/metabolism/microbiology ; Disease Models, Animal ; Humans ; Permeability ; },
abstract = {Diet is a robust entrainment cue that regulates diurnal rhythms of the gut microbiome. We and others have shown that disruption of the circadian clock drives the progression of colorectal cancer (CRC). While certain bacterial species have been suggested to play driver roles in CRC, it is unknown whether the intestinal clock impinges on the microbiome to accelerate CRC pathogenesis. To address this, genetic disruption of the circadian clock, in an Apc-driven mouse model of CRC, was used to define the impact on the gut microbiome. When clock disruption is combined with CRC, metagenomic sequencing identified dysregulation of many bacterial genera including Bacteroides, Helicobacter, and Megasphaera. We identify functional changes to microbial pathways including dysregulated nucleic acid, amino acid, and carbohydrate metabolism, as well as disruption of intestinal barrier function. Our findings suggest that clock disruption impinges on microbiota composition and intestinal permeability that may contribute to CRC pathogenesis.},
}

Animals
*Colorectal Neoplasms/microbiology/metabolism/pathology
*Gastrointestinal Microbiome
*Dysbiosis/microbiology
Mice
*Circadian Clocks/genetics
Intestinal Mucosa/metabolism/microbiology
Disease Models, Animal
Humans
Permeability

@article {pmid39331699,
year = {2024},
author = {Yang, Z and Shan, Y and Liu, X and Chen, G and Pan, Y and Gou, Q and Zou, J and Chang, Z and Zeng, Q and Yang, C and Kong, J and Sun, Y and Li, S and Zhang, X and Wu, WC and Li, C and Peng, H and Holmes, EC and Guo, D and Shi, M},
title = {VirID: Beyond Virus Discovery - An Integrated Platform for Comprehensive RNA Virus Characterization.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msae202},
pmid = {39331699},
issn = {1537-1719},
abstract = {RNA viruses exhibit vast phylogenetic diversity and can significantly impact public health and agriculture. However, current bioinformatics tools for viral discovery from metagenomic data frequently generate false positive virus results, overestimate viral diversity, and misclassify virus sequences. Additionally, current tools often fail to determine virus-host associations, which hampers investigation of the potential threat posed by a newly detected virus. To address these issues we developed VirID, a software tool specifically designed for the discovery and characterization of RNA viruses from metagenomic data. The basis of VirID is a comprehensive RNA-dependent RNA polymerase (RdRP) database to enhance a workflow that includes RNA virus discovery, phylogenetic analysis, and phylogeny-based virus characterization. Benchmark tests on a simulated data set demonstrated that VirID had high accuracy in profiling viruses and estimating viral richness. In evaluations with real-world samples, VirID was able to identity RNA viruses of all type, but also provided accurate estimations of viral genetic diversity and virus classification, as well as comprehensive insights into virus associations with humans, animals, and plants. VirID therefore offers a robust tool for virus discovery and serves as a valuable resource in basic virological studies, pathogen surveillance, and early warning systems for infectious disease outbreaks.},
}

@article {pmid39329142,
year = {2024},
author = {Khomutovska, N and Jasser, I and Sarapultseva, P and Spirina, V and Zaitsev, A and Masłowiecka, J and Isidorov, VA},
title = {Seasonal dynamics in leaf litter decomposing microbial communities in temperate forests: a whole-genome- sequencing-based study.},
journal = {PeerJ},
volume = {12},
number = {},
pages = {e17769},
pmid = {39329142},
issn = {2167-8359},
mesh = {*Plant Leaves/microbiology/metabolism ; *Forests ; *Seasons ; *Microbiota/genetics/physiology ; Bacteria/genetics/classification/metabolism ; Fungi/genetics/classification/metabolism/isolation & purification ; Whole Genome Sequencing ; Metagenome/genetics ; Trees/microbiology ; },
abstract = {Leaf litter decomposition, a crucial component of the global carbon cycle, relies on the pivotal role played by microorganisms. However, despite their ecological importance, leaf-litter-decomposing microorganism taxonomic and functional diversity needs additional study. This study explores the taxonomic composition, dynamics, and functional role of microbial communities that decompose leaf litter of forest-forming tree species in two ecologically unique regions of Europe. Twenty-nine microbial metagenomes isolated from the leaf litter of eight forest-forming species of woody plants were investigated by Illumina technology using read- and assembly-based approaches of sequences analysis. The taxonomic structure of the microbial community varies depending on the stage of litter decomposition; however, the community's core is formed by Pseudomonas, Sphingomonas, Stenotrophomonas, and Pedobacter genera of Bacteria and by Aureobasidium, Penicillium, Venturia genera of Fungi. A comparative analysis of the taxonomic structure and composition of the microbial communities revealed that in both regions, seasonal changes in structure take place; however, there is no clear pattern in its dynamics. Functional gene analysis of MAGs revealed numerous metabolic profiles associated with leaf litter degradation. This highlights the diverse metabolic capabilities of microbial communities and their implications for ecosystem processes, including the production of volatile organic compounds (VOCs) during organic matter decomposition. This study provides important advances in understanding of ecosystem processes and the carbon cycle, underscoring the need to unravel the intricacies of microbial communities within these contexts.},
}

*Plant Leaves/microbiology/metabolism
*Forests
*Seasons
*Microbiota/genetics/physiology
Bacteria/genetics/classification/metabolism
Fungi/genetics/classification/metabolism/isolation & purification
Whole Genome Sequencing
Metagenome/genetics
Trees/microbiology

@article {pmid37052201,
year = {2023},
author = {Jansen, D and Falony, G and Vieira-Silva, S and Simsek, C and Marcelis, T and Caenepeel, C and Machiels, K and Raes, J and Vermeire, S and Matthijnssens, J},
title = {Community Types of the Human Gut Virome are Associated with Endoscopic Outcome in Ulcerative Colitis.},
journal = {Journal of Crohn's & colitis},
volume = {17},
number = {9},
pages = {1504-1513},
pmid = {37052201},
issn = {1876-4479},
support = {1S78021N//Fonds Wetenschappelijk Onderzoek/ ; },
mesh = {Humans ; *Virome ; *Gastrointestinal Microbiome ; *Colitis, Ulcerative/virology/therapy ; Male ; Female ; *Feces/virology/microbiology ; Adult ; Middle Aged ; Bacteriophages/isolation & purification ; Dysbiosis/virology ; Treatment Outcome ; High-Throughput Nucleotide Sequencing ; },
abstract = {BACKGROUND: Inflammatory bowel disease [IBD] is a major debilitating disease. Recently, the gut microbiota has gained attention as an important factor involved in the pathophysiology of IBD. As a complement to the established bacterial 'enterotypes' associated with IBD, we focused here on viruses. We investigated the intestinal virome of IBD patients undergoing biological therapy for the presence of virome configurations associated with IBD, and to uncover how those configurations are associated with therapeutic success.

METHODS: Viral-like particle enrichment followed by deep sequencing was performed on 432 faecal samples from 181 IBD patients starting biological therapy. Redundancy analysis and Dirichlet Multinomial Mixtures were applied to determine covariates of the virome composition and to condense the gut virota into 'viral community types', respectively.

RESULTS: Patients were stratified based on unsupervised clustering into two viral community types. Community type CA showed a low α-diversity and a high relative abundance of Caudoviricetes [non-CrAss] phages and was associated with the dysbiotic Bact2-enterotype. Community type CrM showed a high α-diversity and a high relative abundance of Crassvirales and Malgrandaviricetes phages. During post-interventional analysis, endoscopic outcome was associated with gut virome composition. Remitting UC patients had a high percentage of community type CrM, a high Shannon diversity and a low lysogenic potential. Pre-interventional analyses also identified five novel phages associated with treatment success.

CONCLUSIONS: This study proposed two gut virome configurations that may be involved in the pathophysiology of IBD. Interestingly, those viral configurations are further associated with therapeutic success, suggesting a potential clinical relevance.},
}

Humans
*Virome
*Gastrointestinal Microbiome
*Colitis, Ulcerative/virology/therapy
Male
Female
*Feces/virology/microbiology
Adult
Middle Aged
Bacteriophages/isolation & purification
Dysbiosis/virology
Treatment Outcome
High-Throughput Nucleotide Sequencing

@article {pmid39327438,
year = {2024},
author = {Schmartz, GP and Rehner, J and Gund, MP and Keller, V and Molano, LG and Rupf, S and Hannig, M and Berger, T and Flockerzi, E and Seitz, B and Fleser, S and Schmitt-Grohé, S and Kalefack, S and Zemlin, M and Kunz, M and Götzinger, F and Gevaerd, C and Vogt, T and Reichrath, J and Diehl, L and Hecksteden, A and Meyer, T and Herr, C and Gurevich, A and Krug, D and Hegemann, J and Bozhueyuek, K and Gulder, TAM and Fu, C and Beemelmanns, C and Schattenberg, JM and Kalinina, OV and Becker, A and Unger, M and Ludwig, N and Seibert, M and Stein, ML and Hanna, NL and Martin, MC and Mahfoud, F and Krawczyk, M and Becker, SL and Müller, R and Bals, R and Keller, A},
title = {Decoding the diagnostic and therapeutic potential of microbiota using pan-body pan-disease microbiomics.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {8261},
pmid = {39327438},
issn = {2041-1723},
mesh = {Humans ; *Microbiota/genetics ; *Metagenome/genetics ; *Metagenomics/methods ; Bacteria/genetics/isolation & purification/classification ; Feces/microbiology ; Male ; Female ; Multigene Family ; Saliva/microbiology ; Adult ; },
abstract = {The human microbiome emerges as a promising reservoir for diagnostic markers and therapeutics. Since host-associated microbiomes at various body sites differ and diseases do not occur in isolation, a comprehensive analysis strategy highlighting the full potential of microbiomes should include diverse specimen types and various diseases. To ensure robust data quality and comparability across specimen types and diseases, we employ standardized protocols to generate sequencing data from 1931 prospectively collected specimens, including from saliva, plaque, skin, throat, eye, and stool, with an average sequencing depth of 5.3 gigabases. Collected from 515 patients, these samples yield an average of 3.7 metagenomes per patient. Our results suggest significant microbial variations across diseases and specimen types, including unexpected anatomical sites. We identify 583 unexplored species-level genome bins (SGBs) of which 189 are significantly disease-associated. Of note, the existence of microbial resistance genes in one specimen was indicative of the same resistance genes in other specimens of the same patient. Annotated and previously undescribed SGBs collectively harbor 28,315 potential biosynthetic gene clusters (BGCs), with 1050 significant correlations to diseases. Our combinatorial approach identifies distinct SGBs and BGCs, emphasizing the value of pan-body pan-disease microbiomics as a source for diagnostic and therapeutic strategies.},
}

Humans
*Microbiota/genetics
*Metagenome/genetics
*Metagenomics/methods
Bacteria/genetics/isolation & purification/classification
Feces/microbiology
Male
Female
Multigene Family
Saliva/microbiology
Adult

@article {pmid39327011,
year = {2024},
author = {Ruff, SE and Schwab, L and Vidal, E and Hemingway, J and Kraft, B and Murali, R},
title = {Widespread occurrence of dissolved oxygen anomalies, aerobic microbes, and oxygen-producing metabolic pathways in apparently anoxic environments.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiae132},
pmid = {39327011},
issn = {1574-6941},
abstract = {Nearly all molecular oxygen (O2) on Earth is produced via oxygenic photosynthesis by plants or photosynthetically active microorganisms. Light-independent O2 production, which occurs both abiotically, e.g., through water radiolysis, or biotically, e.g., through the dismutation of nitric oxide or chlorite, has been thought to be negligible to the Earth system. However, recent work indicates that O2 is produced and consumed in dark and apparently anoxic environments at a much larger scale than assumed. Studies have shown that isotopically light O2 can accumulate in old groundwaters; that strictly aerobic microorganisms are present in many apparently anoxic habitats; and that microbes and metabolisms that can produce O2 without light are widespread and abundant in diverse ecosystems. Analysis of published metagenomic data reveals that the enzyme putatively capable of nitric oxide dismutation (NOD) forms four major phylogenetic clusters and occurs in at least 16 bacterial phyla most notably the Bacteroidota. Similarly, a re-analysis of published isotopic signatures of dissolved O2 in groundwater suggests in-situ production in up to half of the studied ecosystems. Geochemical and microbiological data supports the conclusion that "dark oxygen" production is an important and widespread yet overlooked process in apparently anoxic environments with far-reaching implications for subsurface biogeochemistry and ecology.},
}

@article {pmid39238368,
year = {2024},
author = {Hansen, AK and Argondona, JA and Miao, S and Percy, DM and Degnan, PH},
title = {Rapid Loss of Nutritional Symbionts in an Endemic Hawaiian Herbivore Radiation Is Associated with Plant Galling Habit.},
journal = {Molecular biology and evolution},
volume = {41},
number = {9},
pages = {},
doi = {10.1093/molbev/msae190},
pmid = {39238368},
issn = {1537-1719},
mesh = {Animals ; *Symbiosis ; *Herbivory ; *Hemiptera/microbiology ; RNA, Ribosomal, 16S/genetics ; Hawaii ; Phylogeny ; Biological Evolution ; Microbiota ; },
abstract = {Insect herbivores frequently cospeciate with symbionts that enable them to survive on nutritionally unbalanced diets. While ancient symbiont gain and loss events have been pivotal for insect diversification and feeding niche specialization, evidence of recent events is scarce. We examine the recent loss of nutritional symbionts (in as little as 1 MY) in sap-feeding Pariaconus, an endemic Hawaiian insect genus that has undergone adaptive radiation, evolving various galling and free-living ecologies on a single host-plant species, Metrosideros polymorpha within the last ∼5 MY. Using 16S rRNA sequencing, we investigated the bacterial microbiomes of 19 Pariaconus species and identified distinct symbiont profiles associated with specific host-plant ecologies. Phylogenetic analyses and metagenomic reconstructions revealed significant differences in microbial diversity and functions among psyllids with different host-plant ecologies. Within a few millions of years, Pariaconus species convergently evolved the closed-gall habit twice. This shift to enclosed galls coincided with the loss of the Morganella-like symbiont that provides the essential amino acid arginine to free-living and open-gall sister species. After the Pariaconus lineage left Kauai and colonized younger islands, both open- and closed-gall species lost the Dickeya-like symbiont. This symbiont is crucial for synthesizing essential amino acids (phenylalanine, tyrosine, and lysine) as well as B vitamins in free-living species. The recurrent loss of these symbionts in galling species reinforces evidence that galls are nutrient sinks and, combined with the rapidity of the evolutionary timeline, highlights the dynamic role of insect-symbiont relationships during the diversification of feeding ecologies. We propose new Candidatus names for the novel Morganella-like and Dickeya-like symbionts.},
}

Animals
*Symbiosis
*Herbivory
*Hemiptera/microbiology
RNA, Ribosomal, 16S/genetics
Hawaii
Phylogeny
Biological Evolution
Microbiota

@article {pmid38954516,
year = {2024},
author = {Banerjee, G and Papri, SR and Banerjee, P},
title = {Protocol for the construction and functional profiling of metagenome-assembled genomes for microbiome analyses.},
journal = {STAR protocols},
volume = {5},
number = {3},
pages = {103167},
pmid = {38954516},
issn = {2666-1667},
mesh = {*Metagenome/genetics ; *Microbiota/genetics ; Humans ; *Metagenomics/methods ; Computational Biology/methods ; Sequence Analysis, DNA/methods ; },
abstract = {Constructing metagenome-assembled genomes (MAGs) from complex metagenomic samples involves a series of bioinformatics operations, each requiring deep bioinformatics knowledge. Here, we present a protocol for constructing MAGs and conducting functional profiling to address biological questions. We describe steps for system configuration, data downloads, read processing, removal of human DNA contamination, metagenomic assembly, and statistical quality assessment of the final assembly. Additionally, we detail procedures for the construction and refinement of MAGs, as well as the functional profiling of MAGs.},
}

*Metagenome/genetics
*Microbiota/genetics
Humans
*Metagenomics/methods
Computational Biology/methods
Sequence Analysis, DNA/methods

@article {pmid37591518,
year = {2023},
author = {Liu, X and Wu, J and Tang, J and Xu, Z and Zhou, B and Liu, Y and Hu, F and Zhang, G and Cheng, R and Xia, X and Chen, Y and Wu, H and Wang, D and Yue, J and Dong, B and Fu, J and Yu, H and Dong, B},
title = {Prevotella copri alleviates sarcopenia via attenuating muscle mass loss and function decline.},
journal = {Journal of cachexia, sarcopenia and muscle},
volume = {14},
number = {5},
pages = {2275-2288},
pmid = {37591518},
issn = {2190-6009},
support = {32100927//National Natural Science Foundation of China/ ; 82101653//National Natural Science Foundation of China/ ; 2021YFS0158//Project of the Sichuan Province Science and Technology/ ; Z2018B09//National Clinical Research Center for Geriatric, West China Hospital, Sichuan University/ ; 2020HXBH011//West China Hospital Postdoctoral Fund/ ; HXYS19005//1.3.5 Project for Disciplines of Excellence, West China Hospital, Sichuan University, Project of Max Cynader Academy of Brain Workstation, WCHSCU/ ; 2019YF0900083SN//Chengdu Science and Technology Bureau Major Science and Technology Application Demonstration Project/ ; CSC 202108510037//China Scholarship Council/ ; CVON2018-27//Dutch Heart Foundation IN-CONTROL/ ; 101001678//ERC Consolidator Grant/ ; VI.C.202.022//NWO-VICI Grant/ ; 024.003.001//The Netherlands Organ-on-Chip Initiative, an NWO Gravitation Project/ ; },
mesh = {*Sarcopenia/metabolism ; Humans ; Male ; Female ; Aged ; Animals ; Mice ; *Gastrointestinal Microbiome ; *Prevotella ; Middle Aged ; Muscle, Skeletal/metabolism ; Feces/microbiology ; China ; },
abstract = {BACKGROUND: The gut microbiome and fecal metabolites have been found to influence sarcopenia, but whether there are potential bacteria that can alleviate sarcopenia has been under-investigated, and the molecular mechanism remains unclear.

METHODS: To investigate the relationships between the gut microbiome, fecal metabolites and sarcopenia, subjects were selected from observational multi-ethnic study conducted in Western China. Sarcopenia was diagnosed according to the criteria of the Asian Working Group for Sarcopenia 2014. The gut microbiome was profiled by shotgun metagenomic sequencing. Untargeted metabolomic analysis was performed to analyse the differences in fecal metabolites. We investigated bacterium with the greatest relative abundance difference between healthy individuals and sarcopenia patients, and the differences in metabolites associated with the bacteria, to verify its effects on muscle mass and function in a mouse model.

RESULTS: The study included 283 participants (68.90% females, mean age: 66.66 years old) with and without sarcopenia (141 and 142 participants, respectively) and from the Han (98 participants), Zang (88 participants) and Qiang (97 participants) ethnic groups. This showed an overall reduction (15.03% vs. 20.77%, P = 0.01) of Prevotella copri between the sarcopenia and non-sarcopenia subjects across the three ethnic groups. Functional characterization of the differential bacteria showed enrichment (odds ratio = 15.97, P = 0.0068) in branched chain amino acid (BCAA) metabolism in non-sarcopenia group. A total of 13 BCAA and their derivatives have relatively low levels in sarcopenia. In the in vivo experiment, we found that the blood BCAA level was higher in the mice gavaged with live P. copri (LPC) (P < 0.001). The LPC mice had significantly longer wire and grid hanging time (P < 0.02), longer time on rotor (P = 0.0001) and larger grip strength (P < 0.0001), indicating better muscle function. The weight of gastrocnemius mass and rectus femoris mass (P < 0.05) was higher in LPC mice. The micro-computed tomography showed a larger leg area (P = 0.0031), and a small animal analyser showed a higher lean mass ratio in LPC mice (P = 0.0157), indicating higher muscle mass.

CONCLUSIONS: The results indicated that there were lower levels of both P. copri and BCAA in sarcopenia individuals. In vivo experiments, gavage with LPC could attenuate muscle mass and function decline, indicating alleviating sarcopenia. This suggested that P. copri may play a therapeutic potential role in the management of sarcopenia.},
}

*Sarcopenia/metabolism
Humans
Male
Female
Aged
Animals
Mice
*Gastrointestinal Microbiome
*Prevotella
Middle Aged
Muscle, Skeletal/metabolism
Feces/microbiology
China

@article {pmid39322959,
year = {2024},
author = {Wirbel, J and Essex, M and Forslund, SK and Zeller, G},
title = {A realistic benchmark for differential abundance testing and confounder adjustment in human microbiome studies.},
journal = {Genome biology},
volume = {25},
number = {1},
pages = {247},
pmid = {39322959},
issn = {1474-760X},
mesh = {Humans ; *Microbiota ; *Benchmarking ; RNA, Ribosomal, 16S/genetics ; Computer Simulation ; },
abstract = {BACKGROUND: In microbiome disease association studies, it is a fundamental task to test which microbes differ in their abundance between groups. Yet, consensus on suitable or optimal statistical methods for differential abundance testing is lacking, and it remains unexplored how these cope with confounding. Previous differential abundance benchmarks relying on simulated datasets did not quantitatively evaluate the similarity to real data, which undermines their recommendations.

RESULTS: Our simulation framework implants calibrated signals into real taxonomic profiles, including signals mimicking confounders. Using several whole meta-genome and 16S rRNA gene amplicon datasets, we validate that our simulated data resembles real data from disease association studies much more than in previous benchmarks. With extensively parametrized simulations, we benchmark the performance of nineteen differential abundance methods and further evaluate the best ones on confounded simulations. Only classic statistical methods (linear models, the Wilcoxon test, t-test), limma, and fastANCOM properly control false discoveries at relatively high sensitivity. When additionally considering confounders, these issues are exacerbated, but we find that adjusted differential abundance testing can effectively mitigate them. In a large cardiometabolic disease dataset, we showcase that failure to account for covariates such as medication causes spurious association in real-world applications.

CONCLUSIONS: Tight error control is critical for microbiome association studies. The unsatisfactory performance of many differential abundance methods and the persistent danger of unchecked confounding suggest these contribute to a lack of reproducibility among such studies. We have open-sourced our simulation and benchmarking software to foster a much-needed consolidation of statistical methodology for microbiome research.},
}

Humans
*Microbiota
*Benchmarking
RNA, Ribosomal, 16S/genetics
Computer Simulation

@article {pmid39260494,
year = {2024},
author = {Ejaz, MR and Badr, K and Hassan, ZU and Al-Thani, R and Jaoua, S},
title = {Metagenomic approaches and opportunities in arid soil research.},
journal = {The Science of the total environment},
volume = {953},
number = {},
pages = {176173},
doi = {10.1016/j.scitotenv.2024.176173},
pmid = {39260494},
issn = {1879-1026},
mesh = {*Soil Microbiology ; *Metagenomics ; *Soil/chemistry ; Desert Climate ; Microbiota ; },
abstract = {Arid soils present unique challenges and opportunities for studying microbial diversity and bioactive potential due to the extreme environmental conditions they bear. This review article investigates soil metagenomics as an emerging tool to explore complex microbial dynamics and unexplored bioactive potential in harsh environments. Utilizing advanced metagenomic techniques, diverse microbial populations that grow under extreme conditions such as high temperatures, salinity, high pH levels, and exposure to metals and radiation can be studied. The use of extremophiles to discover novel natural products and biocatalysts emphasizes the role of functional metagenomics in identifying enzymes and secondary metabolites for industrial and pharmaceutical purposes. Metagenomic sequencing uncovers a complex network of microbial diversity, offering significant potential for discovering new bioactive compounds. Functional metagenomics, connecting taxonomic diversity to genetic capabilities, provides a pathway to identify microbes' mechanisms to synthesize valuable secondary metabolites and other bioactive substances. Contrary to the common perception of desert soil as barren land, the metagenomic analysis reveals a rich diversity of life forms adept at extreme survival. It provides valuable findings into their resilience and potential applications in biotechnology. Moreover, the challenges associated with metagenomics in arid soils, such as low microbial biomass, high DNA degradation rates, and DNA extraction inhibitors and strategies to overcome these issues, outline the latest advancements in extraction methods, high-throughput sequencing, and bioinformatics. The importance of metagenomics for investigating diverse environments opens the way for future research to develop sustainable solutions in agriculture, industry, and medicine. Extensive studies are necessary to utilize the full potential of these powerful microbial communities. This research will significantly improve our understanding of microbial ecology and biotechnology in arid environments.},
}

*Soil Microbiology
*Metagenomics
*Soil/chemistry
Desert Climate
Microbiota

@article {pmid39244052,
year = {2024},
author = {Wang, Q and Chen, J and Qi, W and Bai, Y and Mao, J and Qu, J},
title = {Dam construction alters the traits of health-related microbes along the Yangtze River.},
journal = {The Science of the total environment},
volume = {953},
number = {},
pages = {176077},
doi = {10.1016/j.scitotenv.2024.176077},
pmid = {39244052},
issn = {1879-1026},
mesh = {*Rivers/microbiology ; China ; Water Microbiology ; Drug Resistance, Microbial/genetics ; Microbiota ; Environmental Monitoring ; Ecosystem ; Virulence Factors/genetics ; },
abstract = {Dams, constructed globally for energy production and water conservation, fragment rivers, and modify flow regimes, thereby altering the composition of biological communities and ecosystem functions. Despite the extensive use of dams, few studies have explored their potential health impacts, particularly concerning changes in health-related genes, such as antibiotic resistance genes (ARGs) and virulence factor genes (VFGs), and their hosts (i.e., ARB and potential pathogens). Understanding these health-related effects is crucial because they can impact human health through water quality and pathogen prevalence. In this study, we investigated the planktonic microbial community in the Three Gorges Reservoir (TGR) and adjacent upstream and downstream areas of the Yangtze River during both the dry and wet season. Our metagenomic analysis showed that dam construction significantly decreased the abundance of ARGs, but it had an insignificant effect on VFGs. The observed reduction in ARGs abundance could be mainly attributed to the decrease abundance of the major ARGs carrier - Limnohabitansin the TGR and downstream areas due to high grazing pressure and fitness cost. Conversely, the abundance of microbes carrying VFGs (potential pathogens) remained stable from upstream to the dam reservoir, which may explain the negligible impact on VFG abundance. Overall, our results provide a detailed understanding of the ecological health implications of dam construction in large river ecosystems.},
}

*Rivers/microbiology
China
Water Microbiology
Drug Resistance, Microbial/genetics
Microbiota
Environmental Monitoring
Ecosystem
Virulence Factors/genetics

@article {pmid39230261,
year = {2024},
author = {Tu, V and Ren, Y and Tanes, C and Mukhopadhyay, S and Daniel, SG and Li, H and Bittinger, K},
title = {A quantitative approach to measure and predict microbiome response to antibiotics.},
journal = {mSphere},
volume = {9},
number = {9},
pages = {e0048824},
doi = {10.1128/msphere.00488-24},
pmid = {39230261},
issn = {2379-5042},
support = {SAP # 4100068710//Pennsylvania Department of Health (PA DOH)/ ; //Children's Hospital of Philadelphia (CHOP)/ ; },
mesh = {Humans ; *Anti-Bacterial Agents/pharmacology ; *Microbiota/drug effects/genetics ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/drug effects/genetics/classification ; Gastrointestinal Microbiome/drug effects/genetics ; Metagenomics/methods ; Microbial Sensitivity Tests/methods ; Skin/microbiology ; Mouth/microbiology ; Software ; },
abstract = {UNLABELLED: Although antibiotics induce sizable perturbations in the human microbiome, we lack a systematic and quantitative method to measure and predict the microbiome's response to specific antibiotics. Here, we introduce such a method, which takes the form of a microbiome response index (MiRIx) for each antibiotic. Antibiotic-specific MiRIx values quantify the overall susceptibility of the microbiota to an antibiotic, based on databases of bacterial phenotypes and published data on intrinsic antibiotic susceptibility. We applied our approach to five published microbiome studies that carried out antibiotic interventions with vancomycin, metronidazole, ciprofloxacin, amoxicillin, and doxycycline. We show how MiRIx can be used in conjunction with existing microbiome analytical approaches to gain a deeper understanding of the microbiome response to antibiotics. Finally, we generate antibiotic response predictions for the oral, skin, and gut microbiome in healthy humans. Our approach is implemented as open-source software and is readily applied to microbiome data sets generated by 16S rRNA marker gene sequencing or shotgun metagenomics.

IMPORTANCE: Antibiotics are potent influencers of the human microbiome and can be a source for enduring dysbiosis and antibiotic resistance in healthcare. Existing microbiome data analysis methods can quantify perturbations of bacterial communities but cannot evaluate whether the differences are aligned with the expected activity of a specific antibiotic. Here, we present a novel method to quantify and predict antibiotic-specific microbiome changes, implemented in a ready-to-use software package. This has the potential to be a critical tool to broaden our understanding of the relationship between the microbiome and antibiotics.},
}

Humans
*Anti-Bacterial Agents/pharmacology
*Microbiota/drug effects/genetics
*RNA, Ribosomal, 16S/genetics
*Bacteria/drug effects/genetics/classification
Gastrointestinal Microbiome/drug effects/genetics
Metagenomics/methods
Microbial Sensitivity Tests/methods
Skin/microbiology
Mouth/microbiology
Software

@article {pmid39189780,
year = {2024},
author = {Liu, L and He, X and Wang, J and Li, M and Wei, X and Yang, J and Cheng, G and Du, W and Liu, Z and Xiao, X},
title = {Exploring the associations between gut microbiota composition and SARS-CoV-2 inactivated vaccine response in mice with type 2 diabetes mellitus.},
journal = {mSphere},
volume = {9},
number = {9},
pages = {e0038024},
doi = {10.1128/msphere.00380-24},
pmid = {39189780},
issn = {2379-5042},
support = {82002149//MOST | National Natural Science Foundation of China (NSFC)/ ; 2022CFB451//| Natural Science Foundation of Hubei Province ()/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; Mice ; *Diabetes Mellitus, Type 2/immunology ; *Mice, Inbred C57BL ; *Vaccines, Inactivated/immunology ; *COVID-19/prevention & control/immunology ; *SARS-CoV-2/immunology ; *Feces/microbiology ; *COVID-19 Vaccines/immunology ; Immunoglobulin G/blood ; RNA, Ribosomal, 16S/genetics ; Lung/microbiology/immunology ; Female ; Male ; Probiotics/administration & dosage ; Antibodies, Viral/blood ; Vaccine Efficacy ; },
abstract = {UNLABELLED: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccination is crucial for protecting vulnerable individuals, yet individuals with type 2 diabetes mellitus (T2DM) often exhibit impaired vaccine responses. Emerging evidence suggests that the composition of the host microbiota, crucial in immune regulation and development, influences vaccine efficacy. This study aimed to characterize the relationships between the SARS-CoV-2 inactivated vaccine and the host microbiota (specifically, gut and lung microbiota) of C57BL/6 mice with T2DM. Employing 16S rRNA metagenomic sequencing and ultra-high-performance liquid chromatography-mass spectrometry, we observed lower alpha diversity and distinct beta diversity in fecal microbiota before vaccination and in gut microbiota 28 days post-vaccination between T2DM mice and healthy mice. Compared with healthy mice, T2DM mice showed a higher Firmicutes/Bacteroidetes ratio 28 days post-vaccination. Significant alterations in gut microbiota composition were detected following vaccination, while lung microbiota remained unchanged. T2DM was associated with a diminished initial IgG antibody response against the spike protein, which subsequently normalized after 28 days. Notably, the initial IgG response positively correlated with fecal microbiota alpha diversity pre-vaccination. Furthermore, after 28 days, increased relative abundance of gut probiotics (Bifidobacterium and Lactobacillus) and higher levels of the gut bacterial tryptophan metabolite, indole acrylic acid, were positively associated with IgG levels. These findings suggest a potential link between vaccine efficacy and gut microbiota composition. Nonetheless, further research is warranted to elucidate the precise mechanisms underlying the impact of the gut microbiome on vaccine response. Overall, this study enhances our understanding of the intricate relationships among host microbiota, SARS-CoV-2 vaccination, and T2DM, with potential implications for improving vaccine efficacy.

IMPORTANCE: Over 7 million deaths attributed to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by 6 May 2024 underscore the urgent need for effective vaccination strategies. However, individuals with type 2 diabetes mellitus (T2DM) have been identified as particularly vulnerable and display compromised immune responses to vaccines. Concurrently, increasing evidence suggests that the composition and diversity of gut microbiota, crucial regulators of immune function, may influence the efficacy of vaccines. Against this backdrop, our study explores the complex interplay among SARS-CoV-2 inactivated vaccination, T2DM, and host microbiota. We discover that T2DM compromises the initial immune response to the SARS-CoV-2 inactivated vaccine, and this response is positively correlated with specific features of the gut microbiota, such as alpha diversity. We also demonstrate that the vaccination itself induces alterations in the composition and structure of the gut microbiota. These findings illuminate potential links between the gut microbiota and vaccine efficacy in individuals with T2DM, offering valuable insights that could enhance vaccine responses in this high-risk population.},
}

Animals
*Gastrointestinal Microbiome
Mice
*Diabetes Mellitus, Type 2/immunology
*Mice, Inbred C57BL
*Vaccines, Inactivated/immunology
*COVID-19/prevention & control/immunology
*SARS-CoV-2/immunology
*Feces/microbiology
*COVID-19 Vaccines/immunology
Immunoglobulin G/blood
RNA, Ribosomal, 16S/genetics
Lung/microbiology/immunology
Female
Male
Probiotics/administration & dosage
Antibodies, Viral/blood
Vaccine Efficacy

@article {pmid39178987,
year = {2024},
author = {Shukla, V and Singh, S and Verma, S and Verma, S and Rizvi, AA and Abbas, M},
title = {Targeting the microbiome to improve human health with the approach of personalized medicine: Latest aspects and current updates.},
journal = {Clinical nutrition ESPEN},
volume = {63},
number = {},
pages = {813-820},
doi = {10.1016/j.clnesp.2024.08.005},
pmid = {39178987},
issn = {2405-4577},
mesh = {Humans ; *Precision Medicine ; *Fecal Microbiota Transplantation ; *Gastrointestinal Microbiome ; *Probiotics/therapeutic use ; *Prebiotics ; *Dysbiosis/therapy ; Microbiota ; Synbiotics ; },
abstract = {The intricate ecosystem of microorganisms residing within and on the human body, collectively known as the microbiome, significantly influences human health. Imbalances in this microbiome, referred to as dysbiosis, have been associated with various diseases, prompting the exploration of novel therapeutic approaches. Personalized medicine, Tailors treatments to individual patient characteristics, offers a promising avenue for addressing microbiome-related health issues. This review highlights recent developments in utilizing personalized medicine to target the microbiome, aiming to enhance health outcomes. Noteworthy strategies include fecal microbiota transplantation (FMT), where healthy donor microbes are transferred to patients, showing promise in treating conditions such as recurrent Clostridium difficile infection. Additionally, probiotics, which are live microorganisms similar to beneficial gut inhabitants, and prebiotics, non-digestible compounds promoting microbial growth, are emerging as tools to restore microbiome balance. The integration of these approaches, known as synbiotics, enhances microbial colonization and therapeutic effects. Advances in metagenomics and sequencing technologies provide the means to understand individual microbiome profiles, enabling tailored interventions. This paper aims to present the latest insights in leveraging personalized medicine to address microbiome-related health concerns, envisioning a future where microbiome-based therapies reshape disease management and promote human health.},
}

Humans
*Precision Medicine
*Fecal Microbiota Transplantation
*Gastrointestinal Microbiome
*Probiotics/therapeutic use
*Prebiotics
*Dysbiosis/therapy
Microbiota
Synbiotics

@article {pmid39151634,
year = {2024},
author = {Xu, WJ and Meng, L and Zhao, YK and Wu, J and Liu, HM and Wang, JQ and Zheng, N},
title = {Characteristics of psychrophilic bacterial communities and associated metabolism pathways in different environments by a metagenomic analysis.},
journal = {The Science of the total environment},
volume = {953},
number = {},
pages = {175496},
doi = {10.1016/j.scitotenv.2024.175496},
pmid = {39151634},
issn = {1879-1026},
mesh = {China ; *Bacteria/classification/metabolism/genetics ; *Metagenomics ; *Milk/microbiology ; Animals ; Microbiota ; },
abstract = {Psychrophilic bacteria, the dominant spoilage organisms in raw milk, secrete heat-stable extracellular proteases and lipases that lead to the decomposition of milk and dairy products. In this study, we investigated psychrophilic bacteria in 165 raw milk samples collected across four seasons and six regions in China using shotgun metagenomic sequencing and traditional culture methods. The isolated psychrophilic bacteria were classified into 40 genera and 185 species. Pseudomonas was the most prevalent, accounting for 51.13 % of the genera, while Lactococcus and Chryseobacterium were also notably abundant (> 6.0 %). Metagenomic sequencing revealed that Pseudomonas (47.9 %), Stenotrophomonas (9.75 %), Sphingomonas (6.73 %), Latilactobacillus (6.38 %) and Lactococcus (5.16 %) were the dominant genera in the raw milk samples. The diversity of psychrophilic bacteria in raw milk was strongly influenced by seasonal variations, with the sampling region being a less significant factor. KEGG annotation indicated that carbohydrate and amino acid metabolism were the primary metabolic pathways in these bacteria. Metagenomic sequencing not only accurately identifies species but also provides functional insights into psychrophilic bacteria in raw milk, aiding in understanding their activities, promoting their control on farms, and ultimately improving raw milk quality.},
}

China
*Bacteria/classification/metabolism/genetics
*Metagenomics
*Milk/microbiology
Animals
Microbiota

@article {pmid39118488,
year = {2024},
author = {Sanville, J and O'Toole, GA and Madan, J and Coker, M},
title = {Premodulator microbiome alterations associated with postmodulator growth outcomes in pediatric cystic fibrosis: Can we predict outcomes?.},
journal = {Journal of pediatric gastroenterology and nutrition},
volume = {79},
number = {3},
pages = {695-704},
doi = {10.1002/jpn3.12350},
pmid = {39118488},
issn = {1536-4801},
support = {SANVIL19GEO//Cystic Fibrosis Foundation (CFF)/ ; MADAN22A0//Cystic Fibrosis Foundation (CFF)/ ; OTOOLE22G0//Cystic Fibrosis Foundation (CFF)/ ; P30-DK117469//National Institutes of Health (NIH)/ ; ES033988-01A1//National Institutes of Health (NIH)/ ; },
mesh = {Humans ; *Cystic Fibrosis/microbiology/complications ; Female ; Male ; *Gastrointestinal Microbiome ; Child, Preschool ; *Feces/microbiology ; Infant ; Longitudinal Studies ; Infant, Newborn ; Overweight/microbiology ; Body Mass Index ; },
abstract = {OBJECTIVES: The gut microbiota plays an important role in childhood growth. Our longitudinal cohort includes children with cystic fibrosis (CwCF) treated with highly effective modulator therapy. We aimed to elucidate early premodulator microbial signatures associated with postmodulator weight for CwCF later in childhood.

METHODS: Stool samples were collected from CwCF at 13 days to 60 months. Metagenomic sequencing determined differentially abundant taxa. Children with body mass index or weight for length Z-scores within 1 standard deviation of the mean (SD) were considered normal weight, those >1 SD were classified as risk of overweight while children <1 SD were considered undernourished, although no CwCF met this latter criterion here. Multivariate regression models were applied to identify significant associations between metadata and microbial taxonomic relative abundances.

RESULTS: One hundred and eighty-nine stool samples were analyzed from 39 CwCF. We identified statistically significant differences in early microbiome patterns among those at risk of being overweight compared to those who were normal weight when adjusted for age, sex, CF mutation, and early feeding method. Early microbiome was a stronger driver of growth status than current modulator use. Among those at risk of overweight, several taxa that were consistently in lower abundance included Eggerthella lentha, Ruminococcus, Bacteroides, with increase in abundance of Bacteroides stercoris.

CONCLUSIONS: The early microbiome strongly predicts growth in the setting of modulator use for CwCF and we identify microbiome signatures associated with risk of being overweight. We highlight the possibility for interventions or early alternations to nutritional guidance for prevention of comorbid complications.},
}

Humans
*Cystic Fibrosis/microbiology/complications
Female
Male
*Gastrointestinal Microbiome
Child, Preschool
*Feces/microbiology
Infant
Longitudinal Studies
Infant, Newborn
Overweight/microbiology
Body Mass Index

@article {pmid39313592,
year = {2024},
author = {Hemapriya, M and Nataraja, KN and Suryanarayanan, TS and Uma Shaanker, R},
title = {Comparative Metagenomic Analysis of Seed Endobiome of Domesticated and Wild Finger Millet Species (Eleusine spp.): Unveiling Microbial Diversity and Composition.},
journal = {Current microbiology},
volume = {81},
number = {11},
pages = {373},
pmid = {39313592},
issn = {1432-0991},
mesh = {*Seeds/microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Metagenomics ; *Eleusine/microbiology/genetics ; *Domestication ; *Microbiota ; Biodiversity ; Fungi/classification/genetics/isolation & purification ; },
abstract = {Domestication, which involves selective breeding, modern agricultural practices, and specific growing conditions, can influence the microbial and endophytic communities in crop plants. In this study, we examined the microbial diversity and community composition in the seeds of wild and domesticated finger millet species. We employed a metagenomic approach to investigate the seed microbial diversity and community composition of wild (Eleusine africana) and domesticated finger millet species (Eleusine coracana (L.) Gaertn) grown in the same habitat. While our findings indicated no significant change in seed endobiome diversity due to domestication, there were differences in microbial community composition between wild and domesticated species. Seeds of domesticated species had higher relative abundance of certain bacterial genera including Helicobacter, Akkermansia, Streptococcus, Bacteroides, and Pseudomonas, whereas seeds of wild species had higher relative abundance of unclassified Streptophyta. The seed-associated microbiota also varied among domesticated finger millet accessions. Co-occurrence network analysis revealed a strong relationship between bacteria and fungi in domesticated compared to wild species. We discuss the results obtained in the larger context of the importance of seed endobiome and how domestication processes in crop plants may have impacted the seed endobiome diversity, composition, and function compared to their wild counterparts.},
}

*Seeds/microbiology
*Bacteria/classification/genetics/isolation & purification
*Metagenomics
*Eleusine/microbiology/genetics
*Domestication
*Microbiota
Biodiversity
Fungi/classification/genetics/isolation & purification

@article {pmid39313228,
year = {2024},
author = {Kirtipal, N and Seo, Y and Son, J and Lee, S},
title = {Systems Biology of Human Microbiome for the Prediction of Personal Glycaemic Response.},
journal = {Diabetes & metabolism journal},
volume = {48},
number = {5},
pages = {821-836},
doi = {10.4093/dmj.2024.0382},
pmid = {39313228},
issn = {2233-6087},
support = {//Ministry of Science ICT/ ; 2021R1C1C1006336//National Research Foundation of Korea/ ; 2021M3A9G8022959//National Research Foundation of Korea/ ; RS-2024-00419699//National Research Foundation of Korea/ ; //Korea Health Industry Development Institute/ ; HR22C141105//Ministry of Health and Welfare/ ; 2024-ER2108-00//Korea National Institute of Health/ ; 2024-ER0608-00//Korea National Institute of Health/ ; //GIST Research Institute/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Precision Medicine/methods ; *Systems Biology/methods ; Machine Learning ; Dysbiosis ; Blood Glucose/analysis ; Diabetes Mellitus/microbiology ; Diabetes Mellitus, Type 2/microbiology ; Hypoglycemic Agents/therapeutic use ; },
abstract = {The human gut microbiota is increasingly recognized as a pivotal factor in diabetes management, playing a significant role in the body's response to treatment. However, it is important to understand that long-term usage of medicines like metformin and other diabetic treatments can result in problems, gastrointestinal discomfort, and dysbiosis of the gut flora. Advanced sequencing technologies have improved our understanding of the gut microbiome's role in diabetes, uncovering complex interactions between microbial composition and metabolic health. We explore how the gut microbiota affects glucose metabolism and insulin sensitivity by examining a variety of -omics data, including genomics, transcriptomics, epigenomics, proteomics, metabolomics, and metagenomics. Machine learning algorithms and genome-scale modeling are now being applied to find microbiological biomarkers associated with diabetes risk, predicted disease progression, and guide customized therapy. This study holds promise for specialized diabetic therapy. Despite significant advances, some concerns remain unanswered, including understanding the complex relationship between diabetes etiology and gut microbiota, as well as developing user-friendly technological innovations. This mini-review explores the relationship between multiomics, precision medicine, and machine learning to improve our understanding of the gut microbiome's function in diabetes. In the era of precision medicine, the ultimate goal is to improve patient outcomes through personalized treatments.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Precision Medicine/methods
*Systems Biology/methods
Machine Learning
Dysbiosis
Blood Glucose/analysis
Diabetes Mellitus/microbiology
Diabetes Mellitus, Type 2/microbiology
Hypoglycemic Agents/therapeutic use

@article {pmid39180723,
year = {2024},
author = {Jiang, L and Hao, Y and Han, D and Dong, W and Yang, A and Sun, Z and Ge, Y and Duan, S and Zhang, X and Dai, Z},
title = {Gut microbiota dysbiosis deteriorates immunoregulatory effects of tryptophan via colonic indole and LBP/HTR2B-mediated macrophage function.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
doi = {10.1093/ismejo/wrae166},
pmid = {39180723},
issn = {1751-7370},
support = {2022YFA1304204//National Key Research and Development Program of China/ ; 32072689//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Dysbiosis/microbiology ; Mice ; *Colitis/chemically induced/immunology/microbiology ; *Tryptophan/metabolism ; *Indoles/pharmacology ; *Macrophages/immunology/drug effects ; *Mice, Inbred C57BL ; *Colon/microbiology/immunology ; *Disease Models, Animal ; *Carrier Proteins/genetics/metabolism ; *Dextran Sulfate ; Acute-Phase Proteins/metabolism ; Male ; Fecal Microbiota Transplantation ; Anti-Bacterial Agents/pharmacology ; Signal Transduction ; Membrane Glycoproteins ; },
abstract = {Tryptophan (Trp) has been shown to regulate immune function by modulating gut serotonin (5-HT) metabolism and signaling. However, the mechanisms underlying the microbial modulation of gut 5-HT signaling in gut inflammation with gut microbiota dysbiosis require further investigation. Here, we investigated the effects of Trp supplementation on the composition and metabolism of the gut microbiome and 5-HT signaling-related gut immune function using a dextran sodium sulfate (DSS)-induced colitis mouse model coupled with antibiotic exposure. The results showed that antibiotic treatment before but not during DSS treatment decreased the immunoregulatory effects of Trp and aggravated gut inflammation and body weight loss in mice. Metagenomic analysis revealed that the fecal microbiota transplantation of Trp-enriched gut microbiota to recipient mice subject to antibiotic pre-exposure and DSS treatment alleviated inflammation by increasing the relative abundances of Lactobacillus and Parabacteroides and the microbial production of indole coupled with the activation of the 5-HT receptor 2B (HTR2B) in the colon. Transcriptomic analysis showed that HTR2B agonist administration strengthened the beneficial effects of Trp in DSS-induced colitis mice with antibiotic exposure by reducing gut lipopolysaccharide-binding protein (LBP) production, IκB-α/nuclear factor-κB signaling, and M1 macrophage polarization. Indole treatment reduced LBP production and M1 macrophage polarization both in mice with DSS-induced colitis and in lipopolysaccharide-treated mouse macrophages; however, the HTR2B antagonist reversed the effects of indole. Our findings provide the basis for developing new dietary and therapeutic interventions to improve gut microbiota dysbiosis-associated inflammatory gut disorders and diseases.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Dysbiosis/microbiology
Mice
*Colitis/chemically induced/immunology/microbiology
*Tryptophan/metabolism
*Indoles/pharmacology
*Macrophages/immunology/drug effects
*Mice, Inbred C57BL
*Colon/microbiology/immunology
*Disease Models, Animal
*Carrier Proteins/genetics/metabolism
*Dextran Sulfate
Acute-Phase Proteins/metabolism
Male
Fecal Microbiota Transplantation
Anti-Bacterial Agents/pharmacology
Signal Transduction
Membrane Glycoproteins

@article {pmid38862509,
year = {2024},
author = {Overbey, EG and Ryon, K and Kim, J and Tierney, BT and Klotz, R and Ortiz, V and Mullane, S and Schmidt, JC and MacKay, M and Damle, N and Najjar, D and Matei, I and Patras, L and Garcia Medina, JS and Kleinman, AS and Wain Hirschberg, J and Proszynski, J and Narayanan, SA and Schmidt, CM and Afshin, EE and Innes, L and Saldarriaga, MM and Schmidt, MA and Granstein, RD and Shirah, B and Yu, M and Lyden, D and Mateus, J and Mason, CE},
title = {Collection of biospecimens from the inspiration4 mission establishes the standards for the space omics and medical atlas (SOMA).},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {4964},
pmid = {38862509},
issn = {2041-1723},
support = {R01 ES032638/ES/NIEHS NIH HHS/United States ; R01 MH117406/MH/NIMH NIH HHS/United States ; },
mesh = {*Specimen Handling/standards ; Humans ; *Space Flight ; *Biological Specimen Banks/standards ; Exobiology ; *Preservation, Biological/standards ; Metagenomics/standards ; },
abstract = {The SpaceX Inspiration4 mission provided a unique opportunity to study the impact of spaceflight on the human body. Biospecimen samples were collected from four crew members longitudinally before (Launch: L-92, L-44, L-3 days), during (Flight Day: FD1, FD2, FD3), and after (Return: R + 1, R + 45, R + 82, R + 194 days) spaceflight, spanning a total of 289 days across 2021-2022. The collection process included venous whole blood, capillary dried blood spot cards, saliva, urine, stool, body swabs, capsule swabs, SpaceX Dragon capsule HEPA filter, and skin biopsies. Venous whole blood was further processed to obtain aliquots of serum, plasma, extracellular vesicles and particles, and peripheral blood mononuclear cells. In total, 2,911 sample aliquots were shipped to our central lab at Weill Cornell Medicine for downstream assays and biobanking. This paper provides an overview of the extensive biospecimen collection and highlights their processing procedures and long-term biobanking techniques, facilitating future molecular tests and evaluations.As such, this study details a robust framework for obtaining and preserving high-quality human, microbial, and environmental samples for aerospace medicine in the Space Omics and Medical Atlas (SOMA) initiative, which can aid future human spaceflight and space biology experiments.},
}

*Specimen Handling/standards
Humans
*Space Flight
*Biological Specimen Banks/standards
Exobiology
*Preservation, Biological/standards
Metagenomics/standards

@article {pmid38797888,
year = {2024},
author = {Manoil, D and Parga, A and Bostanci, N and Belibasakis, GN},
title = {Microbial diagnostics in periodontal diseases.},
journal = {Periodontology 2000},
volume = {95},
number = {1},
pages = {176-193},
doi = {10.1111/prd.12571},
pmid = {38797888},
issn = {1600-0757},
support = {//University of Geneva/ ; ED6481B-2023/117//Regional Government of Galicia, Spain/ ; 2021-03528//Swedish Research Council/ ; 2022-01014//Swedish Research Council/ ; FoUI-966140//Steering Group for Odontological Research (SOF)/ ; FoUI-978687//Steering Group for Odontological Research (SOF)/ ; },
mesh = {Humans ; *Periodontal Diseases/microbiology/diagnosis ; *Dysbiosis/microbiology ; Microbiota ; Biomarkers ; },
abstract = {Microbial analytical methods have been instrumental in elucidating the complex microbial etiology of periodontal diseases, by shaping our understanding of subgingival community dynamics. Certain pathobionts can orchestrate the establishment of dysbiotic communities that can subvert the host immune system, triggering inflammation and tissue destruction. Yet, diagnosis and management of periodontal conditions still rely on clinical and radiographic examinations, overlooking the well-established microbial etiology. This review summarizes the chronological emergence of periodontal etiological models and the co-evolution with technological advances in microbial detection. We additionally review the microbial analytical approaches currently accessible to clinicians, highlighting their value in broadening the periodontal assessment. The epidemiological importance of obtaining culture-based antimicrobial susceptibility profiles of periodontal taxa for antibiotic resistance surveillance is also underscored, together with clinically relevant analytical approaches to guide antibiotherapy choices, when necessary. Furthermore, the importance of 16S-based community and shotgun metagenomic profiling is discussed in outlining dysbiotic microbial signatures. Because dysbiosis precedes periodontal damage, biomarker identification offers early diagnostic possibilities to forestall disease relapses during maintenance. Altogether, this review highlights the underutilized potential of clinical microbiology in periodontology, spotlighting the clinical areas most conductive to its diagnostic implementation for enhancing prevention, treatment predictability, and addressing global antibiotic resistance.},
}

Humans
*Periodontal Diseases/microbiology/diagnosis
*Dysbiosis/microbiology
Microbiota
Biomarkers

@article {pmid39216995,
year = {2024},
author = {Gekenidis, MT and Vollenweider, V and Joyce, A and Murphy, S and Walser, JC and Ju, F and Bürgmann, H and Hummerjohann, J and Walsh, F and Drissner, D},
title = {Unde venis? Bacterial resistance from environmental reservoirs to lettuce: tracking microbiome and resistome over a growth period.},
journal = {FEMS microbiology ecology},
volume = {100},
number = {10},
pages = {},
doi = {10.1093/femsec/fiae118},
pmid = {39216995},
issn = {1574-6941},
support = {407240_167068//National Research Program "Antimicrobial Resistance"/ ; /SNSF_/Swiss National Science Foundation/Switzerland ; },
mesh = {*Lactuca/microbiology ; *Manure/microbiology ; Animals ; *Soil Microbiology ; *Microbiota/genetics ; *Bacteria/genetics/growth & development/drug effects/classification/isolation & purification ; *RNA, Ribosomal, 16S/genetics ; Drug Resistance, Bacterial/genetics ; Swine ; Plant Leaves/microbiology ; Wastewater/microbiology ; Water Microbiology ; Anti-Bacterial Agents/pharmacology ; Metagenomics ; Agricultural Irrigation ; Soil/chemistry ; Water Quality ; },
abstract = {Fresh produce is suggested to contribute highly to shaping the gut resistome. We investigated the impact of pig manure and irrigation water quality on microbiome and resistome of field-grown lettuce over an entire growth period. Lettuce was grown under four regimes, combining soil amendment with manure (with/without) with sprinkler irrigation using river water with an upstream wastewater input, disinfected by UV (with/without). Lettuce leaves, soil, and water samples were collected weekly and analysed by bacterial cultivation, 16S rRNA gene amplicon sequencing, and shotgun metagenomics from total community DNA. Cultivation yielded only few clinically relevant antibiotic-resistant bacteria (ARB), but numbers of ARB on lettuce increased over time, while no treatment-dependent changes were observed. Microbiome analysis confirmed a temporal trend. Antibiotic resistance genes (ARGs) unique to lettuce and water included multidrug and β-lactam ARGs, whereas lettuce and soil uniquely shared mainly glycopeptide and tetracycline ARGs. Surface water carried clinically relevant ARB (e.g. ESBL-producing Escherichia coli or Serratia fonticola) without affecting the overall lettuce resistome significantly. Resistance markers including biocide and metal resistance were increased in lettuce grown with manure, especially young lettuce (increased soil contact). Overall, while all investigated environments had their share as sources of the lettuce resistome, manure was the main source especially on young plants. We therefore suggest minimizing soil-vegetable contact to minimize resistance markers on fresh produce.},
}

*Lactuca/microbiology
*Manure/microbiology
Animals
*Soil Microbiology
*Microbiota/genetics
*Bacteria/genetics/growth & development/drug effects/classification/isolation & purification
*RNA, Ribosomal, 16S/genetics
Drug Resistance, Bacterial/genetics
Swine
Plant Leaves/microbiology
Wastewater/microbiology
Water Microbiology
Anti-Bacterial Agents/pharmacology
Metagenomics
Agricultural Irrigation
Soil/chemistry
Water Quality

@article {pmid39305563,
year = {2024},
author = {Albuquerque, L and Viver, T and Barroso, C and Claudino, R and Galvan, M and Simões, G and Lobo-da-Cunha, A and Egas, C},
title = {Halorubrum miltondacostae sp. nov., a potential polyhydroxyalkanoate producer isolated from an inland solar saltern in Rio Maior, Portugal.},
journal = {Systematic and applied microbiology},
volume = {47},
number = {6},
pages = {126553},
doi = {10.1016/j.syapm.2024.126553},
pmid = {39305563},
issn = {1618-0984},
abstract = {One hundred and sixty-three extreme halophiles were recovered from a single sample collected from an inland solar saltern in Rio Maior. Based on random amplified polymorphic DNA (RAPD) profiles and partial 16S rRNA gene sequencing 125 isolates were identified as members of the Archaea domain within the genus Halorubrum. Two strains, RMP-11[T] and RMP-47, showed 99.1 % sequence similarity with the species Halorubrum californiense based on phylogenetic analysis of the 16S rRNA gene sequence. However, phylogenetic analysis based on five housekeeping genes, atpB, EF-2, glnA, ppsA and rpoB', showed Halorubrum coriense as the closest related species with 96.7 % similarity. The average nucleotide identity (ANI) of strains RMP-11[T], RMP-47 and species Hrr. coriense were within the range of 90.0-90.5 %, supporting that strains RMP-11[T] and RMP-47 represent a novel species of the genus Halorubrum. These strains formed red-pigmented colonies that were able to grow in a temperature range of 25-50 °C. Polyhydroxyalkanoate (PHA) granules were detected in both strains. The polar lipid profile was identical to the neutrophilic species of the genus Halorubrum. The Rio Maior sample from which both strains were isolated was metagenome sequenced. We identified five metagenome-assembled genomes representing novel Halorubrum species but distinct from the species represented by strains RMP-11[T] and RMP-47. Based on phylogenetic, phylogenomic, comparative genomics, physiological and chemotaxonomic parameters, we describe a new species of the genus Halorubrum represented by strains RMP-11[T] (=CECT 30760[T] = DSM 115521[T]) and RMP-47 (=CECT 30761 = DSM 115541) for which we propose the name Halorubrum miltondacostae sp. nov.},
}

@article {pmid39304820,
year = {2024},
author = {Silva, MH and Batista, LL and Malta, SM and Santos, ACC and Mendes-Silva, AP and Bonetti, AM and Ueira-Vieira, C and Dos Santos, AR},
title = {Unveiling the Brazilian kefir microbiome: discovery of a novel Lactobacillus kefiranofaciens (LkefirU) genome and in silico prospection of bioactive peptides with potential anti-Alzheimer properties.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {884},
pmid = {39304820},
issn = {1471-2164},
mesh = {*Kefir/microbiology ; *Alzheimer Disease ; *Lactobacillus/genetics ; *Genome, Bacterial ; *Microbiota ; Brazil ; *Peptides/chemistry/pharmacology ; Humans ; Molecular Docking Simulation ; Amyloid beta-Peptides/metabolism/genetics ; Amyloid Precursor Protein Secretases/metabolism ; Aspartic Acid Endopeptidases/genetics/metabolism ; Metagenomics/methods ; },
abstract = {BACKGROUND: Kefir is a complex microbial community that plays a critical role in the fermentation and production of bioactive peptides, and has health-improving properties. The composition of kefir can vary by geographic localization and weather, and this paper focuses on a Brazilian sample and continues previous work that has successful anti-Alzheimer properties. In this study, we employed shotgun metagenomics and peptidomics approaches to characterize Brazilian kefir further.

RESULTS: We successfully assembled the novel genome of Lactobacillus kefiranofaciens (LkefirU) and conducted a comprehensive pangenome analysis to compare it with other strains. Furthermore, we performed a peptidome analysis, revealing the presence of bioactive peptides encrypted by L. kefiranofaciens in the Brazilian kefir sample, and utilized in silico prospecting and molecular docking techniques to identify potential anti-Alzheimer peptides, targeting β-amyloid (fibril and plaque), BACE, and acetylcholinesterase. Through this analysis, we identified two peptides that show promise as compounds with anti-Alzheimer properties.

CONCLUSIONS: These findings not only provide insights into the genome of L. kefiranofaciens but also serve as a promising prototype for the development of novel anti-Alzheimer compounds derived from Brazilian kefir.},
}

*Kefir/microbiology
*Alzheimer Disease
*Lactobacillus/genetics
*Genome, Bacterial
*Microbiota
Brazil
*Peptides/chemistry/pharmacology
Humans
Molecular Docking Simulation
Amyloid beta-Peptides/metabolism/genetics
Amyloid Precursor Protein Secretases/metabolism
Aspartic Acid Endopeptidases/genetics/metabolism
Metagenomics/methods

@article {pmid39303138,
year = {2024},
author = {Boukheloua, R and Mukherjee, I and Park, H and Šimek, K and Kasalický, V and Ngochera, M and Grossart, HP and Picazo-Mozo, A and Camacho, A and Cabello-Yeves, PJ and Rodriguez-Valera, F and Callieri, C and Andrei, AS and Pernthaler, J and Posch, T and Alfreider, A and Sommaruga, R and Hahn, MW and Sonntag, B and Lopez-Garcia, P and Moreira, D and Jardillier, L and Lepère, C and Biderre-Petit, C and Bednarska, A and Ślusarczyk, M and Tóth, VR and Banciu, HL and Kormas, K and Orlic, S and Šantić, D and Muyzer, G and Herlemann, DPR and Tammert, H and Bertilsson, S and Langenheder, S and Zechmeister, T and Salmaso, N and Storelli, N and Capelli, C and Lepori, F and Lanta, V and Vieira, HH and Kostanjšek, F and Kabeláčová, K and Chiriac, MC and Haber, M and Shabarova, T and Fernandes, C and Rychtecký, P and Znachor, P and Szőke-Nagy, T and Layoun, P and Wong, HL and Kavagutti, VS and Bulzu, PA and Salcher, MM and Piwosz, K and Ghai, R},
title = {Global freshwater distribution of Telonemia protists.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrae177},
pmid = {39303138},
issn = {1751-7370},
abstract = {Telonemia are one of the oldest identified marine protists that for most part of their history have been recognized as a distinct incertae sedis lineage. Today, their evolutionary proximity to the SAR supergroup (Stramenopiles, Alveolates, and Rhizaria) is firmly established. However, their ecological distribution and importance as a natural predatory flagellate, especially in freshwater food webs, still remains unclear. To unravel the distribution and diversity of the phylum Telonemia in freshwater habitats, we examined over a thousand freshwater metagenomes from all over the world. In addition, to directly quantify absolute abundances, we analysed 407 samples from 97 lakes and reservoirs using Catalyzed Reporter Deposition-Fluorescence in situ Hybridization (CARD-FISH). We recovered Telonemia 18S rRNA gene sequences from hundreds of metagenomic samples from a wide variety of habitats, indicating a global distribution of this phylum. However, even after this extensive sampling, our phylogenetic analysis did not reveal any new major clades, suggesting current molecular surveys are near to capturing the full diversity within this group. We observed excellent concordance between CARD-FISH analyses and estimates of abundances from metagenomes. Both approaches suggest that Telonemia are largely absent from shallow lakes and prefer to inhabit the colder hypolimnion of lakes and reservoirs in the Northern Hemisphere, where they frequently bloom, reaching 10-20% of the total heterotrophic flagellate population, making them important predatory flagellates in the freshwater food web.},
}

@article {pmid39303118,
year = {2024},
author = {Doré, J and Sansonetti, PJ},
title = {[The human microbiome: 340 years of history, 140 years of interrogations, technological innovations and emergence of "microbial medicine"].},
journal = {Medecine sciences : M/S},
volume = {40},
number = {8-9},
pages = {654-660},
doi = {10.1051/medsci/2024101},
pmid = {39303118},
issn = {1958-5381},
mesh = {Humans ; *Microbiota/physiology ; History, 20th Century ; History, 21st Century ; History, 19th Century ; Symbiosis ; Inventions/history/trends ; History, 18th Century ; Gastrointestinal Microbiome/physiology ; },
abstract = {For 350 years, we have known that the human body hosts microbes, then called "animalcules". For over a century, following the demonstration of the role of some of these microbes in diseases, questions have arisen about the role of the largely predominant ones colonizing human skin and mucous surfaces, particularly the rich microbial ecosystem of the intestine, the gut microbiota. From the invention of germ-free life - axenism - which experimentally validated the human-microbe symbiosis, resulting from a long coevolution, to the development of anaerobic culture methods, then to the invention of molecular diagnosis, deep sequencing opening up metagenomic and omics approaches in general, a remarkable race has taken place between technological innovations and conceptual advances. This race, beyond the exhaustive description of the microbiota in its intra- and inter-human diversity, and the essential symbiotic functions of the microbiome, has paved the way for a new field of medicine: microbial medicine.},
}

Humans
*Microbiota/physiology
History, 20th Century
History, 21st Century
History, 19th Century
Symbiosis
Inventions/history/trends
History, 18th Century
Gastrointestinal Microbiome/physiology

@article {pmid39300577,
year = {2024},
author = {Lezcano, MÁ and Bornemann, TLV and Sánchez-García, L and Carrizo, D and Adam, PS and Esser, SP and Cabrol, NA and Probst, AJ and Parro, V},
title = {Hyperexpansion of genetic diversity and metabolic capacity of extremophilic bacteria and archaea in ancient Andean lake sediments.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {176},
pmid = {39300577},
issn = {2049-2618},
support = {FJC2018-037246-I//Spanish Ministry of Science and Innovation/State Agency of Research/ ; RYC2018-023943-I//Spanish Ministry of Science and Innovation/State Agency of Research/ ; RYC-2014-19446//Spanish Ministry of Science and Innovation/State Agency of Research/ ; RTI2018-094368-B-I0//Spanish Ministry of Science and Innovation/State Agency of Research/ ; PEJD-2017- POST/TIC-4119//Spanish Ministry of Science and Innovation/State Agency of Research (EU Youth Employment Initiative)/ ; NAI-CAN7, 13NAI7_2-0018//NASA Astrobiology Institute/ ; DFG PR1603/2-1//German Research Foundation/ ; 161L0285E//German Federal Ministry of Education and Research/ ; },
mesh = {*Lakes/microbiology ; *Archaea/genetics/metabolism/classification ; *Geologic Sediments/microbiology ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Genetic Variation ; Chile ; Phylogeny ; Microbiota ; Extremophiles/metabolism/genetics/classification ; RNA, Ribosomal, 16S/genetics ; },
abstract = {BACKGROUND: The Andean Altiplano hosts a repertoire of high-altitude lakes with harsh conditions for life. These lakes are undergoing a process of desiccation caused by the current climate, leaving terraces exposed to extreme atmospheric conditions and serving as analogs to Martian paleolake basins. Microbiomes in Altiplano lake terraces have been poorly studied, enclosing uncultured lineages and a great opportunity to understand environmental adaptation and the limits of life on Earth. Here we examine the microbial diversity and function in ancient sediments (10.3-11 kyr BP (before present)) from a terrace profile of Laguna Lejía, a sulfur- and metal/metalloid-rich saline lake in the Chilean Altiplano. We also evaluate the physical and chemical changes of the lake over time by studying the mineralogy and geochemistry of the terrace profile.

RESULTS: The mineralogy and geochemistry of the terrace profile revealed large water level fluctuations in the lake, scarcity of organic carbon, and high concentration of SO4[2-]-S, Na, Cl and Mg. Lipid biomarker analysis indicated the presence of aquatic/terrestrial plant remnants preserved in the ancient sediments, and genome-resolved metagenomics unveiled a diverse prokaryotic community with still active microorganisms based on in silico growth predictions. We reconstructed 591 bacterial and archaeal metagenome-assembled genomes (MAGs), of which 98.8% belonged to previously unreported species. The most abundant and widespread metabolisms among MAGs were the reduction and oxidation of S, N, As, and halogenated compounds, as well as aerobic CO oxidation, possibly as a key metabolic trait in the organic carbon-depleted sediments. The broad redox and CO2 fixation pathways among phylogenetically distant bacteria and archaea extended the knowledge of metabolic capacities to previously unknown taxa. For instance, we identified genomic potential for dissimilatory sulfate reduction in Bacteroidota and α- and γ-Proteobacteria, predicted an enzyme for ammonia oxidation in a novel Actinobacteriota, and predicted enzymes of the Calvin-Benson-Bassham cycle in Planctomycetota, Gemmatimonadota, and Nanoarchaeota.

CONCLUSIONS: The high number of novel bacterial and archaeal MAGs in the Laguna Lejía indicates the wide prokaryotic diversity discovered. In addition, the detection of genes in unexpected taxonomic groups has significant implications for the expansion of microorganisms involved in the biogeochemical cycles of carbon, nitrogen, and sulfur. Video Abstract.},
}

*Lakes/microbiology
*Archaea/genetics/metabolism/classification
*Geologic Sediments/microbiology
*Bacteria/classification/genetics/metabolism/isolation & purification
*Genetic Variation
Chile
Phylogeny
Microbiota
Extremophiles/metabolism/genetics/classification
RNA, Ribosomal, 16S/genetics

@article {pmid39300575,
year = {2024},
author = {Li, Q and Ruscheweyh, HJ and Østergaard, LH and Libertella, M and Simonsen, KS and Sunagawa, S and Scoma, A and Schwab, C},
title = {Trait-based study predicts glycerol/diol dehydratases as a key function of the gut microbiota of hindgut-fermenting carnivores.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {178},
pmid = {39300575},
issn = {2049-2618},
support = {9152//EMBO/ ; AUFF-F-2020-7//Aarhus Universitet Forsknings Fonden/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; *Feces/microbiology ; *Fermentation ; *Glycerol/metabolism ; *Metagenomics/methods ; Hydro-Lyases/genetics/metabolism ; Propylene Glycols/metabolism ; Vitamin B 12/metabolism ; Bacteria/classification/genetics/isolation & purification/enzymology ; Phylogeny ; Animals, Wild/microbiology ; },
abstract = {BACKGROUND: Microbial pdu and cob-cbi-hem gene clusters encode the key enzyme glycerol/diol dehydratase (PduCDE), which mediates the transformation of dietary nutrients glycerol and 1,2-propanediol (1,2-PD) to a variety of metabolites, and enzymes for cobalamin synthesis, a co-factor and shared good of microbial communities. It was the aim of this study to relate pdu as a multipurpose functional trait to environmental conditions and microbial community composition. We collected fecal samples from wild animal species living in captivity with different gut physiology and diet (n = 55, in total 104 samples), determined occurrence and diversity of pdu and cob-cbi-hem using a novel approach combining metagenomics with quantification of metabolic and genetic biomarkers, and conducted in vitro fermentations to test for trait-based activity.

RESULTS: Fecal levels of the glycerol transformation product 1,3-propanediol (1,3-PD) were higher in hindgut than foregut fermenters. Gene-based analyses indicated that pduC harboring taxa are common feature of captive wild animal fecal microbiota that occur more frequently and at higher abundance in hindgut fermenters. Phylogenetic analysis of genomes reconstructed from metagenomic sequences identified captive wild animal fecal microbiota as taxonomically rich with a total of 4150 species and > 1800 novel species but pointed at only 56 species that at least partially harbored pdu and cbi-cob-hem. While taxonomic diversity was highest in fecal samples of foregut-fermenting herbivores, higher pduC abundance and higher diversity of pdu/cbi-cob-hem related to higher potential for glycerol and 1,2-PD utilization of the less diverse microbiota of hindgut-fermenting carnivores in vitro.

CONCLUSION: Our approach combining metabolite and gene biomarker analysis with metagenomics and phenotypic characterization identified Pdu as a common function of fecal microbiota of captive wild animals shared by few taxa and stratified the potential of fecal microbiota for glycerol/1,2-PD utilization and cobalamin synthesis depending on diet and physiology of the host. This trait-based study suggests that the ability to utilize glycerol/1,2-PD is a key function of hindgut-fermenting carnivores, which does not relate to overall community diversity but links to the potential for cobalamin formation. Video Abstract.},
}

Animals
*Gastrointestinal Microbiome
*Feces/microbiology
*Fermentation
*Glycerol/metabolism
*Metagenomics/methods
Hydro-Lyases/genetics/metabolism
Propylene Glycols/metabolism
Vitamin B 12/metabolism
Bacteria/classification/genetics/isolation & purification/enzymology
Phylogeny
Animals, Wild/microbiology

@article {pmid39300163,
year = {2024},
author = {Myeong, NR and Choe, YH and Shin, SC and Kim, J and Sul, WJ and Kim, M},
title = {Genomic profiling of Antarctic geothermal microbiomes using long-read, Hi-C, and single-cell techniques.},
journal = {Scientific data},
volume = {11},
number = {1},
pages = {1023},
pmid = {39300163},
issn = {2052-4463},
support = {PE24460//Korea Polar Research Institute (KOPRI)/ ; PE24070//Korea Polar Research Institute (KOPRI)/ ; PE24460//Korea Polar Research Institute (KOPRI)/ ; PE24460//Korea Polar Research Institute (KOPRI)/ ; Graduate Research Scholarship in 2017//Chung-Ang University (CAU)/ ; },
mesh = {Antarctic Regions ; *Microbiota ; *Single-Cell Analysis ; Hot Springs/microbiology ; Metagenomics ; Metagenome ; },
abstract = {Geothermal features in Antarctica provide favorable conditions for diverse microorganisms, yet their genomic diversity remains poorly understood. Here, we present an integrated dataset comprising PacBio HiFi and Hi-C metagenomic sequencing, along with single-cell amplified genomes (SAGs) from two high-altitude geothermal sites, Mount Melbourne and Mount Rittmann, in Antarctica. The long-read HiFi sequencing, coupled with Hi-C, enhances the understanding of microbiome diversity and functionality in this unique ecosystem by providing more complete and accurate genomic information. SAGs complement this by recovering rare microbial taxa and offering a strain-resolved perspective. This dataset aims to deepen our understanding of microbial evolution and ecology in Antarctic geothermal environments, and facilitate cross-comparison with other geothermal environments globally.},
}

Antarctic Regions
*Microbiota
*Single-Cell Analysis
Hot Springs/microbiology
Metagenomics
Metagenome

@article {pmid39298196,
year = {2024},
author = {Barber, DG and Davies, CA and Hartley, IP and Tennant, RK},
title = {Evaluation of commercial RNA extraction kits for long-read metatranscriptomics in soil.},
journal = {Microbial genomics},
volume = {10},
number = {9},
pages = {},
pmid = {39298196},
issn = {2057-5858},
mesh = {*Soil Microbiology ; Microbiota/genetics ; Soil/chemistry ; Transcriptome ; Gene Expression Profiling/methods ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, RNA/methods ; RNA/genetics/isolation & purification ; RNA, Bacterial/genetics/isolation & purification ; },
abstract = {Metatranscriptomic analysis of the soil microbiome has the potential to reveal molecular mechanisms that drive soil processes regulated by the microbial community. Therefore, RNA samples must be of sufficient yield and quality to robustly quantify differential gene expression. While short-read sequencing technology is often favoured for metatranscriptomics, long-read sequencing has the potential to provide several benefits over short-read technologies. The ability to resolve complete transcripts on a portable sequencing platform for a relatively low capital expenditure makes Oxford Nanopore Technology an attractive prospect for addressing many of the challenges of soil metatranscriptomics. To fully enable long-read metatranscriptomic analysis of the functional molecular pathways expressed in these diverse habitats, RNA purification methods from soil must be optimised for long-read sequencing. Here we compare RNA samples purified using five commercially available extraction kits designed for use with soil. We found that the Qiagen RNeasy PowerSoil Total RNA Kit performed the best across RNA yield, quality and purity and was robust across different soil types. We found that sufficient sequencing depth can be achieved to characterise the active community for total RNA samples using Oxford Nanopore Technology, and discuss its current limitations for differential gene expression analysis in soil studies.},
}

*Soil Microbiology
Microbiota/genetics
Soil/chemistry
Transcriptome
Gene Expression Profiling/methods
Metagenomics/methods
High-Throughput Nucleotide Sequencing/methods
Sequence Analysis, RNA/methods
RNA/genetics/isolation & purification
RNA, Bacterial/genetics/isolation & purification

@article {pmid39294312,
year = {2024},
author = {Li, D and Wang, Y and Li, X and Zhang, Z and Wang, G and Zhang, Y and Chen, L},
title = {Exploring microbial diversity and function in companion planting systems of white clover and orchard grass.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {21609},
pmid = {39294312},
issn = {2045-2322},
support = {32172769//National Natural Science Foundation of China/ ; },
mesh = {*Trifolium/microbiology/genetics/growth & development ; *Soil Microbiology ; *Rhizosphere ; *Microbiota/genetics ; Dactylis/genetics/microbiology ; Metagenomics/methods ; Bacteria/genetics/classification ; Biodiversity ; },
abstract = {Companion planting of white clover (Trifolium repens L.) with orchard grass (Dactylis glomerata L.), a famous hay grass, improves the forage quality of orchard grass. Microbiome profiling techniques can reveal the specific role of white clover companion planting with orchard grass. This study aimed to explore the microbiome distribution and gene functions of rhizosphere and non-rhizosphere soil via companion planting systems of white clover and orchard grass. From metagenomics sequencing analysis, we confirmed the significant role of white clover on soil environment modeling during companion planting with orchard grass. Twenty-eight biomarkers of rhizosphere soil organisms were identified during companion planting, including Proteobacteria, Betaproteobacteria, Flavobacteriia, and Caulobacterales. The number of gene functions of nitrogen and carbon fixation in companion planting was higher than that in single plants, indicating new functional flora for companion planting. We characterized specific rhizosphere effects, typical biomarker flora, and potential regulatory mechanisms for white clover-related companion planting by metagenomics analyses.},
}

*Trifolium/microbiology/genetics/growth & development
*Soil Microbiology
*Rhizosphere
*Microbiota/genetics
Dactylis/genetics/microbiology
Metagenomics/methods
Bacteria/genetics/classification
Biodiversity

@article {pmid39294129,
year = {2024},
author = {Bozzi, D and Neuenschwander, S and Cruz Dávalos, DI and Sousa da Mota, B and Schroeder, H and Moreno-Mayar, JV and Allentoft, ME and Malaspinas, AS},
title = {Towards predicting the geographical origin of ancient samples with metagenomic data.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {21794},
pmid = {39294129},
issn = {2045-2322},
mesh = {Humans ; *DNA, Ancient/analysis ; *Metagenomics/methods ; *Metagenome ; Geography ; Microbiota/genetics ; },
abstract = {Reconstructing the history-such as the place of birth and death-of an individual sample is a fundamental goal in ancient DNA (aDNA) studies. However, knowing the place of death can be particularly challenging when samples come from museum collections with incomplete or erroneous archives. While analyses of human DNA and isotope data can inform us about the ancestry of an individual and provide clues about where the person lived, they cannot specifically trace the place of death. Moreover, while ancient human DNA can be retrieved, a large fraction of the sequenced molecules in ancient DNA studies derive from exogenous DNA. This DNA-which is usually discarded in aDNA analyses-is constituted mostly by microbial DNA from soil-dwelling microorganisms that have colonized the buried remains post-mortem. In this study, we hypothesize that remains of individuals buried in the same or close geographic areas, exposed to similar microbial communities, could harbor more similar metagenomes. We propose to use metagenomic data from ancient samples' shotgun sequencing to locate the place of death of a given individual which can also help to solve cases of sample mislabeling. We used a k-mer-based approach to compute similarity scores between metagenomic samples from different locations and propose a method based on dimensionality reduction and logistic regression to assign a geographical origin to target samples. We apply our method to several public datasets and observe that individual samples from closer geographic locations tend to show higher similarities in their metagenomes compared to those of different origin, allowing good geographical predictions of test samples. Moreover, we observe that the genus Streptomyces commonly infiltrates ancient remains and represents a valuable biomarker to trace the samples' geographic origin. Our results provide a proof of concept and show how metagenomic data can also be used to shed light on the place of origin of ancient samples.},
}

Humans
*DNA, Ancient/analysis
*Metagenomics/methods
*Metagenome
Geography
Microbiota/genetics

@article {pmid39289490,
year = {2024},
author = {Bai, B and Tuerxun, G and Tuerdi, A and Maimaiti, R and Sun, Y and Abudukerimu, A},
title = {Analysis of vaginal flora diversity and study on the role of Porphyromonas asaccharolytica in promoting IL-1β in regulating cervical cancer.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {21731},
pmid = {39289490},
issn = {2045-2322},
support = {2022D01C185//Natural Science Foundation of the Xinjiang Uygur Autonomous Region/ ; },
mesh = {Female ; Humans ; *Uterine Cervical Neoplasms/microbiology/virology/pathology/genetics ; *Vagina/microbiology ; *Porphyromonas/genetics/isolation & purification ; *Interleukin-1beta/genetics/metabolism ; *Microbiota/genetics ; Adult ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; Papillomavirus Infections/virology/microbiology/complications ; },
abstract = {Cervical cancer, a prevalent malignancy in the female reproductive tract, exhibits a high incidence. Existing evidence indicates a robust correlation between alterations in vaginal flora composition and the progression of cervical cancer. Nevertheless, there is a lack of clarity concerning the specific microorganisms within the vaginal microbiota that are linked to the onset and development of cervical cancer, as well as the mechanisms through which they exert carcinogenic effects. The 16 S ribosomal (rRNA) and metagenomic sequencing technology were used to analyze vaginal microorganisms, and screening for human papillomavirus (HPV) positive cervical cancer-associated microbial markers using fold change in mean bacterial abundance. Moreover, vaginal microenvironmental factors were detected, and the local vaginal inflammatory state in patients with cervical cancer was subjected to assay via qRT-PCR and ELISA. The hub inflammatory genes were screened by transcriptome sequencing after co-culture of bacteria and normal cervical epithelial cells, and an in vitro model was utilized to assess the impacts of inflammatory factors on cervical cancer. Both cervical cancer patients and HPV-positive patients showed significant changes in the composition of the vaginal flora, characterised by a decrease in the abundance of Lactobacillus and an increase in the abundance of a variety of anaerobic bacteria; The microbial sequencing identified Porphyromonas, Porphyromonas_asaccharolytica, and Porphyromonas_uenonis as microbial markers for HPV-associated cervical cancer. Vaginal inflammatory factors in patients with cervical cancer were overexpressed. After Porphyromonas_asaccharolytica intervention on cervical epithelial H8 cells, interleukin (IL)-1β, a hub differential gene, markedly promoted tumor-associated biological behaviors at the in vitro cytological level in cervical cancer. This study for the first demonstrated that Porphyromonas, Porphyromonas_asaccharolytica, and Porphyromonas_uenonis could serve as novel microbial markers for cervical cancer. Moreover, Porphyromonas_asaccharolytica was identified as having the ability to induce the overexpression of inflammatory genes in cervical epithelial cells to create a favorable microenvironment for the onset and development of cervical cancer. The effects of dysbacteriosis on cervical cancer were microbiologically elucidated.},
}

Female
Humans
*Uterine Cervical Neoplasms/microbiology/virology/pathology/genetics
*Vagina/microbiology
*Porphyromonas/genetics/isolation & purification
*Interleukin-1beta/genetics/metabolism
*Microbiota/genetics
Adult
RNA, Ribosomal, 16S/genetics
Middle Aged
Papillomavirus Infections/virology/microbiology/complications

@article {pmid39289365,
year = {2024},
author = {Peng, X and Wang, S and Wang, M and Feng, K and He, Q and Yang, X and Hou, W and Li, F and Zhao, Y and Hu, B and Zou, X and Deng, Y},
title = {Metabolic interdependencies in thermophilic communities are revealed using co-occurrence and complementarity networks.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {8166},
pmid = {39289365},
issn = {2041-1723},
mesh = {*Metabolic Networks and Pathways/genetics ; *Archaea/genetics/metabolism ; *Bacteria/metabolism/genetics/classification ; *Metagenome/genetics ; *Microbiota ; Hot Springs/microbiology ; Phylogeny ; Microbial Interactions ; Hot Temperature ; },
abstract = {Microbial communities exhibit intricate interactions underpinned by metabolic dependencies. To elucidate these dependencies, we present a workflow utilizing random matrix theory on metagenome-assembled genomes to construct co-occurrence and metabolic complementarity networks. We apply this approach to a temperature gradient hot spring, unraveling the interplay between thermal stress and metabolic cooperation. Our analysis reveals an increase in the frequency of metabolic interactions with rising temperatures. Amino acids, coenzyme A derivatives, and carbohydrates emerge as key exchange metabolites, forming the foundation for syntrophic dependencies, in which commensalistic interactions take a greater proportion than mutualistic ones. These metabolic exchanges are most prevalent between phylogenetically distant species, especially archaea-bacteria collaborations, as a crucial adaptation to harsh environments. Furthermore, we identify a significant positive correlation between basal metabolite exchange and genome size disparity, potentially signifying a means for streamlined genomes to leverage cooperation with metabolically richer partners. This phenomenon is also confirmed by another composting system which has a similar wide range of temperature fluctuations. Our workflow provides a feasible way to decipher the metabolic complementarity mechanisms underlying microbial interactions, and our findings suggested environmental stress regulates the cooperative strategies of thermophiles, while these dependencies have been potentially hardwired into their genomes during co-evolutions.},
}

*Metabolic Networks and Pathways/genetics
*Archaea/genetics/metabolism
*Bacteria/metabolism/genetics/classification
*Metagenome/genetics
*Microbiota
Hot Springs/microbiology
Phylogeny
Microbial Interactions
Hot Temperature

@article {pmid39287279,
year = {2024},
author = {Xing, W and Yu, J and Cui, S and Liu, L and Zhi, Y and Zhang, T and Zhou, J},
title = {Analysis of the correlation between gut microbiome imbalance and the development of endometrial cancer based on metagenomics.},
journal = {Medicine},
volume = {103},
number = {37},
pages = {e39596},
pmid = {39287279},
issn = {1536-5964},
mesh = {Humans ; Female ; *Endometrial Neoplasms/microbiology/genetics ; *Gastrointestinal Microbiome/genetics ; Case-Control Studies ; Middle Aged ; Prospective Studies ; *Metagenomics/methods ; Aged ; Adult ; },
abstract = {Endometrial cancer (EC) is the most prevalent gynecologic malignancy, with a higher risk in obese women, suggesting the potential involvement of gut microbiota in the progression of EC. However, there is no direct evidence of a connection between EC and the human gut microbiota. Using metagenomic sequencing, we investigated the relationship between gut microbiome imbalance and cancer development in patients with EC. In this prospective case-control study, we included 15 patients with EC based on endometrial biopsy in the case group and 15 women admitted to the hospital for female pelvic floor issues during the same time who did not have endometrial lesions from January 2023 to June 2023 in control group. The microbiota structure of EC cases and controls without benign or malignant endometrial lesions during the same time period was analyzed using metagenomic sequencing technology. We employed Alpha diversity analysis to reflect the richness and diversity of microbial communities. Statistical algorithm Bray-Curtis was utilized to calculate pairwise distances between samples, obtaining a beta diversity distance matrix. Subsequently, hierarchical clustering analysis was conducted based on the distance matrix. The results showed that the composition of bacterial colonies in both groups was dominated by Firmicutes, which had a higher proportion in the control group, followed by Bacteroidetes in the control group and Proteobacteria and Bacteroidetes in the case group. The abundance of Klebsiella (P = .02) was significantly higher, and the abundance of Alistipes (P = .04), Anearobutyricum (P = .01), and bacteria in Firmicutes such as Oscillospira and Catenibacterium was markedly lower in the case group than in the control group. These results demonstrated conclusively that a gut microbiome imbalance was associated with the development of EC.},
}

Humans
Female
*Endometrial Neoplasms/microbiology/genetics
*Gastrointestinal Microbiome/genetics
Case-Control Studies
Middle Aged
Prospective Studies
*Metagenomics/methods
Aged
Adult

@article {pmid39277616,
year = {2024},
author = {Jia, Y and Shi, Y and Wang, J and Liu, H and Huang, Y and Wang, H and Liu, Y and Peng, J},
title = {Integrating metagenomics with metabolomics for gut microbiota and metabolites profiling in acute pancreatitis.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {21491},
pmid = {39277616},
issn = {2045-2322},
support = {GZC20242045//Postdoctoral Fellowship Program of CPSF/ ; 2023zzts896//Fundamental Research Funds for Central Universities of the Central South University/ ; 82170661//National Natural Science Foundation of China/ ; 2023DK2002//Key Project of Research and Development Plan of Hunan Province/ ; },
mesh = {*Gastrointestinal Microbiome ; *Pancreatitis/microbiology/metabolism ; Animals ; *Metabolomics/methods ; *Metagenomics/methods ; Mice ; Metabolome ; Disease Models, Animal ; Dysbiosis/microbiology/metabolism ; Mice, Inbred C57BL ; Male ; Acute Disease ; },
abstract = {Acute pancreatitis (AP) is an inflammatory disease of the pancreas. Despite of a steadily increasing in morbidity and mortality, there is still no effective therapy. Gut microbial dysbiosis and its derived-metabolites disorder have been shown to play an important role in the development of AP, however, little is known regarding the crosstalk between gut microbiota and metabolites. In this study, we assessed the alterations in gut microbiota and metabolites by constructing three AP mouse models by means of metagenomic and metabolomic sequencing, and further clarified their relationship by correlation analysis. The results revealed that each model exhibited unique flora and metabolite profiles. KEGG analysis showed that the differential flora and metabolite-enriched pathway functions were correlated with lipid metabolism and amino acid metabolism. Moreover, two core differential bacterial species on Burkholderiales bacterium YL45 and Bifidobacterium pseudolongum along with eleven differential metabolites appeared to exert certain effects during the course of AP. In conclusion, further exploration of the crosstalk between microbiota and derived metabolites may provide novel insights and strategies into the diagnosis and treatment of AP.},
}

*Gastrointestinal Microbiome
*Pancreatitis/microbiology/metabolism
Animals
*Metabolomics/methods
*Metagenomics/methods
Mice
Metabolome
Disease Models, Animal
Dysbiosis/microbiology/metabolism
Mice, Inbred C57BL
Male
Acute Disease

@article {pmid39277613,
year = {2024},
author = {da Silva, S and Vuong, P and Amaral, JRV and da Silva, VAS and de Oliveira, SS and Vermelho, AB and Beale, DJ and Bissett, A and Whiteley, AS and Kaur, P and Macrae, A},
title = {The piranha gut microbiome provides a selective lens into river water biodiversity.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {21518},
pmid = {39277613},
issn = {2045-2322},
support = {Bolsa de Doutorado//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; Bolsa de Iniciacao Cientifica//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; Bolsa de doutordo//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; PRINT 001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; },
mesh = {*Rivers/microbiology ; *Gastrointestinal Microbiome/genetics ; Animals ; *Biodiversity ; Metagenome ; Metagenomics/methods ; Water Microbiology ; Bacteria/genetics/classification/isolation & purification ; },
abstract = {Advances in omics technologies have enabled the in-depth study of microbial communities and their metabolic profiles from all environments. Here metagenomes were sampled from piranha (Serrasalmus rhombeus) and from river water from the Rio São Benedito (Amazon Basin). Shotgun metagenome sequencing was used to explore diversity and to test whether fish microbiomes are a good proxy for river microbiome studies. The results showed that the fish microbiomes were not significantly different from the river water microbiomes at higher taxonomic ranks. However, at the genus level, fish microbiome alpha diversity decreased, and beta diversity increased. This result repeated for functional gene abundances associated with specific metabolic categories (SEED level 3). A clear delineation between water and fish was seen for beta diversity. The piranha microbiome provides a good and representative subset of its river water microbiome. Variations seen in beta biodiversity were expected and can be explained by temporal variations in the fish microbiome in response to stronger selective forces on its biodiversity. Metagenome assembled genomes construction was better from the fish samples. This study has revealed that the microbiome of a piranha tells us a lot about its river water microbiome and function.},
}

*Rivers/microbiology
*Gastrointestinal Microbiome/genetics
Animals
*Biodiversity
Metagenome
Metagenomics/methods
Water Microbiology
Bacteria/genetics/classification/isolation & purification

@article {pmid39267241,
year = {2024},
author = {Doni, L and Azzola, A and Oliveri, C and Bosi, E and Auguste, M and Morri, C and Bianchi, CN and Montefalcone, M and Vezzulli, L},
title = {Genome-resolved metagenomics revealed novel microbial taxa with ancient metabolism from macroscopic microbial mat structures inhabiting anoxic deep reefs of a Maldivian Blue Hole.},
journal = {Environmental microbiology reports},
volume = {16},
number = {5},
pages = {e13315},
pmid = {39267241},
issn = {1758-2229},
support = {CN_00000033//Centro Nazionale di Ricerca - Biodiversità (Italy) project (PNRR CN00000033 - Centro Nazionale Biodiversità/ ; CUP D33C22000960007//Italian Ministry of University and Research/ ; },
mesh = {*Metagenomics ; *Phylogeny ; *Metagenome ; Bacteria/classification/genetics/isolation & purification/metabolism ; Geologic Sediments/microbiology ; Genome, Bacterial/genetics ; Anaerobiosis ; Deltaproteobacteria/genetics/classification/isolation & purification/metabolism ; Chloroflexi/genetics/classification/isolation & purification/metabolism ; Proteobacteria/genetics/classification/isolation & purification ; Microbiota ; },
abstract = {Blue holes are vertical water-filled openings in carbonate rock that exhibit complex morphology, ecology, and water chemistry. In this study, macroscopic microbial mat structures found in complete anoxic conditions in the Faanu Mudugau Blue Hole (Maldives) were studied by metagenomic methods. Such communities have likely been evolutionary isolated from the surrounding marine environment for more than 10,000 years since the Blue Hole formation during the last Ice Age. A total of 48 high-quality metagenome-assembled genomes (MAGs) were recovered, predominantly composed of the phyla Chloroflexota, Proteobacteria and Desulfobacterota. None of these MAGs have been classified to species level (<95% ANI), suggesting the discovery of several new microbial taxa. In particular, MAGs belonging to novel bacterial genera within the order Dehalococcoidales accounted for 20% of the macroscopic mat community. Genome-resolved metabolic analysis of this dominant microbial fraction revealed a mixotrophic lifestyle based on energy conservation via fermentation, hydrogen metabolism and anaerobic CO2 fixation through the Wood-Ljungdahl pathway. Interestingly, these bacteria showed a high proportion of ancestral genes in their genomes providing intriguing perspectives on mechanisms driving microbial evolution in this peculiar environment. Overall, our results provide new knowledge for understanding microbial life under extreme conditions in blue hole environments.},
}

*Metagenomics
*Phylogeny
*Metagenome
Bacteria/classification/genetics/isolation & purification/metabolism
Geologic Sediments/microbiology
Genome, Bacterial/genetics
Anaerobiosis
Deltaproteobacteria/genetics/classification/isolation & purification/metabolism
Chloroflexi/genetics/classification/isolation & purification/metabolism
Proteobacteria/genetics/classification/isolation & purification
Microbiota

@article {pmid39275258,
year = {2024},
author = {Wang, M and Chen, Y and Song, AX and Weng, X and Meng, Y and Lin, J and Mao, YH},
title = {The Combination of Exercise and Konjac Glucomannan More Effectively Prevents Antibiotics-Induced Dysbiosis in Mice Compared with Singular Intervention.},
journal = {Nutrients},
volume = {16},
number = {17},
pages = {},
pmid = {39275258},
issn = {2072-6643},
support = {2023A1515010004//Guangdong Basic and Applied Basic Research Foundation/ ; 2023ZDZX2035//Special Funds in Key Areas of Guangdong Provincial Department of Education/ ; S202410585045//The College Students Innovation and Entrepreneurship Training Program/ ; 202410585015//The College Students Innovation and Entrepreneurship Training Program/ ; 82003434//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Mannans/pharmacology ; *Dysbiosis/prevention & control/chemically induced ; *Mice, Inbred C57BL ; *Anti-Bacterial Agents/pharmacology/adverse effects ; *Gastrointestinal Microbiome/drug effects ; *Physical Conditioning, Animal ; Mice ; Male ; Combined Modality Therapy ; },
abstract = {Our previous studies have demonstrated that konjac glucomannan (KGM) can prevent dysbiosis induced by antibiotics. While exercise may also impact the gut microbiome, there are limited studies reporting its protective effect on antibiotic-induced dysbiosis. Therefore, this study investigated the preventive and regulatory effects of a combination of 6-week exercise and KGM intervention on antibiotic-induced dysbiosis in C57BL/6J mice compared with a single intervention. The results showed that combined exercise and KGM intervention could restore the changes in the relative abundance of Bacteroides (3.73% with CTL versus 14.23% with ATBX versus 4.46% with EK) and Prevotellaceae_Prevotella (0.33% with CTL versus 0.00% with ATBX versus 0.30% with EK) induced by antibiotics (p < 0.05), and minimized the Bray-Curtis distance induced by antibiotics (0.55 with CTL versus 0.81 with ATBX versus 0.80 with EXC versus 0.83 with KGM versus 0.75 with EK). Compared with the combined intervention, exercise intervention also produced a certain level of recovery effects; the relative abundance of Rikenellaceae (1.96% with CTL versus 0.09% with ATBX versus 0.49% with EXC) was restored, while KGM supplementation showed the best preventive effect. In addition, the combination of exercise and KGM significantly enriched microbial purine metabolic pathways (p < 0.05). These findings indicate that combining exercise with KGM could be a promising approach to reducing the side effects of antibiotics on the gut microbiome.},
}

Animals
*Mannans/pharmacology
*Dysbiosis/prevention & control/chemically induced
*Mice, Inbred C57BL
*Anti-Bacterial Agents/pharmacology/adverse effects
*Gastrointestinal Microbiome/drug effects
*Physical Conditioning, Animal
Mice
Male
Combined Modality Therapy

@article {pmid39273435,
year = {2024},
author = {Di Chiano, M and Sallustio, F and Fiocco, D and Rocchetti, MT and Spano, G and Pontrelli, P and Moschetta, A and Gesualdo, L and Gadaleta, RM and Gallone, A},
title = {Psychobiotic Properties of Lactiplantibacillus plantarum in Neurodegenerative Diseases.},
journal = {International journal of molecular sciences},
volume = {25},
number = {17},
pages = {},
pmid = {39273435},
issn = {1422-0067},
support = {1062//PON "RICERCA E INNOVAZIONE" 2014-2020-Innovazione/ ; Call for tender No. 341 of 15 March 2022 of Italian Ministry of University and Research funded by the European Union - Next Generation EU//National Recovery and Resilience Plan (NRRP)/ ; Concession Decree No. 1550 of 11 October 2022 adopted by the Italian Ministry of University and Research, CUP D93C22000890001//Italian Ministry of University and Research, CUP D93C22000890001/ ; Codice progetto n. 2022H9MPZ5//MIUR- PRIN Progetti di Ricerca di Rilevante Interesse Nazionale 2022/ ; Id. 23239//AIRC IG 2019/ ; Call for tender No. 3138 of 16/12/2021 of Italian Ministry of University and Research funded by the European Union//National Recovery and Resilience Plan (NRRP)/ ; Project code: CN00000041, CUP H93C22000430007//NextGenerationEU/ ; PNRR-MR1-2022-12376395//European Union - Next Generation EU - PNRR M6C2/ ; "POFACS" - ARS01_00640 -", D.D. 1211/2020 and 1104/2021//Italian Ministry of University and Research (MIUR)/ ; PRA-HE 2021//University of Foggia/ ; },
mesh = {Humans ; *Neurodegenerative Diseases/microbiology/metabolism ; *Gastrointestinal Microbiome ; *Probiotics/therapeutic use ; Dysbiosis/microbiology ; Brain-Gut Axis ; Animals ; },
abstract = {Neurodegenerative disorders are the main cause of cognitive and physical disabilities, affect millions of people worldwide, and their incidence is on the rise. Emerging evidence pinpoints a disturbance of the communication of the gut-brain axis, and in particular to gut microbial dysbiosis, as one of the contributors to the pathogenesis of these diseases. In fact, dysbiosis has been associated with neuro-inflammatory processes, hyperactivation of the neuronal immune system, impaired cognitive functions, aging, depression, sleeping disorders, and anxiety. With the rapid advance in metagenomics, metabolomics, and big data analysis, together with a multidisciplinary approach, a new horizon has just emerged in the fields of translational neurodegenerative disease. In fact, recent studies focusing on taxonomic profiling and leaky gut in the pathogenesis of neurodegenerative disorders are not only shedding light on an overlooked field but are also creating opportunities for biomarker discovery and development of new therapeutic and adjuvant strategies to treat these disorders. Lactiplantibacillus plantarum (LBP) strains are emerging as promising psychobiotics for the treatment of these diseases. In fact, LBP strains are able to promote eubiosis, increase the enrichment of bacteria producing beneficial metabolites such as short-chain fatty acids, boost the production of neurotransmitters, and support the homeostasis of the gut-brain axis. In this review, we summarize the current knowledge on the role of the gut microbiota in the pathogenesis of neurodegenerative disorders with a particular focus on the benefits of LBP strains in Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, autism, anxiety, and depression.},
}

Humans
*Neurodegenerative Diseases/microbiology/metabolism
*Gastrointestinal Microbiome
*Probiotics/therapeutic use
Dysbiosis/microbiology
Brain-Gut Axis
Animals

@article {pmid39273112,
year = {2024},
author = {Druker, S and Sicsic, R and Ravid, S and Scheinin, S and Raz, T},
title = {Reproductive Tract Microbial Transitions from Late Gestation to Early Postpartum Using 16S rRNA Metagenetic Profiling in First-Pregnancy Heifers.},
journal = {International journal of molecular sciences},
volume = {25},
number = {17},
pages = {},
pmid = {39273112},
issn = {1422-0067},
mesh = {Female ; Animals ; Pregnancy ; *RNA, Ribosomal, 16S/genetics ; Cattle ; *Postpartum Period ; *Vagina/microbiology ; *Microbiota/genetics ; *Uterus/microbiology ; Bacteria/classification/genetics/isolation & purification ; Metagenomics/methods ; Metagenome ; },
abstract = {Studies in recent years indicate that reproductive tract microbial communities are crucial for shaping mammals' health and reproductive outcomes. Following parturition, uterine bacterial contamination often occurs due to the open cervix, which may lead to postpartum uterine inflammatory diseases, especially in primiparous individuals. However, investigations into spatio-temporal microbial transitions in the reproductive tract of primigravid females remain limited. Our objective was to describe and compare the microbial community compositions in the vagina at late gestation and in the vagina and uterus at early postpartum in first-pregnancy heifers. Three swab samples were collected from 33 first-pregnancy Holstein Friesian heifers: one vaginal sample at gestation day 258 ± 4, and vaginal and uterine samples at postpartum day 7 ± 2. Each sample underwent 16S rRNA V4 region metagenetic analysis via Illumina MiSeq, with bioinformatics following Mothur MiSeq SOP. The reproductive tract bacterial communities were assigned to 1255 genus-level OTUs across 30 phyla. Dominant phyla, accounting for approximately 90% of the communities, included Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes, and Fusobacteria. However, the results revealed distinct shifts in microbial composition between the prepartum vagina (Vag-pre), postpartum vagina (Vag-post), and postpartum uterus (Utr-post). The Vag-pre and Utr-post microbial profiles were the most distinct. The Utr-post group had lower relative abundances of Proteobacteria but higher abundances of Bacteroidetes, Fusobacteria, and Tenericutes compared to Vag-pre, while Vag-post displayed intermediate values for these phyla, suggesting a transitional profile. Additionally, the Utr-post group exhibited lower bacterial richness and diversity compared to both Vag-pre and Vag-post. The unsupervised probabilistic Dirichlet Multinomial Mixtures model identified two distinct community types: most Vag-pre samples clustered into one type and Utr-post samples into another, while Vag-post samples were distributed evenly between the two. LEfSe analysis revealed distinct microbial profiles at the genus level. Overall, specific microbial markers were associated with anatomical and temporal transitions, revealing a dynamic microbial landscape during the first pregnancy and parturition. These differences highlight the complexity of these ecosystems and open new avenues for research in reproductive biology and microbial ecology.},
}

Female
Animals
Pregnancy
*RNA, Ribosomal, 16S/genetics
Cattle
*Postpartum Period
*Vagina/microbiology
*Microbiota/genetics
*Uterus/microbiology
Bacteria/classification/genetics/isolation & purification
Metagenomics/methods
Metagenome

@article {pmid39268238,
year = {2024},
author = {Wang, J and Su, C and Qian, M and Wang, X and Chen, C and Liu, Y and Liu, W and Xiang, Z and Xu, B},
title = {Subchronic toxic effects of bisphenol A on the gut-liver-hormone axis in rats via intestinal flora and metabolism.},
journal = {Frontiers in endocrinology},
volume = {15},
number = {},
pages = {1415216},
pmid = {39268238},
issn = {1664-2392},
mesh = {Animals ; *Phenols/toxicity ; Male ; Female ; Rats ; *Gastrointestinal Microbiome/drug effects ; *Benzhydryl Compounds/toxicity ; *Liver/drug effects/metabolism/pathology ; *Endocrine Disruptors/toxicity ; Rats, Sprague-Dawley ; Hormones/blood ; },
abstract = {BACKGROUND: Bisphenol A (BPA), a characteristic endocrine disruptor, is a substance that seriously interferes with the human endocrine system and causes reproductive disorders and developmental abnormalities. However, its toxic effects on the gut-liver-hormone axis are still unclear.

METHOD: Male and female rats were exposed to BPA (300 mg/kg) by oral gavage for 60 consecutive days. H&E staining was used for histopathological evaluation, and the serum biochemical indexes were determined using an automatic analyzer. The 16S rRNA gene sequencing was used to detect the intestinal microbial diversity, and the GC-MS was used to analyze the contents of short-chain fatty acids (SCFAs) in colon contents. UPLC-QTOF MS was used to analyze the related metabolites. The ELISA method was used to assess the levels of serum inflammatory factors.

RESULTS: Histopathological analysis indicated that the liver, heart, and testis were affected by BPA. There was a significant effect on alanine aminotransferase (ALT), triglyceride (TG), total cholesterol (TC), and low-density lipoprotein (LDL) in the male-BPA group (P < 0.05), and globulin (GLB), indirect bilirubin (IBIL), alkaline phosphatase (ALP), ALT, TG, TC, high-density lipoprotein (HDL), and creatinine (Cr) in the female-BPA group (P < 0.05). Metagenomics (16S rRNA gene sequencing) analysis indicated that BPA reduced the diversity and changed the composition of gut microbiota in rats significantly. Compared with the control and blank groups, the contents of caproic acid, isobutyric acid, isovaleric acid, and propanoic acid in the colon contents decreased in the male-BPA group (P < 0.05), and caproic acid, isobutyric acid, isovaleric acid, and valeric acid in the colon contents decreased in the female-BPA group (P < 0.05). Metabolomic analysis of the serum indicated that BPA could regulate bile acid levels, especially ursodeoxycholic acid (UDCA) and its conjugated forms. The contents of amino acids, hormones, and lipids were also significantly affected after exposure to BPA. The increase in interleukin-6 (IL-6), interleukin-23 (IL-23), and transforming growth factor-β (TGF-β) in the serum of the male-BPA group suggests that BPA exposure affects the immune system.

CONCLUSION: BPA exposure will cause toxicity to rats via disrupting the gut-liver-hormone axis.},
}

Animals
*Phenols/toxicity
Male
Female
Rats
*Gastrointestinal Microbiome/drug effects
*Benzhydryl Compounds/toxicity
*Liver/drug effects/metabolism/pathology
*Endocrine Disruptors/toxicity
Rats, Sprague-Dawley
Hormones/blood

@article {pmid39267171,
year = {2024},
author = {Gandasegui, J and Fleitas, PE and Petrone, P and Grau-Pujol, B and Novela, V and Rubio, E and Muchisse, O and Cossa, A and Jamine, JC and Sacoor, C and Brienen, EAT and van Lieshout, L and Muñoz, J and Casals-Pascual, C},
title = {Baseline gut microbiota diversity and composition and albendazole efficacy in hookworm-infected individuals.},
journal = {Parasites & vectors},
volume = {17},
number = {1},
pages = {387},
pmid = {39267171},
issn = {1756-3305},
mesh = {*Albendazole/therapeutic use/pharmacology/administration & dosage ; Humans ; *Gastrointestinal Microbiome/drug effects/genetics ; *Anthelmintics/therapeutic use/administration & dosage ; *Hookworm Infections/drug therapy ; *Feces/parasitology/microbiology ; Female ; Male ; RNA, Ribosomal, 16S/genetics ; Adult ; Treatment Outcome ; Animals ; Young Adult ; Middle Aged ; Ancylostomatoidea/drug effects/genetics ; Adolescent ; Child ; },
abstract = {Soil-transmitted helminth (STH) infections account for a significant global health burden, necessitating mass drug administration with benzimidazole-class anthelmintics, such as albendazole (ALB), for morbidity control. However, ALB efficacy shows substantial variability, presenting challenges for achieving consistent treatment outcomes. We have explored the potential impact of the baseline gut microbiota on ALB efficacy in hookworm-infected individuals through microbiota profiling and machine learning (ML) techniques. Our investigation included 89 stool samples collected from hookworm-infected individuals that were analyzed by microscopy and quantitative PCR (qPCR). Of these, 44 were negative by microscopy for STH infection using the Kato-Katz method and qPCR 21 days after treatment, which entails a cure rate of 49.4%. Microbiota characterization was based on amplicon sequencing of the V3-V4 16S ribosomal RNA gene region. Alpha and beta diversity analyses revealed no significant differences between participants who were cured and those who were not cured, suggesting that baseline microbiota diversity does not influence ALB treatment outcomes. Furthermore, differential abundance analysis at the phylum, family and genus levels yielded no statistically significant associations between bacterial communities and ALB efficacy. Utilizing supervised ML models failed to predict treatment response accurately. Our investigation did not provide conclusive insights into the relationship between gut microbiota and ALB efficacy. However, the results highlight the need for future research to incorporate longitudinal studies that monitor changes in the gut microbiota related to the infection and the cure with ALB, as well as functional metagenomics to better understand the interaction of the microbiome with the drug, and its role, if there is any, in modulating anthelmintic treatment outcomes in STH infections. Interdisciplinary approaches integrating microbiology, pharmacology, genetics and data science will be pivotal in advancing our understanding of STH infections and optimizing treatment strategies globally.},
}

*Albendazole/therapeutic use/pharmacology/administration & dosage
Humans
*Gastrointestinal Microbiome/drug effects/genetics
*Anthelmintics/therapeutic use/administration & dosage
*Hookworm Infections/drug therapy
*Feces/parasitology/microbiology
Female
Male
RNA, Ribosomal, 16S/genetics
Adult
Treatment Outcome
Animals
Young Adult
Middle Aged
Ancylostomatoidea/drug effects/genetics
Adolescent
Child

@article {pmid39266528,
year = {2024},
author = {Liu, S and Chen, Q and Hou, C and Dong, C and Qiu, X and Tang, K},
title = {Recovery of 1559 metagenome-assembled genomes from the East China Sea's low-oxygen region.},
journal = {Scientific data},
volume = {11},
number = {1},
pages = {994},
pmid = {39266528},
issn = {2052-4463},
mesh = {China ; *Metagenome ; *Archaea/genetics ; Bacteria/genetics/classification ; Oxygen ; Seawater/microbiology ; Phylogeny ; Metagenomics ; Oceans and Seas ; Microbiota ; },
abstract = {The Changjiang Estuary and adjacent East China Sea are well-known hypoxic aquatic environments. Eutrophication-driven hypoxia frequently occurs in coastal areas, posing a major threat to the ecological environment, including altering community structure and metabolic processes of marine organisms, and enhancing diversion of energy shunt into microbial communities. However, the responses of microbial communities and their metabolic pathways to coastal hypoxia remain poorly understood. Here, we studied the microbial communities collected from spatiotemporal samplings using metagenomic sequencing in the Changjiang Estuary and adjacent East China Sea. This generated 1.31 Tbp of metagenomics data, distributed across 103 samples corresponding to 8 vertical profiles. We further reported 1,559 metagenome-assembled genomes (MAGs), of which 508 were high-quality MAGs (Completeness > 90% and Contamination < 10%). Phylogenomic analysis classified them into 181 archaeal and 1,378 bacterial MAGs. These results provided a valuable metagenomic dataset available for further investigation of the effects of hypoxia on marine microorganisms.},
}

China
*Metagenome
*Archaea/genetics
Bacteria/genetics/classification
Oxygen
Seawater/microbiology
Phylogeny
Metagenomics
Oceans and Seas
Microbiota

@article {pmid39266450,
year = {2024},
author = {Gnimpieba, EZ and Hartman, TW and Do, T and Zylla, J and Aryal, S and Haas, SJ and Agany, DDM and Gurung, BDS and Doe, V and Yosufzai, Z and Pan, D and Campbell, R and Huber, VC and Sani, R and Gadhamshetty, V and Lushbough, C},
title = {Biofilm marker discovery with cloud-based dockerized metagenomics analysis of microbial communities.},
journal = {Briefings in bioinformatics},
volume = {25},
number = {Supplement_1},
pages = {},
pmid = {39266450},
issn = {1477-4054},
support = {#1849206//National Science Foundation/ ; //Institutional Development Award/ ; /GM/NIGMS NIH HHS/United States ; P20GM103443/NH/NIH HHS/United States ; },
mesh = {*Biofilms/growth & development ; *Metagenomics/methods ; Microbiota/genetics ; Cloud Computing ; Humans ; Computational Biology/methods ; },
abstract = {In an environment, microbes often work in communities to achieve most of their essential functions, including the production of essential nutrients. Microbial biofilms are communities of microbes that attach to a nonliving or living surface by embedding themselves into a self-secreted matrix of extracellular polymeric substances. These communities work together to enhance their colonization of surfaces, produce essential nutrients, and achieve their essential functions for growth and survival. They often consist of diverse microbes including bacteria, viruses, and fungi. Biofilms play a critical role in influencing plant phenotypes and human microbial infections. Understanding how these biofilms impact plant health, human health, and the environment is important for analyzing genotype-phenotype-driven rule-of-life functions. Such fundamental knowledge can be used to precisely control the growth of biofilms on a given surface. Metagenomics is a powerful tool for analyzing biofilm genomes through function-based gene and protein sequence identification (functional metagenomics) and sequence-based function identification (sequence metagenomics). Metagenomic sequencing enables a comprehensive sampling of all genes in all organisms present within a biofilm sample. However, the complexity of biofilm metagenomic study warrants the increasing need to follow the Findability, Accessibility, Interoperability, and Reusable (FAIR) Guiding Principles for scientific data management. This will ensure that scientific findings can be more easily validated by the research community. This study proposes a dockerized, self-learning bioinformatics workflow to increase the community adoption of metagenomics toolkits in a metagenomics and meta-transcriptomics investigation. Our biofilm metagenomics workflow self-learning module includes integrated learning resources with an interactive dockerized workflow. This module will allow learners to analyze resources that are beneficial for aggregating knowledge about biofilm marker genes, proteins, and metabolic pathways as they define the composition of specific microbial communities. Cloud and dockerized technology can allow novice learners-even those with minimal knowledge in computer science-to use complicated bioinformatics tools. Our cloud-based, dockerized workflow splits biofilm microbiome metagenomics analyses into four easy-to-follow submodules. A variety of tools are built into each submodule. As students navigate these submodules, they learn about each tool used to accomplish the task. The downstream analysis is conducted using processed data obtained from online resources or raw data processed via Nextflow pipelines. This analysis takes place within Vertex AI's Jupyter notebook instance with R and Python kernels. Subsequently, results are stored and visualized in Google Cloud storage buckets, alleviating the computational burden on local resources. The result is a comprehensive tutorial that guides bioinformaticians of any skill level through the entire workflow. It enables them to comprehend and implement the necessary processes involved in this integrated workflow from start to finish. This manuscript describes the development of a resource module that is part of a learning platform named "NIGMS Sandbox for Cloud-based Learning" https://github.com/NIGMS/NIGMS-Sandbox. The overall genesis of the Sandbox is described in the editorial NIGMS Sandbox [1] at the beginning of this Supplement. This module delivers learning materials on the analysis of bulk and single-cell ATAC-seq data in an interactive format that uses appropriate cloud resources for data access and analyses.},
}

*Biofilms/growth & development
*Metagenomics/methods
Microbiota/genetics
Cloud Computing
Humans
Computational Biology/methods

@article {pmid39264803,
year = {2024},
author = {Tang, D and Hu, W and Fu, B and Zhao, X and You, G and Xie, C and Wang, HY and Guo, X and Zhang, Q and Liu, Z and Ye, L},
title = {Gut microbiota-mediated C-sulfonate metabolism impairs the bioavailability and anti-cholestatic efficacy of andrographolide.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2387402},
pmid = {39264803},
issn = {1949-0984},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Diterpenes/metabolism/pharmacology ; *Biological Availability ; Mice ; Cholestasis/metabolism/drug therapy/microbiology ; Male ; RNA, Ribosomal, 16S/genetics ; Bile Acids and Salts/metabolism ; Bacteria/metabolism/classification/genetics/drug effects/isolation & purification ; Humans ; Mice, Inbred C57BL ; Liver/metabolism/drug effects ; Receptors, Cytoplasmic and Nuclear/metabolism/genetics ; Disease Models, Animal ; },
abstract = {Cholestatic liver injury results from the accumulation of toxic bile acids in the liver, presenting a therapeutic challenge with no effective treatment available to date. Andrographolide (AP) has exhibited potential as a treatment for cholestatic liver disease. However, its limited oral bioavailability poses a significant obstacle to harnessing its potent therapeutic properties and restricts its clinical utility. This limitation is potentially attributed to the involvement of gut microbiota in AP metabolism. In our study, employing pseudo-germ-free, germ-free and strain colonization animal models, along with 16S rRNA and shotgun metagenomic sequencing analysis, we elucidate the pivotal role played by gut microbiota in the C-sulfonate metabolism of AP, a process profoundly affecting its bioavailability and anti-cholestatic efficacy. Subsequent investigations pinpoint a specific enzyme, adenosine-5'-phosphosulfate (APS) reductase, predominantly produced by Desulfovibrio piger, which catalyzes the reduction of SO4[2-] to HSO3[-]. HSO3[-] subsequently interacts with AP, targeting its C=C unsaturated double bond, resulting in the formation of the C-sulfonate metabolite, 14-deoxy-12(R)-sulfo andrographolide (APM). Inhibition of APS reductase leads to a notable enhancement in AP bioavailability and anti-cholestatic efficacy. Furthermore, employing RNA sequencing analysis and farnesoid X receptor (FXR) knockout mice, our findings suggest that AP may exert its anti-cholestatic effects by activating the FXR pathway to promote bile acid efflux. In summary, our study unveils the significant involvement of gut microbiota in the C-sulfonate metabolism of AP and highlights the potential benefits of inhibiting APS reductase to enhance its therapeutic effects. These discoveries provide valuable insights into enhancing the clinical applicability of AP as a promising treatment for cholestatic liver injury.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Diterpenes/metabolism/pharmacology
*Biological Availability
Mice
Cholestasis/metabolism/drug therapy/microbiology
Male
RNA, Ribosomal, 16S/genetics
Bile Acids and Salts/metabolism
Bacteria/metabolism/classification/genetics/drug effects/isolation & purification
Humans
Mice, Inbred C57BL
Liver/metabolism/drug effects
Receptors, Cytoplasmic and Nuclear/metabolism/genetics
Disease Models, Animal

@article {pmid39264513,
year = {2024},
author = {Angebault, C and Botterel, F},
title = {Metagenomics Applied to the Respiratory Mycobiome in Cystic Fibrosis.},
journal = {Mycopathologia},
volume = {189},
number = {5},
pages = {82},
pmid = {39264513},
issn = {1573-0832},
mesh = {*Cystic Fibrosis/microbiology/complications ; Humans ; *Mycobiome ; *Metagenomics/methods ; Fungi/genetics/classification/isolation & purification ; Respiratory System/microbiology ; Bacteria/genetics/classification/isolation & purification ; Lung/microbiology ; Microbiota ; },
abstract = {Cystic fibrosis (CF) is a genetic disorder characterized by chronic microbial colonization and inflammation of the respiratory tract (RT), leading to pulmonary exacerbation (PEx) and lung damage. Although the lung bacterial microbiota has been extensively studied, the mycobiome remains understudied. However, its importance as a contributor to CF pathophysiology has been highlighted. The objective of this review is to provide an overview of the current state of knowledge regarding the mycobiome, as described through NGS-based studies, in patients with CF (pwCF).Several studies have demonstrated that the mycobiome in CF lungs is a dynamic entity, exhibiting a lower diversity and abundance than the bacterial microbiome. Nevertheless, the progression of lung damage is associated with a decrease in fungal and bacterial diversity. The core mycobiome of the RT in pwCFs is mainly composed of yeasts (Candida spp., Malassezia spp.) and molds with lower abundance. Some fungi (Aspergillus, Scedosporium/Pseudallescheria) have been demonstrated to play a role in PEx, while the involvement of others (Candida, Pneumocystis) remains uncertain. The "climax attack" ecological model has been proposed to explain the complexity and interplay of microbial populations in the RT, leading to PEx and lung damage. NGS-based studies also enable the detection of intra- and interkingdom correlations between fungi and bacteria. Further studies are required to ascertain the biological and pathophysiological relevance of these correlations. Finally, with the recent advent of CFTR modulators, our understanding of the pulmonary microbiome and mycobiome in pwCFs is about to change.},
}

*Cystic Fibrosis/microbiology/complications
Humans
*Mycobiome
*Metagenomics/methods
Fungi/genetics/classification/isolation & purification
Respiratory System/microbiology
Bacteria/genetics/classification/isolation & purification
Lung/microbiology
Microbiota

@article {pmid39259188,
year = {2024},
author = {Liu, C and Wang, Y and Zhou, Z and Wang, S and Wei, Z and Ravanbakhsh, M and Shen, Q and Xiong, W and Kowalchuk, GA and Jousset, A},
title = {Protist predation promotes antimicrobial resistance spread through antagonistic microbiome interactions.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrae169},
pmid = {39259188},
issn = {1751-7370},
abstract = {None declared.Conflicts of interestAntibiotic resistance has grown into a major public health threat. In this study, we reveal predation by protists as an overlooked driver of antibiotic resistance dissemination in the soil microbiome. While previous studies have primarily focused on the distribution of antibiotic resistance genes, our work sheds light on the pivotal role of soil protists in shaping antibiotic resistance dynamics. Using a combination of metagenomics and controlled experiments in this study, we demonstrate that protists cause an increase in antibiotic resistance. We mechanistically link this increase to a fostering of antimicrobial activity in the microbiome. Protist predation gives a competitive edge to bacteria capable of producing antagonistic secondary metabolites, which secondary metabolites promote in turn antibiotic-resistant bacteria. This study provides insights into the complex interplay between protists and soil microbiomes in regulating antibiotic resistance dynamics. This study highlights the importance of top-down control on the spread of antibiotic resistance and directly connects it to cross-kingdom interactions within the microbiome. Managing protist communities may become an important tool to control outbreaks of antibiotic resistance in the environment.},
}

@article {pmid39257028,
year = {2024},
author = {Jotta, VFM and García, GJY and Fonseca, PLC and de Mello Ferreira, A and Azevedo, V and Brenig, B and Góes-Neto, A and Badotti, F},
title = {Taxonomic and functional characterization of biofilms from a photovoltaic panel reveals high genetic and metabolic complexity of the communities.},
journal = {Journal of applied microbiology},
volume = {135},
number = {9},
pages = {},
doi = {10.1093/jambio/lxae231},
pmid = {39257028},
issn = {1365-2672},
support = {//Omics Sciences NETWORK/ ; //CEFET-MG/ ; },
mesh = {*Biofilms/growth & development ; Brazil ; *Bacteria/genetics/classification/metabolism/isolation & purification ; Metagenomics ; Ferric Compounds/metabolism ; Microbiota ; Minerals/metabolism ; Bioelectric Energy Sources/microbiology ; Iron Compounds ; },
abstract = {AIMS: Biofilms are complex microbial cell aggregates that attach to different surfaces in nature, industrial environments, or hospital settings. In photovoltaic panels (PVs), biofilms are related to significant energy conversion losses. In this study, our aim was to characterize the communities of microorganisms and the genes involved in biofilm formation.

METHODS AND RESULTS: In this study, biofilm samples collected from a PV system installed in southeastern Brazil were analyzed through shotgun metagenomics, and the microbial communities and genes involved in biofilm formation were investigated. A total of 2030 different genera were identified in the samples, many of which were classified as extremophiles or producers of exopolysaccharides. Bacteria prevailed in the samples (89%), mainly the genera Mucilaginibacter, Microbacterium, Pedobacter, Massilia, and Hymenobacter. The functional annotation revealed >12 000 genes related to biofilm formation and stress response. Genes involved in the iron transport and synthesis of c-di-GMP and c-AMP second messengers were abundant in the samples. The pathways related to these components play a crucial role in biofilm formation and could be promising targets for preventing biofilm formation in the PV. In addition, Raman spectroscopy analysis indicated the presence of hematite, goethite, and ferrite, consistent with the mineralogical composition of the regional soil and metal-resistant bacteria.

CONCLUSIONS: Taken together, our findings reveal that PV biofilms are a promising source of microorganisms of industrial interest and genes of central importance in regulating biofilm formation and persistence.},
}

*Biofilms/growth & development
Brazil
*Bacteria/genetics/classification/metabolism/isolation & purification
Metagenomics
Ferric Compounds/metabolism
Microbiota
Minerals/metabolism
Bioelectric Energy Sources/microbiology
Iron Compounds

@article {pmid39256724,
year = {2024},
author = {Gamage, BD and Ranasinghe, D and Sahankumari, A and Malavige, GN},
title = {Metagenomic analysis of colonic tissue and stool microbiome in patients with colorectal cancer in a South Asian population.},
journal = {BMC cancer},
volume = {24},
number = {1},
pages = {1124},
pmid = {39256724},
issn = {1471-2407},
support = {ASP/01/RE/MED/2018/52//University of Sri Jayewardenepura/ ; ASP/01/RE/MED/2018/52//University of Sri Jayewardenepura/ ; },
mesh = {Adult ; Aged ; Female ; Humans ; Male ; Middle Aged ; Bacteria/classification/isolation & purification ; Colon/microbiology ; *Colorectal Neoplasms/microbiology ; *Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Metagenome ; Metagenomics/methods ; RNA, Ribosomal, 16S/genetics ; South Asian People ; },
abstract = {BACKGROUND: The gut microbiome is thought to play an important role in the development of colorectal cancer (CRC). However, as the gut microbiome varies widely based on diet, we sought to investigate the gut microbiome changes in patients with CRC in a South Asian population.

METHODS: The gut microbiome was assessed by 16s metagenomic sequencing targeting the V4 hypervariable region of the bacterial 16S rRNA in stool samples (n = 112) and colonic tissue (n = 36) in 112 individuals. The cohort comprised of individuals with CRC (n = 24), premalignant lesions (n = 10), healthy individuals (n = 50) and in those with diabetes (n = 28).

RESULTS: Overall, the relative abundances of genus Fusobacterium (p < 0.001), Acinetobacter (p < 0.001), Escherichia-Shigella (p < 0.05) were significantly higher in gut tissue, while Romboutsia (p < 0.01) and Prevotella (p < 0.05) were significantly higher in stool samples. Bacteroides and Fusobacterium were the most abundant genera found in stool samples in patients with CRC. Patients with pre-malignant lesions had significantly high abundances of Christensenellaceae, Enterobacteriaceae, Mollicutes and Ruminococcaceae (p < 0.001) compared to patients with CRC, and healthy individuals. Romboutsia was significantly more abundant (p < 0.01) in stool samples in healthy individuals compared to those with CRC and diabetes.

CONCLUSION: Despite marked differences in the Sri Lankan diet compared to the typical Western diet, Bacteroides and Fusobacterium species were the most abundant in those with CRC, with Prevotella species, being most abundant in many individuals. We believe these results pave the way for possible dietary interventions for prevention of CRC in the South Asian population.},
}

Adult
Aged
Female
Humans
Male
Middle Aged
Bacteria/classification/isolation & purification
Colon/microbiology
*Colorectal Neoplasms/microbiology
*Feces/microbiology
*Gastrointestinal Microbiome/genetics
Metagenome
Metagenomics/methods
RNA, Ribosomal, 16S/genetics
South Asian People

@article {pmid39256682,
year = {2024},
author = {Wu, LH and Hu, CX and Liu, TX},
title = {Metagenomic profiling of gut microbiota in Fall Armyworm (Spodoptera frugiperda) larvae fed on different host plants.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {337},
pmid = {39256682},
issn = {1471-2180},
mesh = {Animals ; *Spodoptera/microbiology/genetics ; *Larva/microbiology ; *Gastrointestinal Microbiome/genetics ; *Metagenomics ; *Zea mays/microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Sorghum/microbiology ; Solanum lycopersicum/microbiology ; Capsicum/microbiology ; Metagenome ; },
abstract = {BACKGROUND: The fall armyworm (FAW, Spodoptera frugiperda) is a polyphagous pest known for causing significant crop damage. The gut microbiota plays a pivotal role in influencing the biology, physiology and adaptation of the host. However, understanding of the taxonomic composition and functional characteristics of the gut microbiota in FAW larvae fed on different host plants remains limited.

METHODS: This study utilized metagenomic sequencing to explore the structure, function and antibiotic resistance genes (ARGs) of the gut microbiota in FAW larvae transferred from an artificial diet to four distinct host plants: maize, sorghum, tomato and pepper.

RESULTS: The results demonstrated significant variations in gut microbiota structure among FAW larvae fed on different host plants. Firmicutes emerged as the dominant phylum, with Enterococcaceae as the dominant family and Enterococcus as the prominent genus. Notably, Enterococcus casseliflavus was frequently observed in the gut microbiota of FAW larvae across host plants. Metabolism pathways, particularly those related to carbohydrate and amino acid metabolism, played a crucial role in the adaptation of the FAW gut microbiota to different host plants. KEGG orthologs associated with the regulation of the peptide/nickel transport system permease protein in sorghum-fed larvae and the 6-phospho-β-glucosidase gene linked to glycolysis/gluconeogenesis as well as starch and sucrose metabolism in pepper-fed larvae were identified. Moreover, the study identified the top 20 ARGs in the gut microbiota of FAW larvae fed on different host plants, with the maize-fed group exhibiting the highest abundance of vanRC.

CONCLUSIONS: Our metagenomic sequencing study reveals significant variations in the gut microbiota composition and function of FAW larvae across diverse host plants. These findings underscore the intricate co-evolutionary relationship between hosts and their gut microbiota, suggesting that host transfer profoundly influences the gut microbiota and, consequently, the adaptability and pest management strategies for FAW.},
}

Animals
*Spodoptera/microbiology/genetics
*Larva/microbiology
*Gastrointestinal Microbiome/genetics
*Metagenomics
*Zea mays/microbiology
*Bacteria/classification/genetics/isolation & purification
*Sorghum/microbiology
Solanum lycopersicum/microbiology
Capsicum/microbiology
Metagenome

@article {pmid39256599,
year = {2024},
author = {Chen, Y and Zhang, KX and Liu, H and Zhu, Y and Bu, QY and Song, SX and Li, YC and Zou, H and You, XY and Zhao, GP},
title = {Impact of ginsenoside Rb1 on gut microbiome and associated changes in pharmacokinetics in rats.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {21168},
pmid = {39256599},
issn = {2045-2322},
support = {TSBICIP-CXRC-042//Tianjin Synthetic Biotechnology Innovation Capacity Improvement Projects/ ; TSBICIP-CXRC-008//Tianjin Synthetic Biotechnology Innovation Capacity Improvement Projects/ ; E2M9560201//Major Project of Haihe Laboratory of Synthetic Biology/ ; 31200035//National Natural Science Foundation of China/ ; XDC 0110300//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; },
mesh = {*Ginsenosides/pharmacokinetics/pharmacology ; Animals ; *Gastrointestinal Microbiome/drug effects ; Rats ; Male ; *Bacteroides/drug effects ; Rats, Sprague-Dawley ; Glycoside Hydrolases/metabolism ; },
abstract = {Ginsenoside Rb1 exhibits a wide range of biological activities, and gut microbiota is considered the main metabolic site for Rb1. However, the impact of gut microbiota on the pharmacokinetics of Rb1 are still uncertain. In this study, we investigated the gut microbiome changes and the pharmacokinetics after a 30 d Rb1 intervention. Results reveal that the systemic exposure and metabolic clearance rate of Rb1 and Rd were substantially affected after orally supplementing Rb1 (60 mg/kg) to rats. Significant increase in the relative abundance of Bacteroides cellulosilyticus in gut microbiota and specific glycoside hydrolase (GH) families, such as GH2, GH92, and GH20 were observed based on microbiome and metagenomic analysis. Moreover, a robust association was identified between the pharmacokinetic parameters of Rb1 and the relative abundance of specific Bacteroides species, and glycoside hydrolase families. Our study demonstrates that Rb1 administration significantly affects the gut microbiome, revealing a complex relationship between B. cellulosilyticus, key GH families, and Rb1 pharmacokinetics.},
}

*Ginsenosides/pharmacokinetics/pharmacology
Animals
*Gastrointestinal Microbiome/drug effects
Rats
Male
*Bacteroides/drug effects
Rats, Sprague-Dawley
Glycoside Hydrolases/metabolism

@article {pmid39256479,
year = {2024},
author = {Campese, L and Russo, L and Abagnale, M and Alberti, A and Bachi, G and Balestra, C and Bellardini, D and Buondonno, A and Cardini, U and Carotenuto, Y and Checcucci, G and Chiusano, ML and D'Ambra, I and d'Ippolito, G and Di Capua, I and Donnarumma, V and Fontana, A and Furia, M and Galarza-Verkovitch, D and Gallia, R and Labadie, K and Leone, S and Licandro, P and Longo, A and Maselli, M and Merquiol, L and Murano, C and Oliveira, PH and Passarelli, A and Percopo, I and Perdereau, A and Piredda, R and Raffini, F and Roncalli, V and Ruscheweyh, HJ and Russo, E and Saggiomo, M and Santinelli, C and Sarno, D and Sunagawa, S and Tramontano, F and Trano, AC and Uttieri, M and Wincker, P and Zampicinini, G and Casotti, R and Conversano, F and D'Alelio, D and Iudicone, D and Margiotta, F and Montresor, M},
title = {The NEREA Augmented Observatory: an integrative approach to marine coastal ecology.},
journal = {Scientific data},
volume = {11},
number = {1},
pages = {989},
pmid = {39256479},
issn = {2052-4463},
mesh = {*Ecosystem ; Plankton ; Metagenome ; Biodiversity ; Metagenomics ; },
abstract = {The NEREA (Naples Ecological REsearch for Augmented observatories) initiative aims to establish an augmented observatory in the Gulf of Naples (GoN), designed to advance the understanding of marine ecosystems through a holistic approach. Inspired by the Tara Oceans expedition and building on the scientific legacy of the MareChiara Long-Term Ecological Research (LTER-MC) site, NEREA integrates traditional physical, chemical, and biological measurements with state-of-the-art methodologies such as metabarcoding and metagenomics. Here we present the first 10 months of NEREA data, collected from April 2019 to January 2020, encompassing physico-chemical parameters, plankton biodiversity (e.g., microscopy and flow cytometry), prokaryotic and eukaryotic metabarcoding, a prokaryotic gene catalogue, and a collection of 3818 prokaryotic Metagenome-Assembled Genomes (MAGs). NEREA's efforts produce a significant volume of multifaceted data, which enhances our understanding of marine ecosystems and promotes the development of scientific hypotheses and ideas.},
}

*Ecosystem
Plankton
Metagenome
Biodiversity
Metagenomics

@article {pmid39256206,
year = {2024},
author = {Ashade, AO and Obayori, OS and Salam, LB and Fashola, MO and Nwaokorie, FO},
title = {Effects of anthropogenic activities on the microbial community diversity of Ologe Lagoon sediment in Lagos State, Nigeria.},
journal = {Environmental monitoring and assessment},
volume = {196},
number = {10},
pages = {918},
pmid = {39256206},
issn = {1573-2959},
mesh = {Nigeria ; *Geologic Sediments/microbiology/chemistry ; *Environmental Monitoring ; *Microbiota ; *Water Pollutants, Chemical/analysis ; Metals, Heavy/analysis ; Anthropogenic Effects ; Bacteria/classification/genetics ; Hydrocarbons/analysis ; },
abstract = {The impact of pollution on the Ologe Lagoon was assessed by comparing physicochemical properties, hydrocarbon concentrations and microbial community structures of the sediments obtained from distinct sites of the lagoon. The locations were the human activity site (OLHAS), industrial-contaminated sites (OLICS) and relatively undisturbed site (OLPS). The physicochemical properties, heavy metal concentrations and hydrocarbon profiles were determined using standard methods. The microbial community structures of the sediments were determined using shotgun next-generation sequencing (NGS), taxonomic profiling was performed using centrifuge and statistical analysis was done using statistical analysis for metagenomics profile (STAMP) and Microsoft Excel. The result showed acidic pH across all sampling points, while the nitrogen content at OLPS was low (7.44 ± 0.085 mg/L) as compared with OLHAS (44.380 ± 0.962 mg/L) and OLICS (59.485 ± 0.827 mg/L). The levels of the cadmium, lead and nickel in the three sites were above the regulatory limits. The gas chromatography flame ionization detector (GC-FID) profile revealed hydrocarbon contaminations with nC14 tetradecane > alpha xylene > nC9 nonane > acenaphthylene more enriched at OLPS. Structurally, the sediments metagenomes consisted of 43 phyla,75 classes each, 165, 161, 166 orders, 986, 927 and 866 bacterial genera and 1476, 1129, 1327 species from OLHAS, OLICS and OLPS, respectively. The dominant phyla in the sediments were Proteobacteria, Firmicutes, Actinobacteria, and Chloroflexi. The principal component ordination (PCO) showed that OLPS microbial community had a total variance of 87.7% PCO1, setting it apart from OLHAS and OLICS. OLICS and OLHAS were separated by PCO2 accounting for 12.3% variation, and the most polluted site is the OLPS.},
}

Nigeria
*Geologic Sediments/microbiology/chemistry
*Environmental Monitoring
*Microbiota
*Water Pollutants, Chemical/analysis
Metals, Heavy/analysis
Anthropogenic Effects
Bacteria/classification/genetics
Hydrocarbons/analysis

@article {pmid39255397,
year = {2024},
author = {Park, G and Kadyan, S and Hochuli, N and Salazar, G and Laitano, O and Chakrabarty, P and Efron, PA and Zafar, MA and Wilber, A and Nagpal, R},
title = {An Enteric Bacterial Infection Triggers Neuroinflammation and Neurobehavioral Impairment in 3xTg-AD Transgenic Mice.},
journal = {The Journal of infectious diseases},
volume = {230},
number = {Supplement_2},
pages = {S95-S108},
pmid = {39255397},
issn = {1537-6613},
support = {23A02//Florida Department of Health/ ; R01 AG070094/NH/NIH HHS/United States ; R01 AG070094/AG/NIA NIH HHS/United States ; //Foundation/ ; R21 AI166642/AI/NIAID NIH HHS/United States ; 440658//US Department of Agriculture/ ; R01 AI173244/AI/NIAID NIH HHS/United States ; //Infectious Diseases Society of America/ ; //Florida State University/ ; R01AI173244//US Public Health Service/ ; },
mesh = {Animals ; Mice ; *Mice, Transgenic ; *Klebsiella pneumoniae ; *Disease Models, Animal ; *Dysbiosis/microbiology/chemically induced ; *Alzheimer Disease/microbiology ; *Neuroinflammatory Diseases/microbiology ; *Gastrointestinal Microbiome/drug effects ; *Klebsiella Infections/microbiology ; *Blood-Brain Barrier/microbiology ; Brain/pathology/microbiology ; Anti-Bacterial Agents/pharmacology ; Brain-Gut Axis ; Male ; Humans ; },
abstract = {BACKGROUND: Klebsiella pneumoniae is infamous for hospital-acquired infections and sepsis, which have also been linked to Alzheimer disease (AD)-related neuroinflammatory and neurodegenerative impairment. However, its causative and mechanistic role in AD pathology remains unstudied.

METHODS: A preclinical model of K. pneumoniae enteric infection and colonization is developed in an AD model (3xTg-AD mice) to investigate whether and how K. pneumoniae pathogenesis exacerbates neuropathogenesis via the gut-blood-brain axis.

RESULTS: K. pneumoniae, particularly under antibiotic-induced dysbiosis, was able to translocate from the gut to the bloodstream by penetrating the gut epithelial barrier. Subsequently, K. pneumoniae infiltrated the brain by breaching the blood-brain barrier. Significant neuroinflammatory phenotype was observed in mice with K. pneumoniae brain infection. K. pneumoniae-infected mice also exhibited impaired neurobehavioral function and elevated total tau levels in the brain. Metagenomic analyses revealed an inverse correlation of K. pneumoniae with gut biome diversity and commensal bacteria, highlighting how antibiotic-induced dysbiosis triggers an enteroseptic "pathobiome" signature implicated in gut-brain perturbations.

CONCLUSIONS: The findings demonstrate how infectious agents following hospital-acquired infections and consequent antibiotic regimen may induce gut dysbiosis and pathobiome and increase the risk of sepsis, thereby increasing the predisposition to neuroinflammatory and neurobehavioral impairments via breaching the gut-blood-brain barrier.},
}

Animals
Mice
*Mice, Transgenic
*Klebsiella pneumoniae
*Disease Models, Animal
*Dysbiosis/microbiology/chemically induced
*Alzheimer Disease/microbiology
*Neuroinflammatory Diseases/microbiology
*Gastrointestinal Microbiome/drug effects
*Klebsiella Infections/microbiology
*Blood-Brain Barrier/microbiology
Brain/pathology/microbiology
Anti-Bacterial Agents/pharmacology
Brain-Gut Axis
Male
Humans

@article {pmid39254265,
year = {2024},
author = {Anandakumar, H and Rauch, A and Wimmer, MI and Yarritu, A and Koch, G and McParland, V and Bartolomaeus, H and Wilck, N},
title = {Segmental patterning of microbiota and immune cells in the murine intestinal tract.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2398126},
pmid = {39254265},
issn = {1949-0984},
mesh = {Animals ; *Gastrointestinal Microbiome ; Mice ; *Mice, Inbred C57BL ; *Bacteria/classification/genetics/isolation & purification/immunology ; Intestines/microbiology/immunology/cytology ; Metagenomics ; Germ-Free Life ; Female ; T-Lymphocyte Subsets/immunology ; Male ; Intestinal Mucosa/microbiology/immunology/cytology ; },
abstract = {The intestine exhibits distinct characteristics along its length, with a substantial immune cell reservoir and diverse microbiota crucial for maintaining health. This study investigates how anatomical location and regional microbiota influence intestinal immune cell abundance. Using conventionally colonized and germ-free mice, segment-specific immune cell composition and microbial communities were assessed. Metagenomic sequencing analyzed microbiome variations, while flow cytometry and immunofluorescence examined immune cell composition. Microbiome composition varied significantly along the intestine, with diversity and abundance increasing from upper to lower segments. Immune cells showed distinct segment-specific patterning influenced by microbial colonization and localization. T cell subsets displayed varied dependence on microbiome presence and anatomical location. This study highlights locoregional differences in intestinal immune cell and microbiome composition, identifying immune subsets susceptible to microbiota presence. The findings provide context for understanding immune cell alterations in disease models.},
}

Animals
*Gastrointestinal Microbiome
Mice
*Mice, Inbred C57BL
*Bacteria/classification/genetics/isolation & purification/immunology
Intestines/microbiology/immunology/cytology
Metagenomics
Germ-Free Life
Female
T-Lymphocyte Subsets/immunology
Male
Intestinal Mucosa/microbiology/immunology/cytology

@article {pmid39252078,
year = {2024},
author = {Vojvoda Zeljko, T and Kajan, K and Jalžić, B and Hu, A and Cukrov, N and Marguš, M and Cukrov, N and Marković, T and Sabatino, R and Di Cesare, A and Orlić, S},
title = {Genome-centric metagenomes unveiling the hidden resistome in an anchialine cave.},
journal = {Environmental microbiome},
volume = {19},
number = {1},
pages = {67},
pmid = {39252078},
issn = {2524-6372},
support = {KK.01.2.1.02.0335//European Union through the European Regional Development Fund/ ; KK.01.1.1.01.0003//European Union through the European Regional Development Fund/ ; KK.01.2.1.02.0335//European Union through the European Regional Development Fund/ ; CN_00000033//European Union - NextGenerationEU/ ; CN_00000033//European Union - NextGenerationEU/ ; },
abstract = {BACKGROUND: Antibiotic resistance is a critical global concern, posing significant challenges to human health and medical treatments. Studying antibiotic resistance genes (ARGs) is essential not only in clinical settings but also in diverse environmental contexts. However, ARGs in unique environments such as anchialine caves, which connect both fresh and marine water, remain largely unexplored despite their intriguing ecological characteristics.

RESULTS: We present the first study that comprehensively explores the occurrence and distribution of ARGs and mobile genetic elements (MGEs) within an anchialine cave. Utilizing metagenomic sequencing we uncovered a wide array of ARGs with the bacitracin resistance gene, bacA and multidrug resistance genes, being the most dominant. The cave's microbial community and associated resistome were significantly influenced by the salinity gradient. The discovery of novel β-lactamase variants revealed the cave's potential as a reservoir for previously undetected resistance genes. ARGs in the cave demonstrated horizontal transfer potential via plasmids, unveiling ecological implications.

CONCLUSIONS: These findings highlight the need for further exploration of the resistome in unique environments like anchialine caves. The interconnected dynamics of ARGs and MGEs within anchialine caves offer valuable insights into potential reservoirs and mechanisms of antibiotic resistance in natural ecosystems. This study not only advances our fundamental understanding but also highlights the need for a comprehensive approach to address antibiotic resistance in diverse ecological settings.},
}

@article {pmid39251745,
year = {2024},
author = {Serwecińska, L and Font-Nájera, A and Strapagiel, D and Lach, J and Tołoczko, W and Bołdak, M and Urbaniak, M},
title = {Sewage sludge fertilization affects microbial community structure and its resistome in agricultural soils.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {21034},
pmid = {39251745},
issn = {2045-2322},
support = {No. 2020/39/B/NZ9/01772//Narodowe Centrum Nauki/ ; No. 2020/39/B/NZ9/01772//Narodowe Centrum Nauki/ ; },
mesh = {*Sewage/microbiology ; *Soil Microbiology ; *Agriculture/methods ; *Fertilizers ; *Soil/chemistry ; *Microbiota/genetics/drug effects ; Bacteria/genetics/drug effects/classification ; Metagenomics/methods ; Drug Resistance, Microbial/genetics ; Poland ; },
abstract = {Global sewage sludge production is rapidly increasing, and its safe disposal is becoming an increasingly serious issue. One of the main methods of municipal sewage sludge management is based on its agricultural use. The wastewater and sewage sludge contain numerous antibiotic resistance genes (ARGs), and its microbiome differs significantly from the soil microbial community. The aim of the study was to assess the changes occurring in the soil microbial community and resistome after the addition of sewage sludge from municipal wastewater treatment plant (WWTP) in central Poland, from which the sludge is used for fertilizing agricultural soils on a regular basis. This study used a high-throughput shotgun metagenomics approach to compare the microbial communities and ARGs present in two soils fertilized with sewage sludge. The two soils represented different land uses and different physicochemical and granulometric properties. Both soils were characterized by a similar taxonomic composition of the bacterial community, despite dissimilarities between soils properties. Five phyla predominated, viz. Planctomycetes, Actinobacteria, Proteobacteria, Chloroflexi and Firmicutes, and they were present in comparable proportions in both soils. Network analysis revealed that the application of sewage sludge resulted in substantial qualitative and quantitative changes in bacterial taxonomic profile, with most abundant phyla being considerably depleted and replaced by Proteobacteria and Spirochaetes. In addition, the ratio of oligotrophic to copiotrophic bacteria substantially decreased in both amended soils. Furthermore, fertilized soils demonstrated greater diversity and richness of ARGs compared to control soils. The increased abundance concerned mainly genes of resistance to antibiotics most commonly used in human and animal medicine. The level of heavy metals in sewage sludge was low and did not exceed the standards permitted in Poland for sludge used in agriculture, and their level in fertilized soils was still inconsiderable.},
}

*Sewage/microbiology
*Soil Microbiology
*Agriculture/methods
*Fertilizers
*Soil/chemistry
*Microbiota/genetics/drug effects
Bacteria/genetics/drug effects/classification
Metagenomics/methods
Drug Resistance, Microbial/genetics
Poland

@article {pmid39251728,
year = {2024},
author = {Cai, X and Dai, J and Xie, Y and Xu, S and Liu, M},
title = {Multi-omics study unravels gut microbiota and metabolites alteration in patients with Wilson's disease.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {21025},
pmid = {39251728},
issn = {2045-2322},
support = {JCYJ20220530165400002//Shenzhen Science and Technology Innovation Program/ ; 2021R01132//Shenzhen Guangming District Economic Development Special Fund/ ; },
mesh = {Humans ; *Hepatolenticular Degeneration/metabolism/microbiology/genetics ; *Gastrointestinal Microbiome ; Female ; Male ; Adult ; RNA, Ribosomal, 16S/genetics ; Metabolomics/methods ; Feces/microbiology ; Metabolome ; Young Adult ; Bacteria/classification/metabolism/genetics/isolation & purification ; Metagenomics/methods ; Adolescent ; Multiomics ; },
abstract = {Hepatolenticular degeneration (HLD), also known as Wilson's disease (WD), is a rare autosomal recessive disorder regarding copper metabolism. Whether gut microbiota imbalance is involved in developing HLD remains unknown. A comprehensive 16S rRNA amplicon sequencing, metagenomic sequencing, and metabonomic analysis were undertaken in patients with WD to analyze the composition and function profiles of gut microbiota in patients with WD. The data demonstrated differences in gut microbiota and metabolic pathways between WD patients and normal individuals, significantly decreasing bacterial richness and diversity. The levels of Selenomonaceae and Megamonas in WD patients are significantly higher than those in healthy individuals. The relative abundances of Roseburia inulinivorans in patients with WD are lower than in healthy individuals. Compared with healthy people, the level of metabolites in patients with WD is abnormal. Leucylproline, 5-Phenylvaleric Acid and N-Desmethylclobazam, which have nutritional and protective effects, are significantly reduced fecal metabolites in patients with WD. D-Gluconic acid, which can chelate metal ions, may be a potential treatment for WD. The positive correlation it demonstrates with Alistipes indistinctus and Prevotella stercora indicates potential bacteria able to treat WD. These metabolites are mainly related to the biosynthesis of antibiotics, alpha-linolenic acid metabolism, one carbon pool by folate, nicotinate and nicotinamide metabolism. In conclusion, the data from this study elucidate novel mechanisms describing how abnormal gut miccrobiota contribute to the pathogenesis of WD and outlines new molecules for the treatment of WD.},
}

Humans
*Hepatolenticular Degeneration/metabolism/microbiology/genetics
*Gastrointestinal Microbiome
Female
Male
Adult
RNA, Ribosomal, 16S/genetics
Metabolomics/methods
Feces/microbiology
Metabolome
Young Adult
Bacteria/classification/metabolism/genetics/isolation & purification
Metagenomics/methods
Adolescent
Multiomics

@article {pmid39250478,
year = {2024},
author = {Pusa, T and Rousu, J},
title = {Stable biomarker discovery in multi-omics data via canonical correlation analysis.},
journal = {PloS one},
volume = {19},
number = {9},
pages = {e0309921},
pmid = {39250478},
issn = {1932-6203},
mesh = {Humans ; *Biomarkers/metabolism ; *Inflammatory Bowel Diseases/metabolism ; *Metabolomics/methods ; Metagenomics/methods ; Machine Learning ; Gastrointestinal Microbiome ; Multiomics ; },
abstract = {Multi-omics analysis offers a promising avenue to a better understanding of complex biological phenomena. In particular, untangling the pathophysiology of multifactorial health conditions such as the inflammatory bowel disease (IBD) could benefit from simultaneous consideration of several omics levels. However, taking full advantage of multi-omics data requires the adoption of suitable new tools. Multi-view learning, a machine learning technique that natively joins together heterogeneous data, is a natural source for such methods. Here we present a new approach to variable selection in unsupervised multi-view learning by applying stability selection to canonical correlation analysis (CCA). We apply our method, StabilityCCA, to simulated and real multi-omics data, and demonstrate its ability to find relevant variables and improve the stability of variable selection. In a case study on an IBD microbiome data set, we link together metagenomics and metabolomics, revealing a connection between their joint structure and the disease, and identifying potential biomarkers. Our results showcase the usefulness of multi-view learning in multi-omics analysis and demonstrate StabilityCCA as a powerful tool for biomarker discovery.},
}

Humans
*Biomarkers/metabolism
*Inflammatory Bowel Diseases/metabolism
*Metabolomics/methods
Metagenomics/methods
Machine Learning
Gastrointestinal Microbiome
Multiomics

@article {pmid39250184,
year = {2024},
author = {Pallen, MJ},
title = {The dynamic history of prokaryotic phyla: discovery, diversity and division.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {74},
number = {9},
pages = {},
pmid = {39250184},
issn = {1466-5034},
mesh = {*Bacteria/genetics/classification ; *Phylogeny ; Archaea/genetics/classification ; History, 20th Century ; History, 21st Century ; Prokaryotic Cells/classification ; Classification/methods ; },
abstract = {Here, I review the dynamic history of prokaryotic phyla. Following leads set by Darwin, Haeckel and Woese, the concept of phylum has evolved from a group sharing common phenotypes to a set of organisms sharing a common ancestry, with modern taxonomy based on phylogenetic classifications drawn from macromolecular sequences. Phyla came as surprising latecomers to the formalities of prokaryotic nomenclature in 2021. Since then names have been validly published for 46 prokaryotic phyla, replacing some established names with neologisms, prompting criticism and debate within the scientific community. Molecular barcoding enabled phylogenetic analysis of microbial ecosystems without cultivation, leading to the identification of candidate divisions (or phyla) from diverse environments. The introduction of metagenome-assembled genomes marked a significant advance in identifying and classifying uncultured microbial phyla. The lumper-splitter dichotomy has led to disagreements, with experts cautioning against the pressure to create a profusion of new phyla and prominent databases adopting a conservative stance. The Candidatus designation has been widely used to provide provisional status to uncultured prokaryotic taxa, with phyla named under this convention now clearly surpassing those with validly published names. The Genome Taxonomy Database (GTDB) has offered a stable, standardized prokaryotic taxonomy with normalized taxonomic ranks, which has led to both lumping and splitting of pre-existing phyla. The GTDB framework introduced unwieldy alphanumeric placeholder labels, prompting recent publication of over 100 user-friendly Latinate names for unnamed prokaryotic phyla. Most candidate phyla remain 'known unknowns', with limited knowledge of their genomic diversity, ecological roles, or environments. Whether phyla still reflect significant evolutionary and ecological partitions across prokaryotic life remains an area of active debate. However, phyla remain of practical importance for microbiome analyses, particularly in clinical research. Despite potential diminishing returns in discovery of biodiversity, prokaryotic phyla offer extensive research opportunities for microbiologists for the foreseeable future.},
}

*Bacteria/genetics/classification
*Phylogeny
Archaea/genetics/classification
History, 20th Century
History, 21st Century
Prokaryotic Cells/classification
Classification/methods

@article {pmid39248279,
year = {2024},
author = {Ohuchi, H and Asano, R and Mori, A and Ishibashi, T and Motooka, D and Nakai, M and Nakaoka, Y},
title = {Gut Dysbiosis in Patients With Fontan Circulation.},
journal = {Journal of the American Heart Association},
volume = {13},
number = {18},
pages = {e034538},
doi = {10.1161/JAHA.124.034538},
pmid = {39248279},
issn = {2047-9980},
mesh = {Humans ; Male ; *Dysbiosis ; *Fontan Procedure/adverse effects ; Female ; *Gastrointestinal Microbiome/physiology ; Adolescent ; Child ; Heart Defects, Congenital/surgery ; Case-Control Studies ; Young Adult ; Feces/microbiology ; Hemodynamics ; Biomarkers/blood/metabolism ; Adult ; },
abstract = {BACKGROUND: The process underlying Fontan pathophysiology is multifactorial and may include gut dysbiosis (GD). We investigated the presence of GD and elucidated its correlation with Fontan pathophysiology.

METHODS AND RESULTS: Gut microbiomes of 155 consecutive patients with Fontan pathophysiology and 44 healthy individuals were analyzed using 16S rRNA sequencing of bacterial DNA extracted from fecal samples. GD was evaluated on the basis of α and ß diversities of the gut microbiome and was compared with natural log-transformed C-reactive protein, hemodynamics, von Willebrand factor antigen (a bacterial translocation marker), Mac-2 binding protein glycosylation isomer (a liver fibrosis indicator), peak oxygen uptake, and heart failure hospitalization. Patients with Fontan exhibited GD in terms of α and ß diversities as compared with controls (P<0.01). Reduced α diversity was associated with a failed hemodynamic phenotype, hypoxia, high natural log-transformed C-reactive protein levels, and elevated von Willebrand factor antigen and Mac-2 binding protein glycosylation isomer levels (P<0.05-0.01). In addition to elevated von Willebrand factor antigen and hypoxia, decreased α diversity was independently correlated with a high natural log-transformed C-reactive protein level (P<0.05), which was associated with liver imaging abnormalities and a heightened risk of heart failure hospitalization (P<0.01 for both).

CONCLUSIONS: Patients with Fontan pathophysiology exhibited GD compared with healthy individuals, and GD was linked to failed hemodynamics and systemic inflammation with a poor prognosis. Therefore, GD may play a pivotal role in a failing Fontan status, including Fontan-associated liver disease, through GD-associated systemic inflammation.},
}

Humans
Male
*Dysbiosis
*Fontan Procedure/adverse effects
Female
*Gastrointestinal Microbiome/physiology
Adolescent
Child
Heart Defects, Congenital/surgery
Case-Control Studies
Young Adult
Feces/microbiology
Hemodynamics
Biomarkers/blood/metabolism
Adult

@article {pmid39248272,
year = {2024},
author = {Chen, X and He, Y and Zhou, L and Li, X and Jiang, M and Wu, M and Li, J and Chen, L and Xu, H and Gui, L and Zhou, Z},
title = {Microbial Heterogeneity Identification of Cerebral Thrombi Via Metagenomic Next-Generation Sequencing-Based Strategy.},
journal = {Journal of the American Heart Association},
volume = {13},
number = {18},
pages = {e033221},
doi = {10.1161/JAHA.123.033221},
pmid = {39248272},
issn = {2047-9980},
mesh = {Humans ; *High-Throughput Nucleotide Sequencing ; *Metagenomics/methods ; Female ; Male ; Middle Aged ; *Intracranial Thrombosis/microbiology/genetics ; Aged ; Ischemic Stroke/microbiology/genetics ; Bacteria/genetics/isolation & purification ; Microbiota/genetics ; },
abstract = {BACKGROUND: Diagnosis of the cause of cerebral thrombi is vital for recurrence prevention but also challenging. The presence of the microbiome has recently been confirmed in thrombus, suggesting a novel approach to distinguish cerebral thrombi of different origins. However, little is known about whether there is heterogeneity in microbiological colonization of cerebral thrombi of different sources.

METHODS AND RESULTS: Forty patients experiencing acute ischemic stroke were included and clinical data were collected. Metagenomic next-generation sequencing was adopted to detect bacterial and genomic signatures of human cerebral thrombi samples. We found similar species diversity between the large-artery atherosclerosis thrombi and cardioembolic thrombi but different species composition and distribution of cerebral thrombus microbiota. Compared with the group with cardioembolism, the group with large-artery atherosclerosis showed a significantly higher relative abundance of Ralstonia insidiosa among the top 10 bacterial species in cerebral thrombi. Twenty operational taxonomy units were correlated with 11 clinical indicators of ischemic stroke. The Gene Ontology enrichment analysis revealed 9 different enriched biological processes (translation and carbohydrate metabolic process, etc). The enriched Kyoto Encyclopedia of Genes and Genomes pathways included ribosome, butanoate metabolism, and sulfur metabolism.

CONCLUSIONS: This study, based on the approach of metagenomic next-generation sequencing, provides a diagnostic microbiological method to discriminate individuals with cardioembolic thrombi from those with large-artery atherosclerosis thrombi with human cerebral thrombi samples. Our findings provide a fresh perspective on microbial heterogeneity of cerebral thrombi and demonstrate biological processes and pathway features of cerebral thrombi.},
}

Humans
*High-Throughput Nucleotide Sequencing
*Metagenomics/methods
Female
Male
Middle Aged
*Intracranial Thrombosis/microbiology/genetics
Aged
Ischemic Stroke/microbiology/genetics
Bacteria/genetics/isolation & purification
Microbiota/genetics

@article {pmid39247916,
year = {2024},
author = {Lyu, X and Xu, X and Shen, S and Qin, F},
title = {Genetics causal analysis of oral microbiome on type 2 diabetes in East Asian populations: a bidirectional two-sample Mendelian randomized study.},
journal = {Frontiers in endocrinology},
volume = {15},
number = {},
pages = {1452999},
pmid = {39247916},
issn = {1664-2392},
mesh = {Humans ; *Diabetes Mellitus, Type 2/microbiology/genetics ; East Asian People/genetics ; Genetic Predisposition to Disease ; *Genome-Wide Association Study ; *Mendelian Randomization Analysis ; *Microbiota/genetics ; Mouth/microbiology ; *Saliva/microbiology ; Tongue/microbiology ; },
abstract = {INTRODUCTION: The dysbiosis of the oral microbiome is associated with the progression of various systemic diseases, including diabetes. However, the precise causal relationships remain elusive. This study aims to investigate the potential causal associations between oral microbiome and type 2 diabetes (T2D) using Mendelian randomization (MR) analyses.

METHODS: We conducted bidirectional two-sample MR analyses to investigate the impact of oral microbiome from saliva and the tongue T2D. This analysis was based on metagenome-genome-wide association studies (mgGWAS) summary statistics of the oral microbiome and a large meta-analysis of GWAS of T2D in East Asian populations. Additionally, we utilized the T2D GWAS summary statistics from the Biobank Japan (BBJ) project for replication. The MR methods employed included Wald ratio, inverse variance weighting (IVW), weighted median, MR-Egger, contamination mixture (ConMix), and robust adjusted profile score (RAPS).

RESULTS: Our MR analyses revealed genetic associations between specific bacterial species in the oral microbiome of saliva and tongue with T2D in East Asian populations. The MR results indicated that nine genera were shared by both saliva and tongue. Among these, the genera Aggregatibacter, Pauljensenia, and Prevotella were identified as risk factors for T2D. Conversely, the genera Granulicatella and Haemophilus D were found to be protective elements against T2D. However, different species within the genera Catonella, Lachnoanaerobaculum, Streptococcus, and Saccharimonadaceae TM7x exhibited multifaceted influences; some species were positively correlated with the risk of developing T2D, while others were negatively correlated.

DISCUSSION: This study utilized genetic variation tools to confirm the causal effect of specific oral microbiomes on T2D in East Asian populations. These findings provide valuable insights for the treatment and early screening of T2D, potentially informing more targeted and effective therapeutic strategies.},
}

Humans
*Diabetes Mellitus, Type 2/microbiology/genetics
East Asian People/genetics
Genetic Predisposition to Disease
*Genome-Wide Association Study
*Mendelian Randomization Analysis
*Microbiota/genetics
Mouth/microbiology
*Saliva/microbiology
Tongue/microbiology