@article {pmid39390034,
year = {2024},
author = {Delanghe, L and De Boeck, I and Van Malderen, J and Allonsius, CN and Van Rillaer, T and Bron, PA and Claes, I and Hagendorens, M and Lebeer, S and Leysen, J},
title = {Mild atopic dermatitis is characterized by increase in non-staphylococcus pathobionts and loss of specific species.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {23659},
pmid = {39390034},
issn = {2045-2322},
support = {HBC.2020.2873//Agentschap Innoveren en Ondernemen/ ; HBC.2020.2873//Agentschap Innoveren en Ondernemen/ ; 12S4222N//Fonds Wetenschappelijk Onderzoek/ ; 1S08523N//Fonds Wetenschappelijk Onderzoek/ ; 852600/ERC_/European Research Council/International ; },
mesh = {*Dermatitis, Atopic/microbiology ; Humans ; *Microbiota ; *Skin/microbiology/pathology ; Female ; Adult ; Male ; Staphylococcus aureus/genetics/isolation & purification/pathogenicity ; Bacteria/classification/genetics ; Middle Aged ; Metagenomics/methods ; },
abstract = {Atopic dermatitis is the most common inflammatory skin condition with a severe negative impact on patients' quality of life. The etiology of AD is complex and depends on age, genetics, the immune system, environmental factors, and the skin microbiome, with a key role for pathogenic Staphylococcus aureus in the development of severe AD. However, the composition of the skin microbiome in mild AD is understudied. Here, using metagenomic shallow shotgun sequencing, we showed that mild AD lesions did not show a significant difference in the diversity of the skin microbiome compared to samples from non-AD patients and that the relative abundance of S. aureus did not differ in these mild AD lesions. However, when we assessed other taxa, Mycobacterium ostraviense, Pedobacter panaciterrae_A and four Streptomyces species were identified with higher abundances in mild AD lesions and species of 15 genera were decreased in abundance. The highest fold decreases were observed for Paracoccus marcusii, Microbacterium lacticum, Micrococcus luteus, and Moraxella sp002478835. These microbiome compositional insights are a first step towards novel microbiome-based diagnostics and therapeutics for early intervention at the stage of mild AD and provide a path forward for the functional study of species involved in this often-overlooked patient population.},
}

*Dermatitis, Atopic/microbiology
Humans
*Microbiota
*Skin/microbiology/pathology
Female
Adult
Male
Staphylococcus aureus/genetics/isolation & purification/pathogenicity
Bacteria/classification/genetics
Middle Aged
Metagenomics/methods

@article {pmid39341154,
year = {2024},
author = {Gough, EK and Edens, TJ and Carr, L and Robertson, RC and Mutasa, K and Ntozini, R and Chasekwa, B and Geum, HM and Baharmand, I and Gill, SK and Mutasa, B and Mbuya, MNN and Majo, FD and Tavengwa, N and Francis, F and Tome, J and Evans, C and Kosek, M and Prendergast, AJ and Manges, AR and , },
title = {Bifidobacterium longum and microbiome maturation modify a nutrient intervention for stunting in Zimbabwean infants.},
journal = {EBioMedicine},
volume = {108},
number = {},
pages = {105362},
pmid = {39341154},
issn = {2352-3964},
mesh = {Humans ; Infant ; *Gastrointestinal Microbiome ; *Growth Disorders/prevention & control/microbiology ; Female ; Male ; Zimbabwe ; Fucosyltransferases/genetics ; Feces/microbiology ; Bifidobacterium ; Dietary Supplements ; Nutrients ; },
abstract = {BACKGROUND: Small-quantity lipid-based nutrient supplements (SQ-LNS), which has been widely tested to reduce child stunting, has largely modest effects to date, but the mechanisms underlying these modest effects are unclear. Child stunting is a longstanding indicator of chronic undernutrition and it remains a prevalent public health problem. The infant gut microbiome may be a key contributor to stunting; and mother and infant fucosyltransferase (FUT) phenotypes are important determinants of infant microbiome composition.

METHODS: We investigated whether mother-infant FUT status (n = 792) and infant gut microbiome composition (n = 354 fecal specimens from 172 infants) modified the impact of an infant and young child feeding (IYCF) intervention, that included SQ-LNS, on stunting at age 18 months in secondary analysis of a randomized trial in rural Zimbabwe.

FINDINGS: We found that the impact of the IYCF intervention on stunting was modified by: (i) mother-infant FUT2+/FUT3- phenotype (difference-in-differences -32.6% [95% CI: -55.3%, -9.9%]); (ii) changes in species composition that reflected microbiome maturation (difference-in-differences -68.1% [95% CI: -99.0%, -28.5%); and (iii) greater relative abundance of B. longum (differences-in-differences 49.1% [95% CI: 26.6%, 73.6%]). The dominant strains of B. longum when the intervention started were most similar to the proficient milk oligosaccharide utilizer subspecies infantis, which decreased with infant age and differed by mother-infant FUT2+/FUT3- phenotypes.

INTERPRETATION: These findings indicate that a persistently "younger" microbiome at initiation of the intervention reduced its benefits on stunting in areas with a high prevalence of growth restriction.

FUNDING: Bill and Melinda Gates Foundation, UK DFID/Aid, Wellcome Trust, Swiss Agency for Development and Cooperation, US National Institutes of Health, UNICEF, and Nutricia Research Foundation.},
}

Humans
Infant
*Gastrointestinal Microbiome
*Growth Disorders/prevention & control/microbiology
Female
Male
Zimbabwe
Fucosyltransferases/genetics
Feces/microbiology
Bifidobacterium
Dietary Supplements
Nutrients

@article {pmid39047732,
year = {2024},
author = {Yang, Z and Ma, J and Han, J and Li, A and Liu, G and Sun, Y and Zheng, J and Zhang, J and Chen, G and Xu, R and Sun, L and Meng, C and Gao, J and Bai, Z and Deng, W and Zhang, C and Su, J and Yao, H and Zhang, Z},
title = {Gut microbiome model predicts response to neoadjuvant immunotherapy plus chemoradiotherapy in rectal cancer.},
journal = {Med (New York, N.Y.)},
volume = {5},
number = {10},
pages = {1293-1306.e4},
doi = {10.1016/j.medj.2024.07.002},
pmid = {39047732},
issn = {2666-6340},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Rectal Neoplasms/therapy/microbiology/pathology ; Male ; Female ; Middle Aged ; *Neoadjuvant Therapy/methods ; Prospective Studies ; Aged ; *Immunotherapy/methods ; *Chemoradiotherapy/methods ; Adult ; Treatment Outcome ; Feces/microbiology ; },
abstract = {BACKGROUND: Accurate evaluation of the response to preoperative treatment enables the provision of a more appropriate personalized therapeutic schedule for locally advanced rectal cancer (LARC), which remains an enormous challenge, especially neoadjuvant immunotherapy plus chemoradiotherapy (nICRT).

METHODS: This prospective, multicenter cohort study enrolled patients with LARC from 6 centers who received nICRT. The dynamic variation in the gut microbiome during nICRT was evaluated. A species-level gut microbiome prediction (SPEED) model was developed and validated to predict the pathological complete response (pCR) to nICRT.

FINDINGS: A total of 50 patients were enrolled, 75 fecal samples were collected from 33 patients at different time points, and the pCR rate reached 42.4% (14/33). Lactobacillus and Eubacterium were observed to increase after nICRT. Additionally, significant differences in the gut microbiome were observed between responders and non-responders at baseline. Significantly higher abundances of Lachnospiraceae bacterium and Blautia wexlerae were found in responders, while Bacteroides, Prevotella, and Porphyromonas were found in non-responders. The SPEED model showcased a superior predictive performance with areas under the curve of 98.80% (95% confidence interval [CI]: 95.67%-100%) in the training cohort and 77.78% (95% CI: 65.42%-88.29%) in the validation cohort.

CONCLUSIONS: Programmed death 1 (PD-1) blockade plus concurrent long-course CRT showed a favorable pCR rate and is well tolerated in microsatellite-stable (MSS)/mismatch repair-proficient (pMMR) patients with LARC. The SPEED model can be used to predict the pCR to nICRT based on the baseline gut microbiome with high robustness and accuracy, thereby assisting clinical physicians in providing individualized management for patients with LARC.

FUNDING: This research was funded by the China National Natural Science Foundation (82202884).},
}

Humans
*Gastrointestinal Microbiome/drug effects
*Rectal Neoplasms/therapy/microbiology/pathology
Male
Female
Middle Aged
*Neoadjuvant Therapy/methods
Prospective Studies
Aged
*Immunotherapy/methods
*Chemoradiotherapy/methods
Adult
Treatment Outcome
Feces/microbiology

@article {pmid39197454,
year = {2024},
author = {Thänert, R and Schwartz, DJ and Keen, EC and Hall-Moore, C and Wang, B and Shaikh, N and Ning, J and Rouggly-Nickless, LC and Thänert, A and Ferreiro, A and Fishbein, SRS and Sullivan, JE and Radmacher, P and Escobedo, M and Warner, BB and Tarr, PI and Dantas, G},
title = {Clinical sequelae of gut microbiome development and disruption in hospitalized preterm infants.},
journal = {Cell host & microbe},
volume = {32},
number = {10},
pages = {1822-1837.e5},
pmid = {39197454},
issn = {1934-6069},
support = {K99 AI175674/AI/NIAID NIH HHS/United States ; P30 ES030283/ES/NIEHS NIH HHS/United States ; R01 AI184858/AI/NIAID NIH HHS/United States ; R01 AI155893/AI/NIAID NIH HHS/United States ; UH3 AI083265/AI/NIAID NIH HHS/United States ; 2021081/DDCF/Doris Duke Charitable Foundation/United States ; R01 HD092414/HD/NICHD NIH HHS/United States ; P30 DK052574/DK/NIDDK NIH HHS/United States ; K08 AI159384/AI/NIAID NIH HHS/United States ; T32 HD007409/HD/NICHD NIH HHS/United States ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Infant, Premature ; Infant, Newborn ; *Feces/microbiology ; *Enterocolitis, Necrotizing/microbiology ; Female ; *Metagenomics ; *Anti-Bacterial Agents/pharmacology ; Male ; Clostridioides difficile/genetics ; Intensive Care Units, Neonatal ; Infant ; Hospitalization ; Enterobacteriaceae/genetics ; Enterococcus/genetics ; Staphylococcus epidermidis ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {Aberrant preterm infant gut microbiota assembly predisposes to early-life disorders and persistent health problems. Here, we characterize gut microbiome dynamics over the first 3 months of life in 236 preterm infants hospitalized in three neonatal intensive care units using shotgun metagenomics of 2,512 stools and metatranscriptomics of 1,381 stools. Strain tracking, taxonomic and functional profiling, and comprehensive clinical metadata identify Enterobacteriaceae, enterococci, and staphylococci as primarily exploiting available niches to populate the gut microbiome. Clostridioides difficile lineages persist between individuals in single centers, and Staphylococcus epidermidis lineages persist within and, unexpectedly, between centers. Collectively, antibiotic and non-antibiotic medications influence gut microbiome composition to greater extents than maternal or baseline variables. Finally, we identify a persistent low-diversity gut microbiome in neonates who develop necrotizing enterocolitis after day of life 40. Overall, we comprehensively describe gut microbiome dynamics in response to medical interventions in preterm, hospitalized neonates.},
}

Humans
*Gastrointestinal Microbiome
*Infant, Premature
Infant, Newborn
*Feces/microbiology
*Enterocolitis, Necrotizing/microbiology
Female
*Metagenomics
*Anti-Bacterial Agents/pharmacology
Male
Clostridioides difficile/genetics
Intensive Care Units, Neonatal
Infant
Hospitalization
Enterobacteriaceae/genetics
Enterococcus/genetics
Staphylococcus epidermidis
Bacteria/classification/genetics/isolation & purification

@article {pmid39117304,
year = {2024},
author = {Mancin, L and Rollo, I and Golzato, D and Segata, N and Petri, C and Pengue, L and Vergani, L and Cassone, N and Corsini, A and Mota, JF and Sut, S and Dall'Acqua, S and Paoli, A},
title = {Short-Term Cocoa Supplementation Influences Microbiota Composition and Serum Markers of Lipid Metabolism in Elite Male Soccer Players.},
journal = {International journal of sport nutrition and exercise metabolism},
volume = {34},
number = {6},
pages = {349-361},
doi = {10.1123/ijsnem.2024-0012},
pmid = {39117304},
issn = {1543-2742},
mesh = {Humans ; Male ; *Soccer/physiology ; *Gastrointestinal Microbiome/drug effects ; Young Adult ; *Dietary Supplements ; *Lipid Metabolism/drug effects ; *Biomarkers/blood ; Polyphenols/administration & dosage/pharmacology ; Chocolate ; Cacao ; Arachidonic Acid/blood ; Adult ; Feces/microbiology/chemistry ; Eicosapentaenoic Acid/blood/administration & dosage ; Triglycerides/blood ; Sports Nutritional Physiological Phenomena ; Athletes ; },
abstract = {OBJECTIVES: Dietary strategies to improve arachidonic acid:eicosapentaenoic acid (AA:EPA) ratios are of interest due to potential reductions in inflammation and oxidative stress following exercise. The aim of this study was to investigate the impact of a novel dietary intervention, that is, the ingestion of 30 g of dark chocolate, on blood lipid profiles and gut microbiota composition in elite male soccer players.

METHODS: Professional male soccer players were randomly assigned to the experimental group (DC) provided with 30 g of dark chocolate or to the control group (WC), provided with 30 g of white chocolate, for 30 days. Before and after intervention, blood, fecal sample, and anthropometry data were collected. For each outcome, two-way repeated-measure analysis of variance was used to identify differences between baseline and endpoint (Week 4), considering treatment (dark chocolate, white chocolate) as intersubjects' factors. Metagenomic analysis was performed following the general guidelines, which relies on the bioBakery computational environment.

RESULTS: DC group showed increased plasma polyphenols (from 154.7 ± 18.6 μg gallic acid equivalents/ml to 185.11 ± 57.6 μg gallic acid equivalents/ml, Δ pre vs. post = +30.41 ± 21.50) and significant improvements in lipid profiles: total cholesterol (Δ -32.47 ± 17.18 mg/dl DC vs. Δ -2.84 ± 6.25 mg/dl WC, Time × Treatment interaction p < .001), triglycerides (Δ -6.32 ± 4.96 mg/dl DC vs. Δ -0.42 ± 6.47 mg/dl WC, Time × Treatment interaction p < .001), low-density lipoprotein (Δ -18.42 ± 17.13 mg/dl vs. Δ -2.05 ± 5.19 mg/dl WC, Time × Treatment interaction p < .001), AA/EPA ratio (Δ -5.26 ± 2.35; -54.1% DC vs. Δ -0.47 ± 0.73, -6.41% WC, Time × Treatment interaction p < .001) compared with WC group. In addition, 4 weeks of intervention showed a significant increase in high-density lipoprotein concentration in DC group (Δ + 3.26 ± 4.49 mg/dl DC vs. Δ -0.79 ± 5.12 mg/dl WC). Microbial communities in the DC group maintained a slightly higher microbial stability over time (exhibiting lower within-subject community dissimilarity).

CONCLUSION: Ingesting 30 g of dark chocolate over 4 weeks positively improved AA:EPA ratio and maintained gut microbial stability. Dark chocolate ingestion represents an effective nutritional strategy to improve blood lipid profiles in professional soccer players. What Are the Findings? Ingesting 30 g of dark chocolate for 4 weeks positively influences blood lipid AA: EPA ratio while maintaining gut microbial stability. What This Study Adds? Dietary intake of specific foods such as dark chocolate represents an alternative strategy to support the health and recovery of elite soccer players. What Impact Might This Have on Clinical Practice in the Future? From a clinical and translational perspective, dark chocolate ingestion positively modulates favorable blood lipid profiles and polyunsaturated fatty acid metabolism while maintaining gut microbial stability. Dark chocolate ingestion may be considered as an effective nutritional strategy in elite sport environments during periods of high-intensity training and congested competitions. Further research is required to determine functional outcomes associated with the observed improvements in blood lipid profiles.},
}

Humans
Male
*Soccer/physiology
*Gastrointestinal Microbiome/drug effects
Young Adult
*Dietary Supplements
*Lipid Metabolism/drug effects
*Biomarkers/blood
Polyphenols/administration & dosage/pharmacology
Chocolate
Cacao
Arachidonic Acid/blood
Adult
Feces/microbiology/chemistry
Eicosapentaenoic Acid/blood/administration & dosage
Triglycerides/blood
Sports Nutritional Physiological Phenomena
Athletes

@article {pmid39390025,
year = {2024},
author = {Larsson, A and Ericson, U and Jönsson, D and Miari, M and Athanasiadis, P and Baldanzi, G and Brunkwall, L and Hellstrand, S and Klinge, B and Melander, O and Nilsson, PM and Fall, T and Maziarz, M and Orho-Melander, M},
title = {New connections of medication use and polypharmacy with the gut microbiota composition and functional potential in a large population.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {23723},
pmid = {39390025},
issn = {2045-2322},
mesh = {*Gastrointestinal Microbiome/drug effects ; Humans ; *Polypharmacy ; Male ; Female ; Middle Aged ; Sweden ; Aged ; Adult ; },
abstract = {Medication can affect the gut microbiota composition and function. The aim of this study was to investigate connections between use of common non-antibiotic medicines and the gut microbiota composition and function in a large Swedish cohort (N = 2223). Use of 67 medications and polypharmacy (≥ 5 medications), based on self-reported and prescription registry data, were associated with the relative abundance of 881 gut metagenomic species (> 5% prevalence) and 103 gut metabolic modules (GMMs). Altogether, 97 associations of 26 medications with 40 species and of four medications with five GMMs were observed (false discovery rate < 5%). Several earlier findings were replicated like the positive associations of proton pump inhibitors (PPIs) with numerous oral species, and those of metformin with Escherichia species and with lactate consumption I and arginine degradation II. Several new associations were observed between, among others, use of antidepressants, beta-blockers, nonsteroidal anti-inflammatory drugs and calcium channel blockers, and specific species. Polypharmacy was positively associated with Enterococcus faecalis, Bacteroides uniformis, Rothia mucilaginosa, Escherichia coli and Limosilactobacillus vaginalis, and with 13 GMMs. We confirmed several previous findings and identified numerous new associations between use of medications/polypharmacy and the gut microbiota composition and functional potential. Further studies are needed to confirm the new findings.},
}

*Gastrointestinal Microbiome/drug effects
Humans
*Polypharmacy
Male
Female
Middle Aged
Sweden
Aged
Adult

@article {pmid39390011,
year = {2024},
author = {Kim, HS and Oh, SJ and Kim, BK and Kim, JE and Kim, BH and Park, YK and Yang, BG and Lee, JY and Bae, JW and Lee, CK},
title = {Dysbiotic signatures and diagnostic potential of gut microbial markers for inflammatory bowel disease in Korean population.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {23701},
pmid = {39390011},
issn = {2045-2322},
support = {2017R1A5A2014768//National Research Foundation of Korea/ ; 2021R1C1C2008556//National Research Foundation of Korea/ ; HI23C0661//Korea Health Industry Development Institute/Republic of Korea ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Dysbiosis/diagnosis/microbiology ; Female ; Male ; Republic of Korea/epidemiology ; Adult ; Middle Aged ; *Biomarkers ; *RNA, Ribosomal, 16S/genetics ; *Feces/microbiology ; *Inflammatory Bowel Diseases/microbiology/diagnosis ; Colitis, Ulcerative/microbiology/diagnosis ; Metagenomics/methods ; Crohn Disease/microbiology/diagnosis ; Case-Control Studies ; Cross-Sectional Studies ; Young Adult ; Aged ; },
abstract = {Fecal samples were collected from 640 individuals in Korea, including 523 patients with IBD (223 with Crohn's disease [CD] and 300 with ulcerative colitis [UC]) and 117 healthy controls. The samples were subjected to cross-sectional gut metagenomic analysis using 16 S rRNA sequencing and bioinformatics analysis. Patients with IBD, particularly those with CD, exhibited significantly lower alpha diversities than the healthy subjects. Differential abundance analysis revealed dysbiotic signatures, characterized by an expansion of the genus Escherichia-Shigella in patients with CD. Functional annotations showed that functional pathways related to bacterial pathogenesis and production of hydrogen sulfide (H2S) were strongly upregulated in patients with CD. A dysbiosis score, calculated based on functional characteristics, highly correlated with disease severity. Markers distinguishing between healthy subjects and patients with IBD showed accurate classification based on a small number of microbial taxa, which may be used to diagnose ambiguous cases. These findings confirm the taxonomic and functional dysbiosis of the gut microbiota in patients with IBD, especially those with CD. Taxa indicative of dysbiosis may have significant implications for future clinical research on the management and diagnosis of IBD.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Dysbiosis/diagnosis/microbiology
Female
Male
Republic of Korea/epidemiology
Adult
Middle Aged
*Biomarkers
*RNA, Ribosomal, 16S/genetics
*Feces/microbiology
*Inflammatory Bowel Diseases/microbiology/diagnosis
Colitis, Ulcerative/microbiology/diagnosis
Metagenomics/methods
Crohn Disease/microbiology/diagnosis
Case-Control Studies
Cross-Sectional Studies
Young Adult
Aged

@article {pmid39389770,
year = {2024},
author = {Xu, Y and Yan, Y and Zhou, T and Lu, Y and Yang, X and Tang, K and Liu, F},
title = {Synergy between Arbuscular Mycorrhizal Fungi and Rhizosphere Bacterial Communities Increases the Utilization of Insoluble Phosphorus and Potassium in the Soil by Maize.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.4c07428},
pmid = {39389770},
issn = {1520-5118},
abstract = {Arbuscular mycorrhizal (AM) fungi can enhance plant uptake of phosphorus (P) and potassium (K), but it is not yet clear whether rhizosphere bacteria can enhance the ability of AM fungi to acquire insoluble P and K from the soil. Here, pot experiments confirmed that AM fungus-promoted insoluble P and K uptake by plants requires rhizosphere bacteria. The changes of rhizosphere bacterial communities associated with AM fungi were explored by 16S rRNA amplicon sequencing and metagenomic sequencing. Five core bacteria genera identified were involved in P and K cycles. Synthetic community (SynCom) inoculation revealed that SynCom increased soil available P and K and its coinoculation with AM fungi increased P and K concentration in the plants. This study revealed that AM fungi interact with rhizosphere bacteria and promote insoluble P and K acquisition, which provided a foundation for the application of AM fungal-bacterial biofertilizers and was beneficial for the sustainable development of agriculture.},
}

@article {pmid39389057,
year = {2024},
author = {Hou, X and He, Y and Fang, P and Mei, SQ and Xu, Z and Wu, WC and Tian, JH and Zhang, S and Zeng, ZY and Gou, QY and Xin, GY and Le, SJ and Xia, YY and Zhou, YL and Hui, FM and Pan, YF and Eden, JS and Yang, ZH and Han, C and Shu, YL and Guo, D and Li, J and Holmes, EC and Li, ZR and Shi, M},
title = {Using artificial intelligence to document the hidden RNA virosphere.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2024.09.027},
pmid = {39389057},
issn = {1097-4172},
abstract = {Current metagenomic tools can fail to identify highly divergent RNA viruses. We developed a deep learning algorithm, termed LucaProt, to discover highly divergent RNA-dependent RNA polymerase (RdRP) sequences in 10,487 metatranscriptomes generated from diverse global ecosystems. LucaProt integrates both sequence and predicted structural information, enabling the accurate detection of RdRP sequences. Using this approach, we identified 161,979 potential RNA virus species and 180 RNA virus supergroups, including many previously poorly studied groups, as well as RNA virus genomes of exceptional length (up to 47,250 nucleotides) and genomic complexity. A subset of these novel RNA viruses was confirmed by RT-PCR and RNA/DNA sequencing. Newly discovered RNA viruses were present in diverse environments, including air, hot springs, and hydrothermal vents, with virus diversity and abundance varying substantially among ecosystems. This study advances virus discovery, highlights the scale of the virosphere, and provides computational tools to better document the global RNA virome.},
}

@article {pmid39389029,
year = {2024},
author = {Qian, J and Yeo, EN and Olm, MR},
title = {Hospitalization throws the preterm gut microbiome off-key.},
journal = {Cell host & microbe},
volume = {32},
number = {10},
pages = {1651-1653},
doi = {10.1016/j.chom.2024.09.009},
pmid = {39389029},
issn = {1934-6069},
mesh = {*Gastrointestinal Microbiome ; Humans ; Infant, Newborn ; *Feces/microbiology ; *Intensive Care Units, Neonatal ; *Metagenomics ; *Infant, Premature ; Hospitalization ; Infant ; },
abstract = {Environmental exposures substantially influence the infant gut microbiome. In this issue of Cell Host & Microbe, Thänert et al.[1] characterize how medical interventions in the neonatal intensive care unit (NICU) shape gut microbiome dynamics in the first months of life by analyzing over 2,500 fecal samples with metagenomics and metatranscriptomics.},
}

*Gastrointestinal Microbiome
Humans
Infant, Newborn
*Feces/microbiology
*Intensive Care Units, Neonatal
*Metagenomics
*Infant, Premature
Hospitalization
Infant

@article {pmid39384807,
year = {2024},
author = {Minot, SS and Li, N and Srinivasan, H and Ayers, JL and Yu, M and Koester, ST and Stangis, MM and Dominitz, JA and Halberg, RB and Grady, WM and Dey, N},
title = {Colorectal cancer-associated bacteria are broadly distributed in global microbiomes and drivers of precancerous change.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {23646},
pmid = {39384807},
issn = {2045-2322},
support = {K08 DK111941/DK/NIDDK NIH HHS/United States ; U54 CA274374/CA/NCI NIH HHS/United States ; R50CA233042//U.S. Department of Health and Human Services | NIH | National Cancer Institute (NCI)/ ; },
mesh = {*Colorectal Neoplasms/microbiology/genetics ; *Gastrointestinal Microbiome/genetics ; Animals ; Humans ; Mice ; *Bacteria/genetics/classification ; *Precancerous Conditions/microbiology ; Metagenomics/methods ; },
abstract = {The gut microbiome is implicated in the pathogenesis of colorectal cancer (CRC), but the full scope of this dialogue is unknown. Here we aimed to define the scale and membership of the body of CRC- and health-associated gut bacteria in global populations. We performed a microbiome-CRC correlation analysis of published ultra-deep shotgun metagenomic sequencing data from global microbiome surveys, utilizing a de novo (reference-agnostic) gene-level clustering approach to identify protein-coding co-abundant gene (CAGs) clusters. We link an unprecedented ~ 23-40% of gut bacteria to CRC or health, split nearly evenly as CRC- or health-associated. These microbes encode 2319 CAGs encompassing 427,261 bacterial genes significantly enriched or depleted in CRC. We identified many microbes that had not previously been linked to CRC, thus expanding the scope of "known unknowns" of CRC-associated microbes. We performed an agnostic CAG-based screen of bacterial isolates and validated predicted effects of previously unimplicated bacteria in preclinical models, in which we observed differential induction of precancerous adenomas and field effects. Single-cell RNA sequencing disclosed microbiome-induced senescence-associated gene expression signatures in discrete colonic populations including fibroblasts. In organoid co-cultures, primary colon fibroblasts from mice with microbiomes promoted significantly greater growth than fibroblasts from microbiome-depleted mice. These results offer proof-of-principle for gene-level metagenomic analysis enabling discovery of microbiome links to health and demonstrate that the microbiome can drive precancer states, thereby potentially revealing novel cancer prevention opportunities.},
}

*Colorectal Neoplasms/microbiology/genetics
*Gastrointestinal Microbiome/genetics
Animals
Humans
Mice
*Bacteria/genetics/classification
*Precancerous Conditions/microbiology
Metagenomics/methods

@article {pmid39307865,
year = {2024},
author = {Gundogdu, A and Nalbantoglu, OU and Karis, G and Sarikaya, I and Erdogan, MN and Hora, M and Aslan, H},
title = {Comparing microbial communities in mucilage and seawater samples: Metagenomic insights into mucilage formation in the Marmara Sea.},
journal = {Environmental science and pollution research international},
volume = {31},
number = {48},
pages = {58363-58374},
pmid = {39307865},
issn = {1614-7499},
support = {121G128//The Scientific and Technological Research Council of Turkey (TUBITAK)/ ; },
mesh = {*Seawater/microbiology ; *Microbiota ; Metagenomics ; Bacteria/genetics ; },
abstract = {Marine environments are subject to various naturally occurring phenomena, including marine snow and mucilage. In 2021, the rapid emergence of mucilage in the Marmara Sea raised concerns about its environmental impact. This study investigates the microbial communities in mucilage and seawater samples from the Marmara Sea using metagenomic-scale comparative analyses. The results indicate significant differences in microbial composition and diversity, with mucilage samples showing higher levels of polysaccharide biosynthesis-related enzymes. Over 50% of reads in mucilage samples remained unclassified (dark matter), highlighting unknown microbial taxa. Clean seawater was characterized by a higher presence of Euryarchaeota, Proteobacteria, and Rhodothermaeota, while Chlamydiae and Fusobacteria were dominant in mucilage. The study underscores the necessity for comprehensive metagenomic analyses to understand microbial roles in mucilage formation and persistence. Early detection of microbial shifts could serve as a warning system for mucilage outbreaks, aiding in the development of management strategies.},
}

*Seawater/microbiology
*Microbiota
Metagenomics
Bacteria/genetics

@article {pmid39044605,
year = {2024},
author = {Xu, H and Zhang, J and Wang, F and Chen, Y and Chen, H and Feng, Y and Hou, G and Zi, J and Zhang, M and Zhou, J and Deng, L and Lin, L and Zhang, X and Liu, S},
title = {Integration of metagenomics and metaproteomics in the intestinal lavage fluids benefits construction of discriminative model and discovery of biomarkers for HBV liver diseases.},
journal = {Proteomics},
volume = {24},
number = {20},
pages = {e2400002},
doi = {10.1002/pmic.202400002},
pmid = {39044605},
issn = {1615-9861},
support = {2023YFC3402900//National Key Research and Development Program of China/ ; 2022YFA1304500//National Key Research and Development Program of China/ ; 2020YFE0202200//National Key Research and Development Program of China/ ; },
mesh = {Humans ; *Biomarkers/analysis/metabolism ; *Proteomics/methods ; *Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; Hepatitis B/virology/genetics/microbiology ; Female ; Adult ; Male ; Hepatitis B virus/genetics ; Machine Learning ; Middle Aged ; },
abstract = {Intestinal lavage fluid (IVF) containing the mucosa-associated microbiota instead of fecal samples was used to study the gut microbiota using different omics approaches. Focusing on the 63 IVF samples collected from healthy and hepatitis B virus-liver disease (HBV-LD), a question is prompted whether omics features could be extracted to distinguish these samples. The IVF-related microbiota derived from the omics data was classified into two enterotype sets, whereas the genomics-based enterotypes were poorly overlapped with the proteomics-based one in either distribution of microbiota or of IVFs. There is lack of molecular features in these enterotypes to specifically recognize healthy or HBV-LD. Running machine learning against the omics data sought the appropriate models to discriminate the healthy and HBV-LD IVFs based on selected genes or proteins. Although a single omics dataset is basically workable in such discrimination, integration of the two datasets enhances discrimination efficiency. The protein features with higher frequencies in the models are further compared between healthy and HBV-LD based on their abundance, bringing about three potential protein biomarkers. This study highlights that integration of metaomics data is beneficial for a molecular discriminator of healthy and HBV-LD, and reveals the IVF samples are valuable for microbiome in a small cohort.},
}

Humans
*Biomarkers/analysis/metabolism
*Proteomics/methods
*Metagenomics/methods
*Gastrointestinal Microbiome/genetics
Hepatitis B/virology/genetics/microbiology
Female
Adult
Male
Hepatitis B virus/genetics
Machine Learning
Middle Aged

@article {pmid39380016,
year = {2024},
author = {Ju, Y and Zhang, Z and Liu, M and Lin, S and Sun, Q and Song, Z and Liang, W and Tong, X and Jie, Z and Lu, H and Cai, K and Chen, P and Jin, X and Zhang, W and Xu, X and Yang, H and Wang, J and Hou, Y and Xiao, L and Jia, H and Zhang, T and Guo, R},
title = {Integrated large-scale metagenome assembly and multi-kingdom network analyses identify sex differences in the human nasal microbiome.},
journal = {Genome biology},
volume = {25},
number = {1},
pages = {257},
pmid = {39380016},
issn = {1474-760X},
mesh = {Humans ; Male ; Female ; *Metagenome ; *Microbiota ; Adult ; Nose/microbiology ; Sex Characteristics ; Young Adult ; Bacteria/genetics/classification ; Sex Factors ; Metagenomics/methods ; },
abstract = {BACKGROUND: Respiratory diseases impose an immense health burden worldwide. Epidemiological studies have revealed extensive disparities in the incidence and severity of respiratory tract infections between men and women. It has been hypothesized that there might also be a nasal microbiome axis contributing to the observed sex disparities.

RESULTS: Here, we study the nasal microbiome of healthy young adults in the largest cohort to date with 1593 individuals, using shotgun metagenomic sequencing. We compile the most comprehensive reference catalog for the nasal bacterial community containing 4197 metagenome-assembled genomes and integrate the mycobiome, to provide a valuable resource and a more holistic perspective for the understudied human nasal microbiome. We systematically evaluate sex differences and reveal extensive sex-specific features in both taxonomic and functional levels in the nasal microbiome. Through network analyses, we capture markedly higher ecological stability and antagonistic potentials in the female nasal microbiome compared to the male's. The analysis of the keystone bacteria reveals that the sex-dependent evolutionary characteristics might have contributed to these differences.

CONCLUSIONS: In summary, we construct the most comprehensive catalog of metagenome-assembled-genomes for the nasal bacterial community to provide a valuable resource for the understudied human nasal microbiome. On top of that, comparative analysis in relative abundance and microbial co-occurrence networks identify extensive sex differences in the respiratory tract community, which may help to further our understanding of the observed sex disparities in the respiratory diseases.},
}

Humans
Male
Female
*Metagenome
*Microbiota
Adult
Nose/microbiology
Sex Characteristics
Young Adult
Bacteria/genetics/classification
Sex Factors
Metagenomics/methods

@article {pmid39379175,
year = {2024},
author = {Zheng, D and Wilén, BM and Öberg, O and Wik, T and Modin, O},
title = {"Metagenomics reveal the potential for geosmin and 2-methylisoborneol production across multiple bacterial phyla in recirculating aquaculture systems".},
journal = {Environmental microbiology},
volume = {26},
number = {10},
pages = {e16696},
doi = {10.1111/1462-2920.16696},
pmid = {39379175},
issn = {1462-2920},
support = {2020-02639//Svenska Forskningsrådet Formas/ ; },
mesh = {*Metagenomics ; *Bacteria/genetics/classification/metabolism ; *Aquaculture ; *Naphthols/metabolism ; *Camphanes/metabolism ; Phylogeny ; Archaea/genetics/metabolism/classification ; Microbiota ; Metagenome ; },
abstract = {Geosmin and 2-methylisoborneol (MIB) are known to cause taste-and-odour problems in recirculating aquaculture systems (RAS). Both geosmin and MIB are microbial metabolites belonging to terpenoids. Precursors for terpenoids are biosynthesized via the methylerythritol phosphate (MEP) and the mevalonate (MVA) pathways. We carried out a metagenomic analysis of 50 samples from five RAS to investigate terpenoid biosynthesis and metabolic potential for geosmin and MIB production in RAS microbiomes. A total of 1008 metagenome-assembled genomes (MAGs) representing 26 bacterial and three archaeal phyla were recovered. Although most archaea are thought to use the MVA pathway for terpenoid precursor biosynthesis, an Iainarchaeota archaeal MAG is shown to harbour a complete set of genes encoding the MEP pathway but lacking genes associated with the MVA pathway. In this study, a total of 16 MAGs affiliated with five bacterial phyla (Acidobacteriota, Actinobacteriota, Bacteroidota, Chloroflexota, and Myxococcota) were identified as possessing potential geosmin or MIB synthases. These putative taste and odour producers were diverse, many were taxonomically unidentified at the genus or species level, and their relative abundance differed between the investigated RAS farms. The metagenomic study of the RAS microbiomes revealed a previously unknown phylogenetic diversity of the potential to produce geosmin and MIB.},
}

*Metagenomics
*Bacteria/genetics/classification/metabolism
*Aquaculture
*Naphthols/metabolism
*Camphanes/metabolism
Phylogeny
Archaea/genetics/metabolism/classification
Microbiota
Metagenome

@article {pmid39327897,
year = {2024},
author = {Dai, Z and Wang, H and Xu, J and Lu, X and Ni, P and Yang, S and Shen, Q and Wang, X and Li, W and Wang, X and Zhou, C and Zhang, W and Shan, T},
title = {Unveiling the Virome of Wild Birds: Exploring CRESS-DNA Viral Dark Matter.},
journal = {Genome biology and evolution},
volume = {16},
number = {10},
pages = {},
doi = {10.1093/gbe/evae206},
pmid = {39327897},
issn = {1759-6653},
support = {2023YFD1801301//National Key Research and Development Programs of China/ ; 82341106//National Natural Science Foundation of China/ ; 20229152//The Special Funds for Science Development of the Clinical Teaching Hospitals of Jiangsu Vocational College of Medicine/ ; },
mesh = {Animals ; *Birds/virology ; *Virome/genetics ; *DNA Viruses/genetics/classification ; Phylogeny ; Animals, Wild/virology ; Metagenomics ; DNA, Viral/genetics ; },
abstract = {Amid global health concerns and the constant threat of zoonotic diseases, this study delves into the diversity of circular replicase-encoding single-stranded DNA (CRESS-DNA) viruses within Chinese wild bird populations. Employing viral metagenomics to tackle the challenge of "viral dark matter," the research collected and analyzed 3,404 cloacal swab specimens across 26 bird families. Metagenomic analysis uncovered a rich viral landscape, with 67.48% of reads classified as viral dark matter, spanning multiple taxonomic levels. Notably, certain viral families exhibited host-specific abundance patterns, with Galliformes displaying the highest diversity. Diversity analysis categorized samples into distinct groups, revealing significant differences in viral community structure, particularly noting higher diversity in terrestrial birds compared to songbirds and unique diversity in migratory birds versus perching birds. The identification of ten novel Circoviridae viruses, seven Smacoviridae viruses, and 167 Genomoviridae viruses, along with 100 unclassified CRESS-DNA viruses, underscores the expansion of knowledge on avian-associated circular DNA viruses. Phylogenetic and structural analyses of Rep proteins offered insights into evolutionary relationships and potential functional variations among CRESS-DNA viruses. In conclusion, this study significantly enhances our understanding of the avian virome, shedding light on the intricate relationships between viral communities and host characteristics in Chinese wild bird populations. The diverse array of CRESS-DNA viruses discovered opens avenues for future research into viral evolution, spread factors, and potential ecosystem impacts.},
}

Animals
*Birds/virology
*Virome/genetics
*DNA Viruses/genetics/classification
Phylogeny
Animals, Wild/virology
Metagenomics
DNA, Viral/genetics

@article {pmid39324627,
year = {2024},
author = {Bigatton, ED and Verdenelli, RA and Haro, RJ and Ayoub, I and Barbero, FM and Martín, MP and Dubini, LE and Jorrín Novo, JV and Lucini, EI and Castillejo, MÁ},
title = {Metagenomic Analysis to Assess the Impact of Plant Growth-Promoting Rhizobacteria on Peanut (Arachis hypogaea L.) Crop Production and Soil Enzymes and Microbial Diversity.},
journal = {Journal of agricultural and food chemistry},
volume = {72},
number = {40},
pages = {22385-22397},
doi = {10.1021/acs.jafc.4c05687},
pmid = {39324627},
issn = {1520-5118},
mesh = {*Arachis/microbiology/growth & development/metabolism/genetics ; *Soil Microbiology ; *Bacillus/genetics/metabolism ; *Bradyrhizobium/genetics/metabolism/growth & development/physiology ; *Pseudomonas/genetics/physiology/growth & development ; *Metagenomics ; *Rhizosphere ; *Soil/chemistry ; Crop Production/methods ; Bacteria/genetics/classification/metabolism/enzymology/isolation & purification ; Biodiversity ; Nitrogen Fixation ; Plant Roots/microbiology/growth & development/metabolism ; },
abstract = {Peanut production could be increased through plant growth-promoting rhizobacteria (PGPR). In this regard, the present field research aimed at elucidating the impact of PGPR on peanut yield, soil enzyme activity, microbial diversity, and structure. Three PGPR strains (Bacillus velezensis, RI3; Bacillus velezensis, SC6; Pseudomonas psychrophila, P10) were evaluated, along with Bradyrhizobium japonicum (BJ), taken as a control. PGPR increased seed yield by 8%, improving the radiation use efficiency (4-14%). PGPR modified soil enzymes (fluorescein diacetate activity by 17% and dehydrogenase activity by 28%) and microbial abundance (12%). However, PGPR did not significantly alter microbial diversity; nonetheless, it modified the relative abundance of key phyla (Actinobacteria > Proteobacteria > Firmicutes) and genera (Bacillus > Arthrobacter > Pseudomonas). PGPRs modified the relative abundance of genes associated with N-fixation and nitrification while increasing genes related to N-assimilation and N-availability. PGPR improved agronomic traits without altering rhizosphere diversity.},
}

*Arachis/microbiology/growth & development/metabolism/genetics
*Soil Microbiology
*Bacillus/genetics/metabolism
*Bradyrhizobium/genetics/metabolism/growth & development/physiology
*Pseudomonas/genetics/physiology/growth & development
*Metagenomics
*Rhizosphere
*Soil/chemistry
Crop Production/methods
Bacteria/genetics/classification/metabolism/enzymology/isolation & purification
Biodiversity
Nitrogen Fixation
Plant Roots/microbiology/growth & development/metabolism

@article {pmid39265854,
year = {2024},
author = {Viglioli, M and Rizzo, SM and Alessandri, G and Fontana, F and Milani, C and Turroni, F and Mancabelli, L and Croci, N and Rivara, S and Vacondio, F and Ventura, M and Mor, M},
title = {Investigating drug-gut microbiota interactions: reductive and hydrolytic metabolism of oral glucocorticoids by in vitro artificial gut microbiota.},
journal = {International journal of pharmaceutics},
volume = {665},
number = {},
pages = {124663},
doi = {10.1016/j.ijpharm.2024.124663},
pmid = {39265854},
issn = {1873-3476},
mesh = {*Gastrointestinal Microbiome/drug effects ; *Glucocorticoids/metabolism/administration & dosage ; Humans ; *Feces/microbiology ; Hydrolysis ; Administration, Oral ; Prodrugs/metabolism ; Fermentation ; },
abstract = {Elucidation of the role of gut microbiota in the metabolism of orally administered drugs may improve therapeutic effectiveness and contribute to the development of personalized medicine. In this study, ten different artificial gut microbiota (AGM), obtained by culturing fecal samples in a continuous fermentation system, were challenged for their metabolizing capacity on a panel of six glucocorticoids selected from either prodrugs or drugs. Data from metabolic stability assays highlighted that, while the hydrolysis-mediated conversion of prodrugs to drugs represented only a minor metabolic pathway, significant differences in the stability of parent compounds and in their conversion rates to multiple reductive metabolites were obtained for the selected drugs. In the latter case, a taxonomic composition-dependent ability to convert parent drugs to metabolites was observed. Indeed, the artificial microbial communities dominated by the genus Bacteroides showed the maximal conversion of parent glucocorticoids to several metabolites. Furthermore, the effect of drugs on AGM was also evaluated through shallow shotgun sequencing and flow cytometry-based total bacterial cell count highlighting that these drugs can affect both the taxonomic composition and growth performances of the human gut microbiota.},
}

*Gastrointestinal Microbiome/drug effects
*Glucocorticoids/metabolism/administration & dosage
Humans
*Feces/microbiology
Hydrolysis
Administration, Oral
Prodrugs/metabolism
Fermentation

@article {pmid39196507,
year = {2024},
author = {Qian, Y and Sorgen, AA and Steffen, KJ and Heinberg, LJ and Reed, K and Carroll, IM},
title = {Intestinal Energy Harvest Mediates Gut Microbiota-Associated Weight Loss Following Bariatric Surgery.},
journal = {Obesity surgery},
volume = {34},
number = {10},
pages = {3771-3780},
pmid = {39196507},
issn = {1708-0428},
support = {1R01DK112585-01//National Institute of Health/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Weight Loss/physiology ; Female ; Male ; *Bariatric Surgery ; *Obesity, Morbid/surgery/microbiology ; Adult ; Middle Aged ; Energy Metabolism ; Feces/microbiology ; },
abstract = {PURPOSE: Metabolic and bariatric surgery (MBS) is the most effective treatment for class III obesity. The capacity to efficiently extract intestinal energy is potentially a determinant of varying weight loss outcomes post-MBS. Prior research indicated that intestinal energy harvest is correlated with post-MBS weight loss. Studies have also demonstrated that the gut microbiota is associated with weight loss post-MBS. We aim to investigate whether gut microbiota-associated weight loss is mediated by intestinal energy harvest in patients post-MBS.

MATERIALS AND METHODS: We examined the relationship between specific gut microbiota, intestinal energy harvest, diet, and weight loss using fecal metagenomic sequence data, bomb calorimetry (fecal energy content as a proxy for calorie absorption), and a validated dietary questionnaire on 67 individuals before and after MBS. Mediation analysis and a machine learning algorithm were conducted.

RESULTS: Intestinal energy harvest was a mediator in the relationship between the intestinal microbiota (Bacteroides caccae) and weight loss outcomes in patients post-MBS at 18 months (M). The association between the abundance of B. caccae and post-MBS weight loss rate at 18 M was partly mediated by 1 M intestinal energy harvest (β = 0.001 ± 0.001, P = 0.020). This mediation represents 2.83% of the total effect (β = 0.050 ± 0.047; P = 0.028). Intestinal microbiota and energy harvest improved random forest model's accuracy in predicting weight loss results.

CONCLUSION: Energy harvest partly mediates the relationship between the intestinal microbiota and weight loss outcomes among patients post-MBS. This study elucidates a potential mechanism regarding how intestinal energy absorption facilitates the effect of intestinal microbiota on energy metabolism and weight loss outcomes.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Weight Loss/physiology
Female
Male
*Bariatric Surgery
*Obesity, Morbid/surgery/microbiology
Adult
Middle Aged
Energy Metabolism
Feces/microbiology

@article {pmid39086104,
year = {2024},
author = {Macher, JN and Martínez, A and Çakir, S and Cholley, PE and Christoforou, E and Curini Galletti, M and van Galen, L and García-Cobo, M and Jondelius, U and de Jong, D and Leasi, F and Lemke, M and Rubio Lopez, I and Sánchez, N and Sørensen, MV and Todaro, MA and Renema, W and Fontaneto, D},
title = {Enhancing metabarcoding efficiency and ecological insights through integrated taxonomy and DNA reference barcoding: A case study on beach meiofauna.},
journal = {Molecular ecology resources},
volume = {24},
number = {7},
pages = {e13997},
doi = {10.1111/1755-0998.13997},
pmid = {39086104},
issn = {1755-0998},
support = {T0206/37197/2021/kg//Stemmler Foundation/ ; },
mesh = {*DNA Barcoding, Taxonomic/methods ; Animals ; *Electron Transport Complex IV/genetics ; Netherlands ; Biodiversity ; North Sea ; Invertebrates/genetics/classification ; Bathing Beaches ; Ecosystem ; Metagenomics/methods ; },
abstract = {Molecular techniques like metabarcoding, while promising for exploring diversity of communities, are often impeded by the lack of reference DNA sequences available for taxonomic annotation. Our study explores the benefits of combining targeted DNA barcoding and morphological taxonomy to improve metabarcoding efficiency, using beach meiofauna as a case study. Beaches are globally important ecosystems and are inhabited by meiofauna, microscopic animals living in the interstitial space between the sand grains, which play a key role in coastal biodiversity and ecosystem dynamics. However, research on meiofauna faces challenges due to limited taxonomic expertise and sparse sampling. We generated 775 new cytochrome c oxidase I DNA barcodes from meiofauna specimens collected along the Netherlands' west coast and combined them with the NCBI GenBank database. We analysed alpha and beta diversity in 561 metabarcoding samples from 24 North Sea beaches, a region extensively studied for meiofauna, using both the enriched reference database and the NCBI database without the additional reference barcodes. Our results show a 2.5-fold increase in sequence annotation and a doubling of species-level Operational Taxonomic Units (OTUs) identification when annotating the metabarcoding data with the enhanced database. Additionally, our analyses revealed a bell-shaped curve of OTU richness across the intertidal zone, aligning more closely with morphological analysis patterns, and more defined community dissimilarity patterns between supralittoral and intertidal sites. Our research highlights the importance of expanding molecular reference databases and combining morphological taxonomy with molecular techniques for biodiversity assessments, ultimately improving our understanding of coastal ecosystems.},
}

*DNA Barcoding, Taxonomic/methods
Animals
*Electron Transport Complex IV/genetics
Netherlands
Biodiversity
North Sea
Invertebrates/genetics/classification
Bathing Beaches
Ecosystem
Metagenomics/methods

@article {pmid39060894,
year = {2024},
author = {Wu, J and Zhang, Y and Duan, J and Wei, Y and Miao, Y},
title = {A metagenomic next-generation sequencing (mNGS)-based analysis of bronchoalveolar lavage samples in patients with an acute exacerbation of chronic obstructive pulmonary disease.},
journal = {Journal of molecular histology},
volume = {55},
number = {5},
pages = {709-719},
pmid = {39060894},
issn = {1567-2387},
support = {MTP2022A008//China Primary Health Care Foundation/ ; },
mesh = {Humans ; *Pulmonary Disease, Chronic Obstructive/microbiology/diagnosis/virology/genetics ; *High-Throughput Nucleotide Sequencing/methods ; *Bronchoalveolar Lavage Fluid/microbiology ; Male ; Female ; *Metagenomics/methods ; Aged ; *Microbiota/genetics ; Middle Aged ; Metagenome ; Bacteria/genetics/isolation & purification/classification ; Disease Progression ; },
abstract = {The role of the bronchoalveolar lavage fluid (BALF) microbiome in acute exacerbations of chronic obstructive pulmonary disease (AECOPD) remains unclear. The advent of the metagenomic next-generation sequencing (mNGS) has made it possible to reveal the complex microbiome composition of the respiratory tract. This study aimed to explore whether there are differences in the BALF microbiome of AECOPD patients with different lung functions. We enrolled 55 AECOPD patients and divided them into a mild group (n = 31) and a severe group (n = 24) according to their lung function. We collected BALF and submitted it to mNGS and bioinformatics analysis. At the species level, mNGS identified 264 bacteria, 13 fungi and 12 viruses in the mild group, and 174 bacteria, 6 fungi and 6 viruses in the severe group. Mixed bacterial and viral infection occurred in both groups. At the genus level, Rothia and Veillonella were more abundant in the mild group, while Pseudomonas and Staphylococcus were more abundant in the severe group. At the species level, compared with the mild group, the relative abundance of Haemophilus influenzae and Pseudomonas aeruginosa was increased in the severe group. Besides, the BALF microbiome composition was similar between the two groups, and there was no significant difference in α and β diversity. Forced expiratory volume in 1 s/forced vital capacity (FEV1/FVC) (%) showed no significant correlation with the Shannon or Simpson index. The microbiome abundance was different between the mild and severe groups; however, microbiome diversity was similar between the two groups. Based on our findings, Haemophilus influenzae and Pseudomonas aeruginosa may be the pathogenic bacteria that cause the difference in lung function in patients with AECOPD.},
}

Humans
*Pulmonary Disease, Chronic Obstructive/microbiology/diagnosis/virology/genetics
*High-Throughput Nucleotide Sequencing/methods
*Bronchoalveolar Lavage Fluid/microbiology
Male
Female
*Metagenomics/methods
Aged
*Microbiota/genetics
Middle Aged
Metagenome
Bacteria/genetics/isolation & purification/classification
Disease Progression

@article {pmid38605646,
year = {2024},
author = {Heston, SM and Hurst, JH and Kelly, MS},
title = {Understanding the influence of the microbiome on childhood infections.},
journal = {Expert review of anti-infective therapy},
volume = {22},
number = {7},
pages = {529-545},
doi = {10.1080/14787210.2024.2340664},
pmid = {38605646},
issn = {1744-8336},
support = {K01 AI173398/AI/NIAID NIH HHS/United States ; K12 HD105253/HD/NICHD NIH HHS/United States ; },
mesh = {Humans ; Child ; *Microbiota/physiology ; *Gastrointestinal Microbiome/physiology ; Adolescent ; Communicable Diseases/microbiology/immunology ; Vaccines/administration & dosage/immunology ; Respiratory Tract Infections/microbiology/immunology ; Disease Susceptibility ; Animals ; Immune System/microbiology ; },
abstract = {INTRODUCTION: The microbiome is known to have a substantial impact on human health and disease. However, the impacts of the microbiome on immune system development, susceptibility to infectious diseases, and vaccine-elicited immune responses are emerging areas of interest.

AREAS COVERED: In this review, we provide an overview of development of the microbiome during childhood. We highlight available data suggesting that the microbiome is critical to maturation of the immune system and modifies susceptibility to a variety of infections during childhood and adolescence, including respiratory tract infections, Clostridioides difficile infection, and sexually transmitted infections. We discuss currently available and investigational therapeutics that have the potential to modify the microbiome to prevent or treat infections among children. Finally, we review the accumulating evidence that the gut microbiome influences vaccine-elicited immune responses among children.

EXPERT OPINION: Recent advances in sequencing technologies have led to an explosion of studies associating the human microbiome with the risk and severity of infectious diseases. As our knowledge of the extent to which the microbiome influences childhood infections continues to grow, microbiome-based diagnostics and therapeutics will increasingly be incorporated into clinical practice to improve the prevention, diagnosis, and treatment of infectious diseases among children.},
}

Humans
Child
*Microbiota/physiology
*Gastrointestinal Microbiome/physiology
Adolescent
Communicable Diseases/microbiology/immunology
Vaccines/administration & dosage/immunology
Respiratory Tract Infections/microbiology/immunology
Disease Susceptibility
Animals
Immune System/microbiology

@article {pmid39378072,
year = {2024},
author = {Koohi-Moghadam, M and Watt, RM and Leung, WK},
title = {Multi-site analysis of biosynthetic gene clusters from the periodontitis oral microbiome.},
journal = {Journal of medical microbiology},
volume = {73},
number = {10},
pages = {},
doi = {10.1099/jmm.0.001898},
pmid = {39378072},
issn = {1473-5644},
mesh = {Humans ; *Periodontitis/microbiology ; *Multigene Family ; *Mouth/microbiology ; *Microbiota/genetics ; *Bacteria/genetics/classification/isolation & purification/metabolism ; Pilot Projects ; Metagenomics/methods ; Saliva/microbiology ; Adult ; Male ; Biosynthetic Pathways/genetics ; Female ; Middle Aged ; High-Throughput Nucleotide Sequencing ; Metagenome ; },
abstract = {Background. Bacteria significantly influence human health and disease, with bacterial biosynthetic gene clusters (BGCs) being crucial in the microbiome-host and microbe-microbe interactions.Gap statement. Despite extensive research into BGCs within the human gut microbiome, their roles in the oral microbiome are less understood.Aim. This pilot study utilizes high-throughput shotgun metagenomic sequencing to examine the oral microbiota in different niches, particularly focusing on the association of BGCs with periodontitis.Methodology. We analysed saliva, subgingival plaque and supragingival plaque samples from periodontitis patients (n=23) and controls (n=16). DNA was extracted from these samples using standardized protocols. The high-throughput shotgun metagenomic sequencing was then performed to obtain comprehensive genetic information from the microbial communities present in the samples.Results. Our study identified 10 742 BGCs, with certain clusters being niche-specific. Notably, aryl polyenes and bacteriocins were the most prevalent BGCs identified. We discovered several 'novel' BGCs that are widely represented across various bacterial phyla and identified BGCs that had different distributions between periodontitis and control subjects. Our systematic approach unveiled the previously unexplored biosynthetic pathways that may be key players in periodontitis.Conclusions. Our research expands the current metagenomic knowledge of the oral microbiota in both healthy and periodontally diseased states. These findings highlight the presence of novel biosynthetic pathways in the oral cavity and suggest a complex network of host-microbe and microbe-microbe interactions, potentially influencing periodontal disease. The BGCs identified in this study pave the way for future investigations into the role of small-molecule-mediated interactions within the human oral microbiota and their impact on periodontitis.},
}

Humans
*Periodontitis/microbiology
*Multigene Family
*Mouth/microbiology
*Microbiota/genetics
*Bacteria/genetics/classification/isolation & purification/metabolism
Pilot Projects
Metagenomics/methods
Saliva/microbiology
Adult
Male
Biosynthetic Pathways/genetics
Female
Middle Aged
High-Throughput Nucleotide Sequencing
Metagenome

@article {pmid39375774,
year = {2024},
author = {Kosmopoulos, JC and Klier, KM and Langwig, MV and Tran, PQ and Anantharaman, K},
title = {Viromes vs. mixed community metagenomes: choice of method dictates interpretation of viral community ecology.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {195},
pmid = {39375774},
issn = {2049-2618},
mesh = {*Virome/genetics ; *Viruses/genetics/classification/isolation & purification ; *Metagenomics/methods ; Humans ; *Metagenome ; *Genome, Viral/genetics ; Microbiota/genetics ; Soil Microbiology ; Fresh Water/virology/microbiology ; Gastrointestinal Microbiome/genetics ; },
abstract = {BACKGROUND: Viruses, the majority of which are uncultivated, are among the most abundant biological entities on Earth. From altering microbial physiology to driving community dynamics, viruses are fundamental members of microbiomes. While the number of studies leveraging viral metagenomics (viromics) for studying uncultivated viruses is growing, standards for viromics research are lacking. Viromics can utilize computational discovery of viruses from total metagenomes of all community members (hereafter metagenomes) or use physical separation of virus-specific fractions (hereafter viromes). However, differences in the recovery and interpretation of viruses from metagenomes and viromes obtained from the same samples remain understudied.

RESULTS: Here, we compare viral communities from paired viromes and metagenomes obtained from 60 diverse samples across human gut, soil, freshwater, and marine ecosystems. Overall, viral communities obtained from viromes had greater species richness and total viral genome abundances than those obtained from metagenomes, although there were some exceptions. Despite this, metagenomes still contained many viral genomes not detected in viromes. We also found notable differences in the predicted lytic state of viruses detected in viromes vs metagenomes at the time of sequencing. Other forms of variation observed include genome presence/absence, genome quality, and encoded protein content between viromes and metagenomes, but the magnitude of these differences varied by environment.

CONCLUSIONS: Overall, our results show that the choice of method can lead to differing interpretations of viral community ecology. We suggest that the choice of whether to target a metagenome or virome to study viral communities should be dependent on the environmental context and ecological questions being asked. However, our overall recommendation to researchers investigating viral ecology and evolution is to pair both approaches to maximize their respective benefits. Video Abstract.},
}

*Virome/genetics
*Viruses/genetics/classification/isolation & purification
*Metagenomics/methods
Humans
*Metagenome
*Genome, Viral/genetics
Microbiota/genetics
Soil Microbiology
Fresh Water/virology/microbiology
Gastrointestinal Microbiome/genetics

@article {pmid39375348,
year = {2024},
author = {Kang, X and Zhang, W and Li, Y and Luo, X and Schönhuth, A},
title = {HyLight: Strain aware assembly of low coverage metagenomes.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {8665},
pmid = {39375348},
issn = {2041-1723},
mesh = {*Metagenome/genetics ; *High-Throughput Nucleotide Sequencing/methods ; Metagenomics/methods ; Microbiota/genetics ; Sequence Analysis, DNA/methods ; Bacteria/genetics/classification ; Genome, Bacterial ; Software ; },
abstract = {Different strains of identical species can vary substantially in terms of their spectrum of biomedically relevant phenotypes. Reconstructing the genomes of microbial communities at the level of their strains poses significant challenges, because sequencing errors can obscure strain-specific variants. Next-generation sequencing (NGS) reads are too short to resolve complex genomic regions. Third-generation sequencing (TGS) reads, although longer, are prone to higher error rates or substantially more expensive. Limiting TGS coverage to reduce costs compromises the accuracy of the assemblies. This explains why prior approaches agree on losses in strain awareness, accuracy, tendentially excessive costs, or combinations thereof. We introduce HyLight, a metagenome assembly approach that addresses these challenges by implementing the complementary strengths of TGS and NGS data. HyLight employs strain-resolved overlap graphs (OG) to accurately reconstruct individual strains within microbial communities. Our experiments demonstrate that HyLight produces strain-aware and contiguous assemblies at minimal error content, while significantly reducing costs because utilizing low-coverage TGS data. HyLight achieves an average improvement of 19.05% in preserving strain identity and demonstrates near-complete strain awareness across diverse datasets. In summary, HyLight offers considerable advances in metagenome assembly, insofar as it delivers significantly enhanced strain awareness, contiguity, and accuracy without the typical compromises observed in existing approaches.},
}

*Metagenome/genetics
*High-Throughput Nucleotide Sequencing/methods
Metagenomics/methods
Microbiota/genetics
Sequence Analysis, DNA/methods
Bacteria/genetics/classification
Genome, Bacterial
Software

@article {pmid39264053,
year = {2024},
author = {Ho, L and Lai, C and Daim, LDJ and Noh, NM and Yap, Y and Ibrahim, J and Teh, C},
title = {Deciphering root-associated microbial communities in asymptomatic oil palm seedlings exposed to Ganoderma boninense: new insight into disease tolerance of oil palms.},
journal = {FEMS microbiology ecology},
volume = {100},
number = {10},
pages = {},
doi = {10.1093/femsec/fiae122},
pmid = {39264053},
issn = {1574-6941},
support = {//SD Guthrie Research Sdn Bhd/ ; },
mesh = {*Ganoderma/genetics ; *Seedlings/microbiology ; *Arecaceae/microbiology ; *Soil Microbiology ; *Plant Diseases/microbiology ; *Microbiota ; *Rhizosphere ; *Plant Roots/microbiology ; Ascomycota/genetics ; Disease Resistance ; Metagenomics ; },
abstract = {Understanding the microbial communities in asymptomatic oil palm seedlings is crucial for developing disease-suppressive microbiota against basal stem rot (BSR) in oil palm. In this study, we compared the microbial communities in bulk soil, rhizosphere, and endosphere of control, asymptomatic, and symptomatic seedlings following inoculation with Ganoderma boninense. Our findings revealed significant shifts in microbial structure and interactions, particularly in asymptomatic seedlings. Both Actinobacteriota and Ascomycota were notably enriched in these samples, with Actinobacteriota identified as keystone taxa. Long-read shotgun metagenomics demonstrated that 67.4% of enriched Actinobacteriota taxa were unique to asymptomatic seedlings. Similarly, Ascomycota members showed significant enrichment, suggesting their potential role in BSR suppression. The consistent identification of these phyla across various analyses underscores their importance in disease resistance. This is the first report detailing the shifts in prokaryotic and fungal communities in asymptomatic and symptomatic seedlings, offering insights into potential disease-suppressive taxa across three compartments: bulk soil, rhizosphere, and endosphere of oil palm seedlings.},
}

*Ganoderma/genetics
*Seedlings/microbiology
*Arecaceae/microbiology
*Soil Microbiology
*Plant Diseases/microbiology
*Microbiota
*Rhizosphere
*Plant Roots/microbiology
Ascomycota/genetics
Disease Resistance
Metagenomics

@article {pmid38006569,
year = {2024},
author = {Aminu, S and Ascandari, A and Laamarti, M and Safdi, NEH and El Allali, A and Daoud, R},
title = {Exploring microbial worlds: a review of whole genome sequencing and its application in characterizing the microbial communities.},
journal = {Critical reviews in microbiology},
volume = {50},
number = {5},
pages = {805-829},
doi = {10.1080/1040841X.2023.2282447},
pmid = {38006569},
issn = {1549-7828},
mesh = {Humans ; *Metagenomics/methods ; *Microbiota/genetics ; *Bacteria/genetics/classification/isolation & purification ; Animals ; *Whole Genome Sequencing ; Genome, Bacterial ; },
abstract = {The classical microbiology techniques have inherent limitations in unraveling the complexity of microbial communities, necessitating the pivotal role of sequencing in studying the diversity of microbial communities. Whole genome sequencing (WGS) enables researchers to uncover the metabolic capabilities of the microbial community, providing valuable insights into the microbiome. Herein, we present an overview of the rapid advancements achieved thus far in the use of WGS in microbiome research. There was an upsurge in publications, particularly in 2021 and 2022 with the United States, China, and India leading the metagenomics research landscape. The Illumina platform has emerged as the widely adopted sequencing technology, whereas a significant focus of metagenomics has been on understanding the relationship between the gut microbiome and human health where distinct bacterial species have been linked to various diseases. Additionally, studies have explored the impact of human activities on microbial communities, including the potential spread of pathogenic bacteria and antimicrobial resistance genes in different ecosystems. Furthermore, WGS is used in investigating the microbiome of various animal species and plant tissues such as the rhizosphere microbiome. Overall, this review reflects the importance of WGS in metagenomics studies and underscores its remarkable power in illuminating the variety and intricacy of the microbiome in different environments.},
}

Humans
*Metagenomics/methods
*Microbiota/genetics
*Bacteria/genetics/classification/isolation & purification
Animals
*Whole Genome Sequencing
Genome, Bacterial

@article {pmid39375018,
year = {2024},
author = {Yang, Q and Zhong, Y and Feng, SW and Wen, P and Wang, H and Wu, J and Yang, S and Liang, JL and Li, D and Yang, Q and Tam, NFY and Peng, P},
title = {Temporal enrichment of comammox Nitrospira and Ca. Nitrosocosmicus in a coastal plastisphere.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrae186},
pmid = {39375018},
issn = {1751-7370},
abstract = {Plastic marine debris is known to harbor a unique microbiome (termed the "plastisphere") that can be important in marine biogeochemical cycles. However, the temporal dynamics in the plastisphere and their implications for marine biogeochemistry remain poorly understood. Here, we characterized the temporal dynamics of nitrifying communities in the plastisphere of plastic ropes exposed to a mangrove intertidal zone. The 39-month colonization experiment revealed that the relative abundances of Nitrospira and Candidatus Nitrosocosmicus representatives increased over time according to 16S rRNA gene amplicon sequencing analysis. The relative abundances of amoA genes in metagenomes implied that comammox Nitrospira were the dominant ammonia oxidizers in the plastisphere, and their dominance increased over time. The relative abundances of two metagenome-assembled genomes of comammox Nitrospira also increased with time and positively correlated with extracellular polymeric substances content of the plastisphere but negatively correlated with NH4+ concentration in seawater, indicating the long-term succession of these two parameters significantly influenced the ammonia-oxidizing community in the coastal plastisphere. At the end of the colonization experiment, the plastisphere exhibited high nitrification activity, leading to the release of N2O (2.52 ng N2O N g-1) in a 3-day nitrification experiment. The predicted relative contribution of comammox Nitrospira to N2O production (17.9%) was higher than that of ammonia-oxidizing bacteria (4.8%) but lower than that of ammonia-oxidizing archaea (21.4%). These results provide evidence that from a long-term perspective, some coastal plastispheres will become dominated by comammox Nitrospira and thereby act as hotspots of ammonia oxidation and N2O production.},
}

@article {pmid39369255,
year = {2024},
author = {Figueroa-Gonzalez, PA and Bornemann, TLV and Hinzke, T and Maaß, S and Trautwein-Schult, A and Starke, J and Moore, CJ and Esser, SP and Plewka, J and Hesse, T and Schmidt, TC and Schreiber, U and Bor, B and Becher, D and Probst, AJ},
title = {Metaproteogenomics resolution of a high-CO2 aquifer community reveals a complex cellular adaptation of groundwater Gracilibacteria to a host-dependent lifestyle.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {194},
pmid = {39369255},
issn = {2049-2618},
support = {CRC 1439/1 426547801//German Research Foundation (DFG)/ ; CRC 1439/1 426547801//German Research Foundation (DFG)/ ; },
mesh = {*Groundwater/microbiology ; Carbon Dioxide/metabolism ; Metagenomics ; Bacteria/genetics/classification/isolation & purification/metabolism ; Germany ; Genome, Bacterial ; Phylogeny ; Microbiota/genetics ; Proteogenomics ; Adaptation, Physiological ; Proteomics ; },
abstract = {BACKGROUND: Bacteria of the candidate phyla radiation (CPR), constituting about 25% of the bacterial biodiversity, are characterized by small cell size and patchy genomes without complete key metabolic pathways, suggesting a symbiotic lifestyle. Gracilibacteria (BD1-5), which are part of the CPR branch, possess alternate coded genomes and have not yet been cultivated. The lifestyle of Gracilibacteria, their temporal dynamics, and activity in natural ecosystems, particularly in groundwater, has remained largely unexplored. Here, we aimed to investigate Gracilibacteria activity in situ and to discern their lifestyle based on expressed genes, using the metaproteogenome of Gracilibacteria as a function of time in the cold-water geyser Wallender Born in the Volcanic Eifel region in Germany.

RESULTS: We coupled genome-resolved metagenomics and metaproteomics to investigate a cold-water geyser microbial community enriched in Gracilibacteria across a 12-day time-series. Groundwater was collected and sequentially filtered to fraction CPR and other bacteria. Based on 725 Gbps of metagenomic data, 1129 different ribosomal protein S3 marker genes, and 751 high-quality genomes (123 population genomes after dereplication), we identified dominant bacteria belonging to Gallionellales and Gracilibacteria along with keystone microbes, which were low in genomic abundance but substantially contributing to proteomic abundance. Seven high-quality Gracilibacteria genomes showed typical limitations, such as limited amino acid or nucleotide synthesis, in their central metabolism but no co-occurrence with potential hosts. The genomes of these Gracilibacteria were encoded for a high number of proteins involved in cell to cell interaction, supporting the previously surmised host-dependent lifestyle, e.g., type IV and type II secretion system subunits, transporters, and features related to cell motility, which were also detected on protein level.

CONCLUSIONS: We here identified microbial keystone taxa in a high-CO2 aquifer, and revealed microbial dynamics of Gracilibacteria. Although Gracilibacteria in this ecosystem did not appear to target specific organisms in this ecosystem due to lack of co-occurrence despite enrichment on 0.2-µm filter fraction, we provide proteomic evidence for the complex machinery behind the host-dependent lifestyle of groundwater Gracilibacteria. Video Abstract.},
}

*Groundwater/microbiology
Carbon Dioxide/metabolism
Metagenomics
Bacteria/genetics/classification/isolation & purification/metabolism
Germany
Genome, Bacterial
Phylogeny
Microbiota/genetics
Proteogenomics
Adaptation, Physiological
Proteomics

@article {pmid39367431,
year = {2024},
author = {Gaber, M and Wilson, AS and Millen, AE and Hovey, KM and LaMonte, MJ and Wactawski-Wende, J and Ochs-Balcom, HM and Cook, KL},
title = {Visceral adiposity in postmenopausal women is associated with a pro-inflammatory gut microbiome and immunogenic metabolic endotoxemia.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {192},
pmid = {39367431},
issn = {2049-2618},
support = {W81XWH-20-1-0014//Congressionally Directed Medical Research Programs/ ; W81XWH-20-1-0014//Congressionally Directed Medical Research Programs/ ; W81XWH-20-1-0014//Congressionally Directed Medical Research Programs/ ; R01 DE013505, R01 DE024523/DE/NIDCR NIH HHS/United States ; R01 DE013505, R01 DE024523/DE/NIDCR NIH HHS/United States ; R01 DE013505, R01 DE024523/DE/NIDCR NIH HHS/United States ; R01 DE013505, R01 DE024523/DE/NIDCR NIH HHS/United States ; R01 DE013505, R01 DE024523/DE/NIDCR NIH HHS/United States ; HHSN268201600018C, HHSN268201600001C, HHSN268201600002C, HHSN268201600003C, and HHSN268201600004C/HL/NHLBI NIH HHS/United States ; HHSN268201600018C, HHSN268201600001C, HHSN268201600002C, HHSN268201600003C, and HHSN268201600004C/HL/NHLBI NIH HHS/United States ; },
mesh = {Female ; *Gastrointestinal Microbiome/drug effects ; *Endotoxemia/immunology/microbiology ; Humans ; *Postmenopause ; Animals ; Aged ; Mice ; *Lipopolysaccharides ; Intra-Abdominal Fat/metabolism/immunology ; Inflammation ; Aged, 80 and over ; Mice, Inbred C57BL ; Adiposity ; Bacteria/classification/isolation & purification/metabolism/genetics ; Acute-Phase Proteins/metabolism ; Feces/microbiology ; Obesity, Abdominal/microbiology/immunology ; Absorptiometry, Photon ; Carrier Proteins ; Membrane Glycoproteins ; },
abstract = {BACKGROUND: Obesity, and in particular abdominal obesity, is associated with an increased risk of developing a variety of chronic diseases. Obesity, aging, and menopause are each associated with differential shifts in the gut microbiome. Obesity causes chronic low-grade inflammation due to increased lipopolysaccharide (LPS) levels which is termed "metabolic endotoxemia." We examined the association of visceral adiposity tissue (VAT) area, circulating endotoxemia markers, and the gut bacterial microbiome in a cohort of aged postmenopausal women.

METHODS: Fifty postmenopausal women (mean age 78.8 ± 5.3 years) who had existing adipose measurements via dual x-ray absorptiometry (DXA) were selected from the extremes of VAT: n = 25 with low VAT area (45.6 ± 12.5 cm[2]) and n = 25 with high VAT area (177.5 ± 31.3 cm[2]). Dietary intake used to estimate the Healthy Eating Index (HEI) score was assessed with a food frequency questionnaire. Plasma LPS, LPS-binding protein (LBP), anti-LPS antibodies, anti-flagellin antibodies, and anti-lipoteichoic acid (LTA) antibodies were measured by ELISA. Metagenomic sequencing was performed on fecal DNA. Female C57BL/6 mice consuming a high-fat or low-fat diet were treated with 0.4 mg/kg diet-derived fecal isolated LPS modeling metabolic endotoxemia, and metabolic outcomes were measured after 6 weeks.

RESULTS: Women in the high VAT group showed increased Proteobacteria abundance and a lower Firmicutes/Bacteroidetes ratio. Plasma LBP concentration was positively associated with VAT area. Plasma anti-LPS, anti-LTA, and anti-flagellin IgA antibodies were significantly correlated with adiposity measurements. Women with high VAT showed significantly elevated LPS-expressing bacteria compared to low VAT women. Gut bacterial species that showed significant associations with both adiposity and inflammation (anti-LPS IgA and LBP) were Proteobacteria (Escherichia coli, Shigella spp., and Klebsiella spp.) and Veillonella atypica. Healthy eating index (HEI) scores negatively correlated with % body fat and anti-LPS IgA antibodies levels. Preclinical murine model showed that high-fat diet-fed mice administered a low-fat diet fecal-derived LPS displayed reduced body weight, decreased % body fat, and improved glucose tolerance test parameters when compared with saline-injected or high-fat diet fecal-derived LPS-treated groups consuming a high-fat diet.

CONCLUSIONS: Increased VAT in postmenopausal women is associated with elevated gut Proteobacteria abundance and immunogenic metabolic endotoxemia markers. Low-fat diet-derived fecal-isolated LPS improved metabolic parameters in high-fat diet-fed mice giving mechanistic insights into potential pro-health signaling mediated by under-acylated LPS isoforms. Video Abstract.},
}

Female
*Gastrointestinal Microbiome/drug effects
*Endotoxemia/immunology/microbiology
Humans
*Postmenopause
Animals
Aged
Mice
*Lipopolysaccharides
Intra-Abdominal Fat/metabolism/immunology
Inflammation
Aged, 80 and over
Mice, Inbred C57BL
Adiposity
Bacteria/classification/isolation & purification/metabolism/genetics
Acute-Phase Proteins/metabolism
Feces/microbiology
Obesity, Abdominal/microbiology/immunology
Absorptiometry, Photon
Carrier Proteins
Membrane Glycoproteins

@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 {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 = {},
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 {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 {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 = {},
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 {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 {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 {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},
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 {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 {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 {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 {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 {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 {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 {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 {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 {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 {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 {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 {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 {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 {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 {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

@article {pmid39245657,
year = {2024},
author = {Lee, S and Meslier, V and Bidkhori, G and Garcia-Guevara, F and Etienne-Mesmin, L and Clasen, F and Park, J and Plaza Oñate, F and Cai, H and Le Chatelier, E and Pons, N and Pereira, M and Seifert, M and Boulund, F and Engstrand, L and Lee, D and Proctor, G and Mardinoglu, A and Blanquet-Diot, S and Moyes, D and Almeida, M and Ehrlich, SD and Uhlen, M and Shoaie, S},
title = {Transient colonizing microbes promote gut dysbiosis and functional impairment.},
journal = {NPJ biofilms and microbiomes},
volume = {10},
number = {1},
pages = {80},
pmid = {39245657},
issn = {2055-5008},
support = {EP/S001301/1//RCUK | Engineering and Physical Sciences Research Council (EPSRC)/ ; BB/S016899/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; N/A//Science for Life Laboratory (SciLifeLab)/ ; },
mesh = {*Dysbiosis/microbiology ; *Gastrointestinal Microbiome ; Humans ; *Metagenomics/methods ; Sweden ; *Bacteria/classification/genetics/isolation & purification ; *Feces/microbiology ; Longitudinal Studies ; Metagenome ; Adult ; Bioreactors/microbiology ; Fermentation ; },
abstract = {Species composition of the healthy adult gut microbiota tends to be stable over time. Destabilization of the gut microbiome under the influence of different factors is the main driver of the microbial dysbiosis and subsequent impacts on host physiology. Here, we used metagenomics data from a Swedish longitudinal cohort, to determine the stability of the gut microbiome and uncovered two distinct microbial species groups; persistent colonizing species (PCS) and transient colonizing species (TCS). We validated the continuation of this grouping, generating gut metagenomics data for additional time points from the same Swedish cohort. We evaluated the existence of PCS/TCS across different geographical regions and observed they are globally conserved features. To characterize PCS/TCS phenotypes, we performed bioreactor fermentation with faecal samples and metabolic modeling. Finally, using chronic disease gut metagenome and other multi-omics data, we identified roles of TCS in microbial dysbiosis and link with abnormal changes to host physiology.},
}

*Dysbiosis/microbiology
*Gastrointestinal Microbiome
Humans
*Metagenomics/methods
Sweden
*Bacteria/classification/genetics/isolation & purification
*Feces/microbiology
Longitudinal Studies
Metagenome
Adult
Bioreactors/microbiology
Fermentation

@article {pmid39245190,
year = {2024},
author = {Huang, J and Liu, S and Li, P and Wei, L and Lin, G and Lin, J and Luo, Y and Liu, Y and Mao, Y and Ruan, H and Qin, B and Fan, P and Lu, T and Cai, W and Yi, H and Mou, X and Lu, Z and Zhao, W and Wu, A},
title = {Multi-omics analysis of gut-brain axis reveals novel microbial and neurotransmitter signatures in patients with arteriosclerotic cerebral small vessel disease.},
journal = {Pharmacological research},
volume = {208},
number = {},
pages = {107385},
doi = {10.1016/j.phrs.2024.107385},
pmid = {39245190},
issn = {1096-1186},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Cerebral Small Vessel Diseases/metabolism/microbiology ; Male ; *Brain-Gut Axis ; Female ; Aged ; Middle Aged ; *Neurotransmitter Agents/metabolism ; *Dysbiosis/microbiology ; Metabolomics ; Bacteria/metabolism/genetics ; Metabolome ; Multiomics ; },
abstract = {Arteriosclerotic cerebral small vessel disease (aCSVD) is a major cause of stroke and dementia. Although its underlying pathogenesis remains poorly understood, both inflammaging and gut microbiota dysbiosis have been hypothesized to play significant roles. This study investigated the role of gut microbiota in the pathogenesis of aCSVD through a comparative analysis of the gut microbiome and metabolome between CSVD patients and healthy controls. The results showed that patients with aCSVD exhibited a marked reduction in potentially beneficial bacterial species, such as Faecalibacterium prausnitzli and Roseburia intestinalis, alongside an increase in taxa from Bacteroides and Proteobacteria. Integrated metagenomic and metabolomic analyses revealed that alterations in microbial metabolic pathways, including LPS biosynthesis and phenylalanine-tyrosine metabolism, were associated with the status of aCSVD. Our findings indicated that microbial LPS biosynthesis and phenylalanine-tyrosine metabolism potentially influenced the symptoms and progression of aCSVD via pro-inflammatory effect and modulation of systemic neurotransmitters, respectively. These results imply that gut microbiota characteristics may serve as indicators for early detection of aCSVD and as potential gut-directed therapeutic intervention target.},
}

Humans
*Gastrointestinal Microbiome
*Cerebral Small Vessel Diseases/metabolism/microbiology
Male
*Brain-Gut Axis
Female
Aged
Middle Aged
*Neurotransmitter Agents/metabolism
*Dysbiosis/microbiology
Metabolomics
Bacteria/metabolism/genetics
Metabolome
Multiomics

@article {pmid39244633,
year = {2024},
author = {Li, F and Liu, J and Maldonado-Gómez, MX and Frese, SA and Gänzle, MG and Walter, J},
title = {Highly accurate and sensitive absolute quantification of bacterial strains in human fecal samples.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {168},
pmid = {39244633},
issn = {2049-2618},
mesh = {Humans ; *Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; *Limosilactobacillus reuteri/genetics/classification ; Reproducibility of Results ; DNA, Bacterial/genetics ; Real-Time Polymerase Chain Reaction/methods ; High-Throughput Nucleotide Sequencing/methods ; Limit of Detection ; Sensitivity and Specificity ; Bacteria/genetics/classification/isolation & purification ; },
abstract = {BACKGROUND: Next-generation sequencing (NGS) approaches have revolutionized gut microbiome research and can provide strain-level resolution, but these techniques have limitations in that they are only semi-quantitative, suffer from high detection limits, and generate data that is compositional. The present study aimed to systematically compare quantitative PCR (qPCR) and droplet digital PCR (ddPCR) for the absolute quantification of Limosilactobacillus reuteri strains in human fecal samples and to develop an optimized protocol for the absolute quantification of bacterial strains in fecal samples.

RESULTS: Using strain-specific PCR primers for L. reuteri 17938, ddPCR showed slightly better reproducibility, but qPCR was almost as reproducible and showed comparable sensitivity (limit of detection [LOD] around 10[4] cells/g feces) and linearity (R[2] > 0.98) when kit-based DNA isolation methods were used. qPCR further had a wider dynamic range and is cheaper and faster. Based on these findings, we conclude that qPCR has advantages over ddPCR for the absolute quantification of bacterial strains in fecal samples. We provide an optimized and easy-to-follow step-by-step protocol for the design of strain-specific qPCR assays, starting from primer design from genome sequences to the calibration of the PCR system. Validation of this protocol to design PCR assays for two L. reuteri strains, PB-W1 and DSM 20016[ T], resulted in a highly accurate qPCR with a detection limit in spiked fecal samples of around 10[3] cells/g feces. Applying our strain-specific qPCR assays to fecal samples collected from human subjects who received live L. reuteri PB-W1 or DSM 20016[ T] during a human trial demonstrated a highly accurate quantification and sensitive detection of these two strains, with a much lower LOD and a broader dynamic range compared to NGS approaches (16S rRNA gene sequencing and whole metagenome sequencing).

CONCLUSIONS: Based on our analyses, we consider qPCR with kit-based DNA extraction approaches the best approach to accurately quantify gut bacteria at the strain level in fecal samples. The provided step-by-step protocol will allow scientists to design highly sensitive strain-specific PCR systems for the accurate quantification of bacterial strains of not only L. reuteri but also other bacterial taxa in a broad range of applications and sample types. Video Abstract.},
}

Humans
*Feces/microbiology
*Gastrointestinal Microbiome/genetics
*Limosilactobacillus reuteri/genetics/classification
Reproducibility of Results
DNA, Bacterial/genetics
Real-Time Polymerase Chain Reaction/methods
High-Throughput Nucleotide Sequencing/methods
Limit of Detection
Sensitivity and Specificity
Bacteria/genetics/classification/isolation & purification

@article {pmid39244624,
year = {2024},
author = {Yang, X and Feng, K and Wang, S and Yuan, MM and Peng, X and He, Q and Wang, D and Shen, W and Zhao, B and Du, X and Wang, Y and Wang, L and Cao, D and Liu, W and Wang, J and Deng, Y},
title = {Unveiling the deterministic dynamics of microbial meta-metabolism: a multi-omics investigation of anaerobic biodegradation.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {166},
pmid = {39244624},
issn = {2049-2618},
support = {No. 2019YFC1905001//National Key Research and Development Program of China/ ; },
mesh = {Anaerobiosis ; *Biodegradation, Environmental ; *Bioreactors/microbiology ; *Metabolomics ; *Microbiota ; Bacteria/metabolism/genetics/classification ; Metagenomics ; Methane/metabolism ; Thermodynamics ; Multiomics ; },
abstract = {BACKGROUND: Microbial anaerobic metabolism is a key driver of biogeochemical cycles, influencing ecosystem function and health of both natural and engineered environments. However, the temporal dynamics of the intricate interactions between microorganisms and the organic metabolites are still poorly understood. Leveraging metagenomic and metabolomic approaches, we unveiled the principles governing microbial metabolism during a 96-day anaerobic bioreactor experiment.

RESULTS: During the turnover and assembly of metabolites, homogeneous selection was predominant, peaking at 84.05% on day 12. Consistent dynamic coordination between microbes and metabolites was observed regarding their composition and assembly processes. Our findings suggested that microbes drove deterministic metabolite turnover, leading to consistent molecular conversions across parallel reactors. Moreover, due to the more favorable thermodynamics of N-containing organic biotransformations, microbes preferentially carried out sequential degradations from N-containing to S-containing compounds. Similarly, the metabolic strategy of C18 lipid-like molecules could switch from synthesis to degradation due to nutrient exhaustion and thermodynamical disadvantage. This indicated that community biotransformation thermodynamics emerged as a key regulator of both catabolic and synthetic metabolisms, shaping metabolic strategy shifts at the community level. Furthermore, the co-occurrence network of microbes-metabolites was structured around microbial metabolic functions centered on methanogenesis, with CH4 as a network hub, connecting with 62.15% of total nodes as 1st and 2nd neighbors. Microbes aggregate molecules with different molecular traits and are modularized depending on their metabolic abilities. They established increasingly positive relationships with high-molecular-weight molecules, facilitating resource acquisition and energy utilization. This metabolic complementarity and substance exchange further underscored the cooperative nature of microbial interactions.

CONCLUSIONS: All results revealed three key rules governing microbial anaerobic degradation. These rules indicate that microbes adapt to environmental conditions according to their community-level metabolic trade-offs and synergistic metabolic functions, further driving the deterministic dynamics of molecular composition. This research offers valuable insights for enhancing the prediction and regulation of microbial activities and carbon flow in anaerobic environments. Video Abstract.},
}

Anaerobiosis
*Biodegradation, Environmental
*Bioreactors/microbiology
*Metabolomics
*Microbiota
Bacteria/metabolism/genetics/classification
Metagenomics
Methane/metabolism
Thermodynamics
Multiomics

@article {pmid39244357,
year = {2024},
author = {Abo-Ismail, M and Sadek, MAA and Humagain, K and Banjara, N and Pokharel, S},
title = {Spatiotemporal distribution of environmental microbiota around animal farms adjacent to produce fields in central coast California.},
journal = {Food microbiology},
volume = {124},
number = {},
pages = {104598},
doi = {10.1016/j.fm.2024.104598},
pmid = {39244357},
issn = {1095-9998},
mesh = {Animals ; *Bacteria/classification/genetics/isolation & purification ; *Microbiota ; *Seasons ; *Soil Microbiology ; *Farms ; California ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; Water Microbiology ; Spatio-Temporal Analysis ; Metagenomics ; },
abstract = {This study aimed to identify different environmental microbiota in animal farms adjacent to produce fields and to understand their potential flow pattern. Soil and water samples were collected from 16 locations during the winter, spring, summer, and fall seasons. In addition, a high-resolution digital elevation model helped to create a stream network to understand the potential flow of the microbiome. Metagenomic analysis of the 16 S rRNA gene revealed that soil and water samples from the four seasons harbor diverse microbiome profiles. The phylogenetic relationship of operational taxonomic units (OTUs) is separated by a maximum of 0.6 Bray-Curtis distance. Similarly, the Principal Component Analysis (P = 0.001) demonstrated the soil and water microbiome clustering across different locations and seasons. The relative abundance of Proteobacteria, Bacteroidetes, and Firmicutes was higher in the water samples than in the soil samples. In contrast, the relative abundance of Actinobacteria and Chloroflexi was higher in the soil compared to the water samples. Soil samples in summer and water samples in spring had the highest abundance of Bacteroidetes and Firmicutes, respectively. A unique microbial community structure was found in water samples, with an increased abundance of Hydrogenophaga and Solirubrobacter. Genera that were significantly abundant at a 1% false discovery rate (FDR) among seasons and soil or water samples, include Nocardioides, Gemmatimonas, JG30-KF-CM45, Massilia, Gaiellales, Sphingomonas, KD4-96, Bacillus, Streptomyces, Gaiella, and Gemmatimonadaceae. The relative abundance of pathogenic genera, including Mycobacterium, Bacteroides, Nocardia, Clostridium, and Corynebacterium, were significantly (at 1% FDR) affected by seasons and environmental type. The elevation-based stream network model suggests the potential flow of microbiomes from the animal farm to the produce fields.},
}

Animals
*Bacteria/classification/genetics/isolation & purification
*Microbiota
*Seasons
*Soil Microbiology
*Farms
California
RNA, Ribosomal, 16S/genetics
Phylogeny
Water Microbiology
Spatio-Temporal Analysis
Metagenomics

@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 {pmid39243135,
year = {2024},
author = {Shi, K and Liu, X and Duan, Y and Ding, J and Jia, Y and Jiang, Z and Feng, C},
title = {Multi-omics analysis reveals associations between host gene expression, gut microbiota, and metabolites in chickens.},
journal = {Journal of animal science},
volume = {102},
number = {},
pages = {},
doi = {10.1093/jas/skae263},
pmid = {39243135},
issn = {1525-3163},
mesh = {Animals ; *Chickens/microbiology/metabolism ; *Gastrointestinal Microbiome ; Female ; *Metabolome ; Transcriptome ; Liver/metabolism ; Gene Expression Profiling ; Gene Expression ; Multiomics ; },
abstract = {Egg-laying is an important trait in chickens, and it is affected by many factors, such as hormones regulated by the hypothalamic-pituitary axis and precursors synthesized by the liver. Recent studies showed that gut microbiota was associated with egg-laying, however, its underlying mechanism remains unclear. We comprehensively analyzed the host transcriptome, gut microbiota, and metabolome in broiler breeder hens during the pre-laying, peak-laying, and late-laying periods. The transcriptome analysis of the tissues related to the hypothalamic-pituitary-liver (HPL) axis revealed dynamic gene expression during egg-laying periods. Differentially expressed genes (DEGs) (i.e., PENK, NPY, AVP, PRL, RLN3, and FST) from the hypothalamus and pituitary gland were involved in female gonadal development, hormone secretion, response to endogenous stimulus, liver development, and amide metabolism. In liver, DEGs (i.e., FABP3, VTG1, LPL, APOA5, APOV1, and RBP5) were enriched in efferocytosis, sphingolipid metabolism, amide, and peptide biosynthesis. Alpha and beta diversity changed significantly in cecum microbiota during different laying periods. The abundance of Firmicutes was decreased and the abundance of Bacteroidota was increased during the peak-laying period. Functional analysis showed that the biosynthesis of secondary metabolites, amino acids, purine, and steroid hormones was altered during laying. The metabolome analysis from cecal contents showed that amino acid metabolism and steroid hormone biosynthesis changed during laying. Integrated analysis of the cecal microbiota and metabolites showed the genus Megasphaera was involved in amino acid metabolism, which included 3-phenyllatic acid, quinic acid, caffeic acid, and folic acid, and the genus Hungatella participated in steroid hormone biosynthesis through its strong correlation with estradiol. These results explored the dynamic changes in tissues related to the HPL axis and cecal microbiota and provided new insights into the interaction between the host and microbiota during egg-laying in chickens.},
}

Animals
*Chickens/microbiology/metabolism
*Gastrointestinal Microbiome
Female
*Metabolome
Transcriptome
Liver/metabolism
Gene Expression Profiling
Gene Expression
Multiomics

@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 = {/WT_/Wellcome Trust/United Kingdom ; 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 {pmid39242698,
year = {2024},
author = {Lu, X and Gong, G and Zhang, Q and Yang, S and Wu, H and Zhao, M and Wang, X and Shen, Q and Ji, L and Liu, Y and Wang, Y and Liu, J and Suolang, S and Ma, X and Shan, T and Zhang, W},
title = {Metagenomic analysis reveals high diversity of gut viromes in yaks (Bos grunniens) from the Qinghai-Tibet Plateau.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {1097},
pmid = {39242698},
issn = {2399-3642},
mesh = {Animals ; Cattle ; *Metagenomics ; *Gastrointestinal Microbiome/genetics ; *Virome/genetics ; Tibet ; Metagenome ; },
abstract = {The Qinghai-Tibet Plateau (QTP), renowned for its exceptional biological diversity, is home to numerous endemic species. However, research on the virology of vulnerable vertebrates like yaks remains limited. In this study, our objective was to use metagenomics to provide a comprehensive understanding of the diversity and evolution of the gut virome in yak populations across different regions of the QTP. Our findings revealed a remarkably diverse array of viruses in the gut of yaks, including those associated with vertebrates and bacteriophages. Notably, some vertebrate-associated viruses, such as astrovirus and picornavirus, showed significant sequence identity across diverse yak populations. Additionally, we observed differences in the functional profiles of genes carried by the yak gut virome across different regions. Moreover, the virus-bacterium symbiotic network that we discovered holds potential significance in maintaining the health of yaks. Overall, this research expands our understanding of the viral communities in the gut of yaks and highlights the importance of further investigating the interactions between viruses and their hosts. These data will be beneficial for revealing the crucial role that viruses play in the yak gut ecology in future studies.},
}

Animals
Cattle
*Metagenomics
*Gastrointestinal Microbiome/genetics
*Virome/genetics
Tibet
Metagenome

@article {pmid39239875,
year = {2024},
author = {Kwan, SY and Gonzales, KA and Jamal, MA and Stevenson, HL and Tan, L and Lorenzi, PL and Futreal, PA and Hawk, ET and McCormick, JB and Fisher-Hoch, SP and Jenq, RR and Beretta, L},
title = {Protection against fibrosis by a bacterial consortium in metabolic dysfunction-associated steatohepatitis and the role of amino acid metabolism.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2399260},
pmid = {39239875},
issn = {1949-0984},
support = {P30 CA016672/CA/NCI NIH HHS/United States ; P50 CA217674/CA/NCI NIH HHS/United States ; UL1 TR000371/TR/NCATS NIH HHS/United States ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; Humans ; *Liver Cirrhosis/microbiology/metabolism ; Mice ; *Amino Acids/metabolism ; *Bacteria/classification/metabolism/genetics/isolation & purification ; Male ; *Liver/metabolism/pathology/microbiology ; Female ; Feces/microbiology ; Mice, Inbred C57BL ; Middle Aged ; Fatty Liver/metabolism/microbiology ; Disease Models, Animal ; Metagenome ; Adult ; },
abstract = {The gut microbiota drives progression to liver fibrosis, the main determinant of mortality in metabolic dysfunction-associated steatohepatitis (MASH). In this study, we aimed to identify bacterial species associated with protection against liver fibrosis in a high-risk population, and test their potential to protect against liver fibrosis in vivo. Based on stool shotgun metagenomic sequencing of 340 subjects from a population cohort disproportionally affected by MASH, we identified bacterial species from the Bacteroidales and Clostridiales orders associated with reduced risk of liver fibrosis. A bacterial consortium was subsequently tested in a mouse model of MASH, which demonstrated protective effects against liver fibrosis. Six of the eight inoculated bacteria were detected in mouse stool and liver. Intrahepatic presence of bacteria was further confirmed by bacterial culture of mouse liver tissue. Changes in liver histological parameters, gut functional profiles, and amino acid profiles were additionally assessed. Comparison between fibrosis-associated human metagenome and bacteria-induced metagenome changes in mice identified microbial functions likely to mediate the protective effect against liver fibrosis. Amino acid profiling confirmed an increase in cysteine synthase activity, associated with reduced fibrosis. Other microbiota-induced changes in amino acids associated with reduced fibrosis included increased gut asparaginase activity and decreased hepatic tryptophan-to-kynurenine conversion. This human-to-mouse study identified bacterial species and their effects on amino acid metabolism as innovative strategies to protect against liver fibrosis in MASH.},
}

Animals
*Gastrointestinal Microbiome
Humans
*Liver Cirrhosis/microbiology/metabolism
Mice
*Amino Acids/metabolism
*Bacteria/classification/metabolism/genetics/isolation & purification
Male
*Liver/metabolism/pathology/microbiology
Female
Feces/microbiology
Mice, Inbred C57BL
Middle Aged
Fatty Liver/metabolism/microbiology
Disease Models, Animal
Metagenome
Adult

@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 = {},
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 {pmid39237540,
year = {2024},
author = {Ravikrishnan, A and Wijaya, I and Png, E and Chng, KR and Ho, EXP and Ng, AHQ and Mohamed Naim, AN and Gounot, JS and Guan, SP and Hanqing, JL and Guan, L and Li, C and Koh, JY and de Sessions, PF and Koh, WP and Feng, L and Ng, TP and Larbi, A and Maier, AB and Kennedy, BK and Nagarajan, N},
title = {Gut metagenomes of Asian octogenarians reveal metabolic potential expansion and distinct microbial species associated with aging phenotypes.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {7751},
pmid = {39237540},
issn = {2041-1723},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Singapore ; Male ; Aged, 80 and over ; Female ; *Aging ; *Metagenome ; Asian People/genetics ; Phenotype ; Metagenomics/methods ; Bacteria/genetics/classification/metabolism/isolation & purification ; Bacteroides/genetics/metabolism ; Cohort Studies ; Feces/microbiology ; },
abstract = {While rapid demographic changes in Asia are driving the incidence of chronic aging-related diseases, the limited availability of high-quality in vivo data hampers our ability to understand complex multi-factorial contributions, including gut microbial, to healthy aging. Leveraging a well-phenotyped cohort of community-living octogenarians in Singapore, we used deep shotgun-metagenomic sequencing for high-resolution taxonomic and functional characterization of their gut microbiomes (n = 234). Joint species-level analysis with other Asian cohorts identified distinct age-associated shifts characterized by reduction in microbial richness, and specific Alistipes and Bacteroides species enrichment (e.g., Alistipes shahii and Bacteroides xylanisolvens). Functional analysis confirmed these changes correspond to metabolic potential expansion in aging towards alternate pathways synthesizing and utilizing amino-acid precursors, vis-à-vis dominant microbial guilds producing butyrate in gut from pyruvate (e.g., Faecalibacterium prausnitzii, Roseburia inulinivorans). Extending these observations to key clinical markers helped identify >10 robust microbial associations to inflammation, cardiometabolic and liver health, including potential probiotic species (e.g., Parabacteroides goldsteinii) and pathobionts (e.g., Klebsiella pneumoniae), highlighting the microbiome's role as biomarkers and potential targets for promoting healthy aging.},
}

Humans
*Gastrointestinal Microbiome/genetics
Singapore
Male
Aged, 80 and over
Female
*Aging
*Metagenome
Asian People/genetics
Phenotype
Metagenomics/methods
Bacteria/genetics/classification/metabolism/isolation & purification
Bacteroides/genetics/metabolism
Cohort Studies
Feces/microbiology

@article {pmid39236827,
year = {2024},
author = {Xu, W and Xu, Y and Sun, R and Rey Redondo, E and Leung, KK and Wan, SH and Li, J and Yung, CCM},
title = {Revealing the intricate temporal dynamics and adaptive responses of prokaryotic and eukaryotic microbes in the coastal South China Sea.},
journal = {The Science of the total environment},
volume = {952},
number = {},
pages = {176019},
doi = {10.1016/j.scitotenv.2024.176019},
pmid = {39236827},
issn = {1879-1026},
mesh = {China ; *Phytoplankton/physiology/genetics ; *Seawater/microbiology ; Microbiota ; Cyanobacteria/genetics/physiology ; Photosynthesis ; Seasons ; Metagenome ; },
abstract = {This comprehensive two-year investigation in the coastal South China Sea has advanced our understanding of marine microbes at both community and genomic levels. By combining metagenomics and metatranscriptomics, we have revealed the intricate temporal dynamics and remarkable adaptability of microbial communities and phytoplankton metagenome-assembled genomes (MAGs) in response to environmental fluctuations. We observed distinct seasonal shifts in microbial community composition and function: cyanobacteria were predominant during warmer months, whereas photosynthetic protists were more abundant during colder seasons. Notably, metabolic marker KOs of photosynthesis were consistently active throughout the year, underscoring the persistent role of these processes irrespective of seasonal changes. Our analysis reveals that environmental parameters such as temperature, salinity, and nitrate concentrations profoundly influence microbial community composition, while temperature and silicate have emerged as crucial factors shaping their functional traits. Through the recovery and analysis of 37 phytoplankton MAGs, encompassing nine prokaryotic cyanobacteria and 28 eukaryotic protists from diverse phyla, we have gained insights into their genetic diversity and metabolic capabilities. Distinct profiles of photosynthesis-related pathways including carbon fixation, carotenoid biosynthesis, photosynthesis-antenna proteins, and photosynthesis among the MAGs indicated their genetic adaptations to changing environmental conditions. This study not only enhances our understanding of microbial dynamics in coastal marine ecosystems but also sheds light on the ecological roles and adaptive responses of different microbial groups to environmental changes.},
}

China
*Phytoplankton/physiology/genetics
*Seawater/microbiology
Microbiota
Cyanobacteria/genetics/physiology
Photosynthesis
Seasons
Metagenome

@article {pmid39235751,
year = {2025},
author = {Lemée, P and Bridier, A},
title = {Bioinformatic Pipeline for Profiling Foodborne Bacterial Ecology and Resistome from Short-Read Metagenomics.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2852},
number = {},
pages = {289-309},
pmid = {39235751},
issn = {1940-6029},
mesh = {*Metagenomics/methods ; *Computational Biology/methods ; *Food Microbiology/methods ; *Bacteria/genetics ; *High-Throughput Nucleotide Sequencing/methods ; Metagenome ; Microbiota/genetics ; },
abstract = {Next-generation sequencing revolutionized food safety management these last years providing access to a huge quantity of valuable data to identify, characterize, and monitor bacterial pathogens on the food chain. Shotgun metagenomics emerged as a particularly promising approach as it enables in-depth taxonomic profiling and functional investigation of food microbial communities. In this chapter, we provide a comprehensive step-by-step bioinformatical workflow to characterize bacterial ecology and resistome composition from metagenomic short-reads obtained by shotgun sequencing.},
}

*Metagenomics/methods
*Computational Biology/methods
*Food Microbiology/methods
*Bacteria/genetics
*High-Throughput Nucleotide Sequencing/methods
Metagenome
Microbiota/genetics

@article {pmid39235268,
year = {2024},
author = {Sudarshan, AS and Dai, Z and Gabrielli, M and Oosthuizen-Vosloo, S and Konstantinidis, KT and Pinto, AJ},
title = {New Drinking Water Genome Catalog Identifies a Globally Distributed Bacterial Genus Adapted to Disinfected Drinking Water Systems.},
journal = {Environmental science & technology},
volume = {58},
number = {37},
pages = {16475-16487},
pmid = {39235268},
issn = {1520-5851},
mesh = {*Drinking Water/microbiology ; Disinfection ; Bacteria/genetics ; Microbiota ; Genome, Bacterial ; Metagenome ; },
abstract = {Genome-resolved insights into the structure and function of the drinking water microbiome can advance the effective management of drinking water quality. To enable this, we constructed and curated thousands of metagenome-assembled and isolate genomes from drinking water distribution systems globally to develop a Drinking Water Genome Catalog (DWGC). The current DWGC disproportionately represents disinfected drinking water systems due to a paucity of metagenomes from nondisinfected systems. Using the DWGC, we identify core genera of the drinking water microbiome including a genus (UBA4765) within the order Rhizobiales that is frequently detected and highly abundant in disinfected drinking water systems. We demonstrate that this genus has been widely detected but incorrectly classified in previous amplicon sequencing-based investigations of the drinking water microbiome. Further, we show that a single genome variant (genomovar) within this genus is detected in 75% of drinking water systems included in this study. We propose a name for this uncultured bacterium as "Raskinella chloraquaticus" and describe the genus as "Raskinella" (endorsed by SeqCode). Metabolic annotation and modeling-based predictions indicate that this bacterium is capable of necrotrophic growth, is able to metabolize halogenated compounds, proliferates in a biofilm-based environment, and shows clear indications of disinfection-mediated selection.},
}

*Drinking Water/microbiology
Disinfection
Bacteria/genetics
Microbiota
Genome, Bacterial
Metagenome

@article {pmid39235252,
year = {2024},
author = {Sweet, P and Burroughs, M and Jang, S and Contreras, L},
title = {TolRad, a model for predicting radiation tolerance using Pfam annotations, identifies novel radiosensitive bacterial species from reference genomes and MAGs.},
journal = {Microbiology spectrum},
volume = {12},
number = {10},
pages = {e0383823},
doi = {10.1128/spectrum.03838-23},
pmid = {39235252},
issn = {2165-0497},
support = {HDTRA1-17-1-0025//DOD | Defense Threat Reduction Agency (DTRA)/ ; FA9550-20-1-0131//DOD | USAF | AMC | Air Force Office of Scientific Research (AFOSR)/ ; W911NF22S0002//DNI | Intelligence Advanced Research Projects Activity (IARPA)/ ; },
mesh = {*Radiation Tolerance/genetics ; *Bacteria/genetics/radiation effects/classification ; *Genome, Bacterial ; Humans ; Radiation, Ionizing ; Bacterial Proteins/genetics/metabolism ; Microbiota/genetics/radiation effects ; Proteome ; Metagenome ; Molecular Sequence Annotation ; },
abstract = {UNLABELLED: The trait of ionizing radiation (IR) tolerance is variable between bacterium, with species succumbing to acute doses as low as 60 Gy and extremophiles able to survive doses exceeding 10,000 Gy. While survival screens have identified multiple highly radioresistant bacteria, such systemic searches have not been conducted for IR-sensitive bacteria. The taxonomy-level diversity of IR sensitivity is poorly understood, as are genetic elements that influence IR sensitivity. Using the protein domain (Pfam) frequencies from 61 bacterial species with experimentally determined D10 values (the dose at which only 10% of the population survives), we trained TolRad, a random forest binary classifier, to distinguish between radiosensitive (D10 < 200 Gy) and radiation-tolerant (D10 > 200 Gy) bacteria. On untrained species, TolRad had an accuracy of 0.900. We applied TolRad to 152 UniProt-hosted bacterial proteomes associated with the human microbiome, including 37 strains from the ATCC Human Microbiome Collection, and classified 34 species as radiosensitive. Whereas IR-sensitive species (D10 < 200 Gy) in the training data set had been confined to the phylum Proteobacterium, this initial TolRad screen identified radiosensitive bacteria in two additional phyla. We experimentally validated the predicted radiosensitivity of a Bacteroidota species from the human microbiome. To demonstrate that TolRad can be applied to metagenome-assembled genomes (MAGs), we tested the accuracy of TolRad on Egg-NOG assembled proteomes (0.965) and partial proteomes. Finally, three collections of MAGs were screened using TolRad, identifying further phyla with radiosensitive species and suggesting that environmental conditions influence the abundance of radiosensitive bacteria.

IMPORTANCE: Bacterial species have vast genetic diversity, allowing for life in extreme environments and the conduction of complex chemistry. The ability to harness the full potential of bacterial diversity is hampered by the lack of high-throughput experimental or bioinformatic methods for characterizing bacterial traits. Here, we present a computational model that uses de novo-generated genome annotations to classify a bacterium as tolerant of ionizing radiation (IR) or as radiosensitive. This model allows for rapid screening of bacterial communities for low-tolerance species that are of interest for both mechanistic studies into bacterial sensitivity to IR and biomarkers of IR exposure.},
}

*Radiation Tolerance/genetics
*Bacteria/genetics/radiation effects/classification
*Genome, Bacterial
Humans
Radiation, Ionizing
Bacterial Proteins/genetics/metabolism
Microbiota/genetics/radiation effects
Proteome
Metagenome
Molecular Sequence Annotation

@article {pmid39232827,
year = {2024},
author = {Sun, C and Hu, G and Yi, L and Ge, W and Yang, Q and Yang, X and He, Y and Liu, Z and Chen, WH},
title = {Integrated analysis of facial microbiome and skin physio-optical properties unveils cutotype-dependent aging effects.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {163},
pmid = {39232827},
issn = {2049-2618},
support = {2019YFA0905600//National Key Research and Development Program of China/ ; },
mesh = {Humans ; *Microbiota ; *Skin/microbiology ; *Face/microbiology ; Middle Aged ; *Skin Aging/physiology ; Female ; Adult ; Male ; *Bacteria/classification/genetics/isolation & purification ; Aged ; Aging ; Metagenome ; Young Adult ; High-Throughput Nucleotide Sequencing ; Sebum/metabolism ; },
abstract = {BACKGROUND: Our facial skin hosts millions of microorganisms, primarily bacteria, crucial for skin health by maintaining the physical barrier, modulating immune response, and metabolizing bioactive materials. Aging significantly influences the composition and function of the facial microbiome, impacting skin immunity, hydration, and inflammation, highlighting potential avenues for interventions targeting aging-related facial microbes amidst changes in skin physiological properties.

RESULTS: We conducted a multi-center and deep sequencing survey to investigate the intricate interplay of aging, skin physio-optical conditions, and facial microbiome. Leveraging a newly-generated dataset of 2737 species-level metagenome-assembled genomes (MAGs), our integrative analysis highlighted aging as the primary driver, influencing both facial microbiome composition and key skin characteristics, including moisture, sebum production, gloss, pH, elasticity, and sensitivity. Further mediation analysis revealed that skin characteristics significantly impacted the microbiome, mostly as a mediator of aging. Utilizing this dataset, we uncovered two consistent cutotypes across sampling cities and identified aging-related microbial MAGs. Additionally, a Facial Aging Index (FAI) was formulated based on the microbiome, uncovering the cutotype-dependent effects of unhealthy lifestyles on skin aging. Finally, we distinguished aging related microbial pathways influenced by lifestyles with cutotype-dependent effect.

CONCLUSIONS: Together, our findings emphasize aging's central role in facial microbiome dynamics, and support personalized skin microbiome interventions by targeting lifestyle, skin properties, and aging-related microbial factors. Video Abstract.},
}

Humans
*Microbiota
*Skin/microbiology
*Face/microbiology
Middle Aged
*Skin Aging/physiology
Female
Adult
Male
*Bacteria/classification/genetics/isolation & purification
Aged
Aging
Metagenome
Young Adult
High-Throughput Nucleotide Sequencing
Sebum/metabolism

@article {pmid39232318,
year = {2024},
author = {Yadav, P and Kumari, SP and Hooda, S and Gupta, RK and Diwan, P},
title = {Comparative assessment of microbiome and resistome of influent and effluent of sewage treatment plant and common effluent treatment plant located in Delhi, India using shotgun approach.},
journal = {Journal of environmental management},
volume = {369},
number = {},
pages = {122342},
doi = {10.1016/j.jenvman.2024.122342},
pmid = {39232318},
issn = {1095-8630},
mesh = {India ; *Microbiota ; *Sewage/microbiology ; *Wastewater/microbiology ; Drug Resistance, Microbial/genetics ; Bacteria/genetics/drug effects ; Waste Disposal, Fluid ; },
abstract = {Antimicrobial resistance (AMR) is a significant threat that demands surveillance to identify and analyze trends of the emerging antibiotic resistance genes (ARGs) and potential microbial carriers. The influent of the wastewater treatment plants (WWTPs) reflects the microbes derived from the population and effluent being the source of dissemination of potential pathogenic microbes and AMR. The present study aimed to monitor microbial communities and antibiotic resistance genes in WWTPs employing a whole metagenome shotgun sequencing approach. The samples were collected from a sewage treatment plant (STP) and a common effluent treatment plant (CETP) in Delhi, India. The results showed the influent of STP to be rich in Bifidobacterium, Bacteroides, Escherichia, Arcobacter, and Pseudomonas residents of gut microbiota and known to cause diseases in humans and animals; whereas the CETP sample was abundant in Aeromonas, Escherichia, and Shewanella known to be involved in the degradation of different compounds. Interestingly, the effluent samples from both STPs and CETP were rich in microbial diversity, comprising organic and xenobiotic compound degrading and disease-causing bacteria, indicating the effluent being the source of dissemination of concerning bacteria to the environment. The functional profile at both sites displayed similarity with an abundance of housekeeping function genes as analyzed by Clusters of Orthologous Genes (COG), KEGG Orthology (KO), and subsystem databases. Resistome profiling by MEGARes showed the dominance of ARGs corresponding to beta-lactams having relative abundance ranging from 16% to 34% in all the metagenome datasets, followed by tetracycline (8%-16%), aminoglycosides (7%-9%), multi-drug (5%-9%), and rifampin (3%-9%). Also, AMR genes oxa, ant3-DPRIME, and rpoB, which are of clinical importance were predominantly and most prevalently present in all the samples. The presence of AMR in effluents from both types of treatment plants indicates that wastewater from both sources contributes to the spread of pathogenic bacteria and resistance genes, increasing the environmental AMR burden and therefore requires tertiary treatment before discharge. This work will facilitate further research towards the identification of suitable biomarkers for monitoring antibiotic resistance.},
}

India
*Microbiota
*Sewage/microbiology
*Wastewater/microbiology
Drug Resistance, Microbial/genetics
Bacteria/genetics/drug effects
Waste Disposal, Fluid

@article {pmid39232089,
year = {2024},
author = {Melo, T and Sousa, CA and Delacour-Estrella, S and Bravo-Barriga, D and Seixas, G},
title = {Characterization of the microbiome of Aedes albopictus populations in different habitats from Spain and São Tomé.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {20545},
pmid = {39232089},
issn = {2045-2322},
mesh = {Animals ; *Aedes/microbiology ; Spain ; *Microbiota ; *Wolbachia/genetics/isolation & purification/physiology ; Female ; *RNA, Ribosomal, 16S/genetics ; Mosquito Vectors/microbiology ; Ecosystem ; Male ; },
abstract = {The mosquito microbiome significantly influences vector competence, including in Aedes albopictus, a globally invasive vector. Describing the microbiome and Wolbachia strains of Ae. albopictus from different regions can guide area-specific control strategies. Mosquito samples from Spain and São Tomé were analyzed using 16S rRNA gene sequencing and metagenomic sequencing. Wolbachia infection patterns were observed by sex and population. Female mosquitoes were blood-fed, a factor considered in analyzing their microbiota. Results revealed a dominance of dual Wolbachia infections, strains A and B, in the microbiome of both populations of Ae. albopictus, especially among females. Both populations shared a core microbiome, although 5 and 9 other genera were only present in Spain and São Tomé populations, respectively. Genera like Pelomonas and Nevskia were identified for the first time in Aedes mosquitoes. This study is the first to describe the Ae. albopictus bacteriome in Spain and São Tomé, offering insights for the development of targeted mosquito control strategies. Understanding the specific microbiome composition can help in designing more effective interventions, such as microbiome manipulation and Wolbachia-based approaches, to reduce vector competence and transmission potential of these mosquitoes.},
}

Animals
*Aedes/microbiology
Spain
*Microbiota
*Wolbachia/genetics/isolation & purification/physiology
Female
*RNA, Ribosomal, 16S/genetics
Mosquito Vectors/microbiology
Ecosystem
Male

@article {pmid39230701,
year = {2024},
author = {Hera, MR and Liu, S and Wei, W and Rodriguez, JS and Ma, C and Koslicki, D},
title = {Metagenomic functional profiling: to sketch or not to sketch?.},
journal = {Bioinformatics (Oxford, England)},
volume = {40},
number = {Suppl 2},
pages = {ii165-ii173},
pmid = {39230701},
issn = {1367-4811},
support = {R01 GM146462/GM/NIGMS NIH HHS/United States ; R01GM146462/GF/NIH HHS/United States ; },
mesh = {*Metagenomics/methods ; *Software ; *Algorithms ; *Metagenome/genetics ; Humans ; Microbiota/genetics ; Databases, Genetic ; },
abstract = {MOTIVATION: Functional profiling of metagenomic samples is essential to decipher the functional capabilities of microbial communities. Traditional and more widely used functional profilers in the context of metagenomics rely on aligning reads against a known reference database. However, aligning sequencing reads against a large and fast-growing database is computationally expensive. In general, k-mer-based sketching techniques have been successfully used in metagenomics to address this bottleneck, notably in taxonomic profiling. In this work, we describe leveraging FracMinHash (implemented in sourmash, a publicly available software), a k-mer-sketching algorithm, to obtain functional profiles of metagenome samples.

RESULTS: We show how pieces of the sourmash software (and the resulting FracMinHash sketches) can be put together in a pipeline to functionally profile a metagenomic sample. We named our pipeline fmh-funprofiler. We report that the functional profiles obtained using this pipeline demonstrate comparable completeness and better purity compared to the profiles obtained using other alignment-based methods when applied to simulated metagenomic data. We also report that fmh-funprofiler is 39-99× faster in wall-clock time, and consumes up to 40-55× less memory. Coupled with the KEGG database, this method not only replicates fundamental biological insights but also highlights novel signals from the Human Microbiome Project datasets.

This fast and lightweight metagenomic functional profiler is freely available and can be accessed here: https://github.com/KoslickiLab/fmh-funprofiler. All scripts of the analyses we present in this manuscript can be found on GitHub.},
}

*Metagenomics/methods
*Software
*Algorithms
*Metagenome/genetics
Humans
Microbiota/genetics
Databases, Genetic

@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},
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 {pmid39230075,
year = {2024},
author = {Kim, N and Kim, CY and Ma, J and Yang, S and Park, DJ and Ha, SJ and Belenky, P and Lee, I},
title = {MRGM: an enhanced catalog of mouse gut microbial genomes substantially broadening taxonomic and functional landscapes.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2393791},
pmid = {39230075},
issn = {1949-0984},
support = {R01 DK125382/DK/NIDDK NIH HHS/United States ; },
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Mice ; *Bacteria/classification/genetics/isolation & purification ; *Genome, Bacterial ; Humans ; Phylogeny ; Diet ; },
abstract = {Mouse gut microbiome research is pivotal for understanding the human gut microbiome, providing insights into disease modeling, host-microbe interactions, and the dietary influence on the gut microbiome. To enhance the translational value of mouse gut microbiome studies, we need detailed and high-quality catalogs of mouse gut microbial genomes. We introduce the Mouse Reference Gut Microbiome (MRGM), a comprehensive catalog with 42,245 non-redundant mouse gut bacterial genomes across 1,524 species. MRGM marks a 40% increase in the known taxonomic diversity of mouse gut microbes, capturing previously underrepresented lineages through refined genome quality assessment techniques. MRGM not only broadens the taxonomic landscape but also enriches the functional landscape of the mouse gut microbiome. Using deep learning, we have elevated the Gene Ontology annotation rate for mouse gut microbial proteins from 3.2% with orthology to 60%, marking an over 18-fold increase. MRGM supports both DNA- and marker-based taxonomic profiling by providing custom databases, surpassing previous catalogs in performance. Finally, taxonomic and functional comparisons between human and mouse gut microbiota reveal diet-driven divergences in their taxonomic composition and functional enrichment. Overall, our study highlights the value of high-quality microbial genome catalogs in advancing our understanding of the co-evolution between gut microbes and their host.},
}

Animals
*Gastrointestinal Microbiome/genetics
Mice
*Bacteria/classification/genetics/isolation & purification
*Genome, Bacterial
Humans
Phylogeny
Diet

@article {pmid39222347,
year = {2024},
author = {Glendinning, L and Wu, Z and Vervelde, L and Watson, M and Balic, A},
title = {Infectious bronchitis virus vaccination, but not the presence of XCR1, is correlated with large differences in chicken caecal microbiota.},
journal = {Microbial genomics},
volume = {10},
number = {9},
pages = {},
doi = {10.1099/mgen.0.001289},
pmid = {39222347},
issn = {2057-5858},
mesh = {Animals ; *Chickens/microbiology ; *Infectious bronchitis virus/immunology/genetics ; *Cecum/microbiology ; *Gastrointestinal Microbiome ; Vaccination ; Poultry Diseases/microbiology/virology/immunology ; Coronavirus Infections/veterinary/prevention & control/immunology ; Viral Vaccines/immunology/genetics ; Receptors, G-Protein-Coupled/genetics ; Metagenome ; Dendritic Cells/immunology ; Bacteria/classification/genetics ; Metagenomics ; },
abstract = {The chicken immune system and microbiota play vital roles in maintaining gut homeostasis and protecting against pathogens. In mammals, XCR1+ conventional dendritic cells (cDCs) are located in the gut-draining lymph nodes and play a major role in gut homeostasis. These cDCs sample antigens in the gut luminal contents and limit the inflammatory response to gut commensal microbes by generating appropriate regulatory and effector T-cell responses. We hypothesized that these cells play similar roles in sustaining gut homeostasis in chickens, and that chickens lacking XCR1 were likely to contain a dysbiotic caecal microbiota. Here we compare the caecal microbiota of chickens that were either heterozygous or homozygous XCR1 knockouts, that had or had not been vaccinated for infectious bronchitis virus (IBV). We used short-read (Illumina) and long-read (PacBio HiFi) metagenomic sequencing to reconstruct 670 high-quality, strain-level metagenome assembled genomes. We found no significant differences between alpha diversity or the abundance of specific microbial taxa between genotypes. However, IBV vaccination was found to correlate with significant differences in the richness and beta diversity of the microbiota, and to the abundance of 40 bacterial genera. In conclusion, we found that a lack of XCR1 was not correlated with significant changes in the chicken microbiota, but IBV vaccination was.},
}