Category Archives: Metabolomics

May 12, 2023

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Today’s digest features studies on human respiratory tract, mouse models, bovine milk microbiome, and more. See you at #MVIF next week!

Respiratory tract microbiome

Review: Ecology of the respiratory tract microbiome – Ana Elena Pérez-Cobas – Trends in Microbiology

Cervicovaginal microbiome

The cervical microbiota of Hispanics living in Puerto Rico is highly volatile and dominated by Lactobacillus iners regardless of HPV status – Daniela Vargas-Robles – bioRxiv

Gut microbiome

Key determinants of success in fecal microbiota transplantation: From microbiome to clinic – Serena Porcari – Cell Host & Microbes

Profiling the human intestinal environment under physiological conditions – Dari Shalon – Nature

Interaction between gut microbiota and sex hormones and their relation to sexual dimorphism in metabolic diseases – Jose Antonio Santos-Marcos – Biology of Sex Differences

Persistent delay in maturation of the developing gut microbiota in infants with cystic fibrosis – Paige Salerno – bioRxiv

Animal microbiome

Metagenomic analysis of milk microbiota in the bovine subclinical mastitis – Giulia Alessandri – bioRxiv

Animal experiments

MetaPhlAn 4 profiling of unknown species-level genome bins improves the characterization of diet-associated microbiome changes in mice – Paolo Manghi – Cell Reports

Bioinformatics

ResMiCo: Increasing the quality of metagenome-assembled genomes with deep learning – Olga Mineeva – Plos Computational Biology

Technique

Catch me if you can: capturing microbial community transformation by extracellular DNA using Hi-C sequencing – David Calderón-Franco – Antonie van Leeuwenhoek

Built environment

The microbiome of an outpatient rehabilitation clinic and predictors of contamination: A pilot study – Gabriella Brigando – PlosOne

February 13, 2023

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Today’s reading recommendation is a microbiota review collection edited by Lindsay Hall and Melanie Schirmer.

Happy Monday and see you at #MVIF!

Vaginal microbiome

Gardnerella Diversity and Ecology in Pregnancy and Preterm Birth – Hanna L. Berman – bioRxiv

Heterogeneity of the group B streptococcal type VII secretion system and influence on colonization of the female genital tract – Brady L. Spencer – bioRxiv

Urinary microbiome

Comparative Genomic Study of Streptococcus anginosus Reveals Distinct Group of Urinary Strains – Ananya Prasad – mSphere

Human gut

Gut microbes predominantly act as symbiotic partners rather than raw nutrients – Nuno Felipe da Silva Soares – bioRxiv

Antibiotic resistance in the commensal human gut microbiota – Lisa E Lamberte, Willem van Schaik – Current Opinion in Microbiology

Identifying glycan consumers in human gut microbiota samples using metabolic labeling coupled with fluorescence-activated cell sorting – Lharbi Dridi – Nature Communications

Animal experiments

Over supplementation with vitamin B12 alters microbe-host interactions in the gut leading to accelerated Citrobacter rodentium colonization and pathogenesis in mice – Andrew J. Forgie – Microbiome

Disturbance of lipid metabolism in germ-free mice transplanted with gut microbiota of DSS-induced colitis mice – Chungho Lee – Plos One

Bioinformatics

Accurate and fast graph-based pangenome annotation and clustering with ggCaller – Samuel T. Horsfield – bioRxiv

Brief report: uBin – a manual refining tool for genomes from metagenomes – Till L V Bornemann – Environmental Microbiology

In-situ metagenomics: A platform for rapid sequencing and analysis of metagenomes in less than one day – Javier Tamames – bioRxiv

The virtual microbiome: A computational framework to evaluate microbiome analyses – Belén Serrano-Antón – Plos One

November 16, 2022

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General microbiome

Enhancing nutritional niche and host defenses by modifying the gut microbiome – Sun et al. – Molecular Systems Biology

Evolution of immune genes is associated with the Black Death – Klunk et al. – Nature

Pregnancy and early life

Cross-generational bacterial strain transfer to an infant after fecal microbiota transplantation to a pregnant patient: a case report – Wei et al. – Microbiome

Multi-site human microbiome

Age-Related Changes, Influencing Factors, and Crosstalk Between Vaginal and Gut Microbiota: A Cross-Sectional Comparative Study of Pre- and Postmenopausal Women – Yoshikata et al. – Journal of Women’s Health

Human oral microbiome

Characterization of oral microbiota in HPV and non-HPV head and neck squamous cell carcinoma and its association with patient outcomes – Chan et al. – Oral Oncology

Human gut microbiome

[REVIEW]Making gut microbiomes from scratch – Tiang & Bisanz – Cell Host &Microbe

Impairments of intestinal arginine and NO metabolisms trigger aging-associated intestinal barrier dysfunction and ‘inflammaging’ – Brandt et al. – Redox Biology

Dietary fiber ameliorates sleep disturbance connected to the gut–brain axis – Tang et al. – Food & Function

Meta-analysis of 16S rRNA microbial data identified alterations of the gut microbiota in COVID-19 patients during the acute and recovery phases – Cheng et al. – BMC Microbiology

Relationships between dietary diversity and gut microbial diversity in the elderly – Amamoto et al. – Beneficial Microbes

Alteration of the faecal microbiota composition in patients with constipation: evidence of American Gut Project – Xu et al. – Beneficial Microbes

Gut microbiome, cognitive function and brain structure: a multi-omics integration analysis – Liang et al. – Translational Neurodegeneration

Microbiome insights into pediatric familial adenomatous polyposis – Attard et al. – Orphanet Journal of Rare Diseases

[REVIEW]The crosstalk between intestinal bacterial microbiota and immune cells in colorectal cancer progression – Wen et al. – Clinical and Translational Oncology

[REVIEW]Epigenetic regulation by metabolites from the gut microbiome – Marin-Tello et al. – Benefical Microbes

Animal experiments (mouse/rat experiments, chickens/pigs on different diets)

A tetrapeptide from maize combined with probiotics exerted strong anti-inflammatory effects and modulated gut microbiota in DSS-induced colitis mice – Li et al. – Food & Function

IGF1R is a mediator of sex-specific metabolism in mice: Effects of age and high-fat diet – Perez-Matute et al. – Front. Endocrinol.

Animal microbiome (for animals in the wild)

Nutrient dynamics in coral symbiosis depend on both the relative and absolute abundance of Symbiodiniaceae species – McIlroy et al. – Microbiome

Plant, root, and soil microbiome

Function-Based Rhizosphere Assembly along a Gradient of Desiccation in the Former Aral Sea – Wicaksono et al. – mSystems

Bioinformatics

Metagenomics versus total RNA sequencing: most accurate data-processing tools, microbial identification accuracy and perspectives for ecological assessments – Hempel et al. – NAR

Metagenome-assembled genome extraction and analysis from microbiomes using KBase – Chivian et al. – Nature Protocols

SourceFinder: a Machine-Learning-Based Tool for Identification of Chromosomal, Plasmid, and Bacteriophage Sequences from Assemblies – Aytan-Aktug et al. – Microbiology Spectrum

TaxiBGC: a Taxonomy-Guided Approach for Profiling Experimentally Characterized Microbial Biosynthetic Gene Clusters and Secondary Metabolite Production Potential in Metagenomes – Gupta et al. – mSystems

Techniques

Optimization of Low-Biomass Sample Collection and Quantitative PCR-Based Titration Impact 16S rRNA Microbiome Resolution – Clokie et al. – Microbiology Spectrum

October 26, 2022

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General microbiome

[BOOK]Human Microbiome in Health and Disease – Part B – Progress in Molecular Biology and Translational Science

Pregnancy and early life

Relationships of the very low birth weight infant microbiome with neurodevelopment at 2 and 4 years of age – Sarkar et al. – Developmental Psychobiology

Human respiratory microbiome

The lower airways microbiota and antimicrobial peptides indicate dysbiosis in sarcoidosis – Knudsen et al. – Microbiome

Human gut microbiome

Profiling the fungal microbiome after FMT for graft-versus-host disease: insights from a phase 1 interventional study – van Lier et al. – Transplantation and Cellular Therapy

Colorectal cancer, Vitamin D and microbiota: A double-blind Phase II randomized trial (ColoViD) in colorectal cancer patients – Bellerba et al. – Neoplasia

Natural and after colon washing fecal samples: the two sides of the coin for investigating the human gut microbiome – Piancone et al. – Scientific Reports

Animal microbiome

[DATA]Effects of heat stress on 16S rDNA, metagenome and metabolome in Holstein cows at different growth stages – Feng et al. – Scientific data

Tick transmission of Borrelia burgdorferi to the murine host is not influenced by environmentally acquired midgut microbiota – Narasimhan et al. – Microbiome

Mining the microbiota to identify gut commensals modulating neuroinflammation in a mouse model of multiple sclerosis – Bianchimano et al. – Microbiome

Microbiomes associated with avian malaria survival differ between susceptible Hawaiian honeycreepers and sympatric malaria-resistant introduced birds – Navine et al. – Molecular Ecology

Impact of Germinated Brown Rice and Brown Rice on Metabolism, Inflammation, and Gut Microbiome in High Fat Diet-Induced Insulin Resistant Mice – Zhao et al. – J. Agric. Food Chem.

Dietary Lactobacillus reuteri prevent from inflammation mediated apoptosis of liver via improving intestinal microbiota and bile acid metabolism – Lin et al. – Food Chemistry

Plant, root, and soil microbiome

Specific metabolites drive the deterministic assembly of diseased rhizosphere microbiome through weakening microbial degradation of autotoxin – Wen et al. – Microbiome

Low-abundance populations distinguish microbiome performance in plant cell wall deconstruction – Tom et al. – Microbiome

Water and extremophile microbiome (sea, rivers, lakes, glaciers, permafrost, high-salt)

Community assembly patterns and processes of microbiome responses to habitats and Mytilopsis sallei invasion in the tidal zones of the Pearl River Estuary – Guo et al. – Science of The Total Environment

Bioinformatics

LotuS2: an ultrafast and highly accurate tool for amplicon sequencing analysis – Özkurt et al. – Microbiome

Techniques

[PREPRINT]Double emulsions as a high-throughput enrichment and isolation platform for slower-growing microbes – McCully et al. – bioRxiv

A novel metagenome-derived viral RNA polymerase and its application in a cell-free expression system for metagenome screening – Han et al. – Scientif Reports

September 18, 2022

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Human and General Microbiome

Neisseria species as pathobionts in bronchiectasis – Liang Li – Cell Host & Microbe

The gut microbiome molecular complex in human health and disease – Paul Wilmes – Cell Host & Microbe

Codiversification of gut microbiota with humans – Taichi A Suzuki – Science

Gut microbiome of multiple sclerosis patients and paired household healthy controls reveal associations with disease risk and course – The iMSMS Consortium – Cell

Composition and diverse differences of intestinal microbiota in ulcerative colitis patients – Siying Zhu – Frontiers in Cellular and Infection Microbiology

A systematic review on omics data (metagenomics, metatranscriptomics, and metabolomics) in the role of microbiome in gallbladder disease – Paola Di Carlo – Frontiers in Physiology

Variability of strain engraftment and predictability of microbiome composition after fecal microbiota transplantation across different diseases – Gianluca Ianiro – Nature Medicine

Drivers and determinants of strain dynamics following fecal microbiota transplantation – Thomas S B Schmidt – Nature Medicine

Long-term ecological and evolutionary dynamics in the gut microbiomes of carbapenemase-producing Enterobacteriaceae colonized subjects – Jonathan T L Kang – Nature Microbiology

Structural and functional dysbiosis of gut microbiota in Tibetan subjects with coronary heart disease – Qi Cheng – Genomics

Growth of succinate consumer Dialister hominis is supported by Bacteroides thetaiotaomicron – Mitsuo Sakamoto – Anaerobe

RhoB affects colitis through modulating cell signaling and intestinal microbiome – Jianming Yang – Microbiome

Review: Diet fuelling inflammatory bowel diseases: preclinical and clinical concepts – Timon E Adolph – Gut

Review: Recent findings in Akkermansia muciniphila-regulated metabolism and its role in intestinal diseases – Meng-Jie Liu – Clinical Nutrition

Beneficial Microbes and Compounds

Comprehensive analysis of microbiome, metabolome and transcriptome revealed the mechanisms of Moringa oleifera polysaccharide on preventing ulcerative colitis – Hanchen Tian – International Journal of Biological Macromolecules

Probiotics ameliorates pulmonary inflammation via modulating gut microbiota and rectifying Th17/Treg imbalance in a rat model of PM2.5 induced lung injury – Yongcan Wu – Ecotoxicology and Environmental Safety

Short-term supplementation with ω-3 polyunsaturated fatty acids modulates primarily mucolytic species from the gut luminal mucin niche in a human fermentation system – Charlène Roussel – Gut Microbes

Model Animal Microbiome

Interactive Effect of Combined Intermittent and Sustained Hypoxia and High-Fat Diet on the Colonic Mucosal Microbiome and Host Gene Expression in Mice – Saif Mashaqi – Nature and Science of Sleep

Non-Model Animal Microbiome

Fungi are more transient than bacteria in caterpillar gut microbiomes – Martin Šigut – Scientific Reports

Adapting to climate with limited genetic diversity: Nucleotide, DNA methylation and microbiome variation among populations of the social spider Stegodyphus dumicola – Anne Aagaard – Molecular Ecology

Bioinformatics and Microbiome Analysis

Filtering ASVs/OTUs via mutual information-based microbiome network analysis – Elham Bayat Mokhtari – BMC Bioinformatics

Batch effects removal for microbiome data via conditional quantile regression – Wodan Ling – Nature Communications

Phylogenetic Analysis of Anti-CRISPR and Member Addition in the Families – Sweta Nidhi – Molecular Biotechnology

Shallow shotgun sequencing of the microbiome recapitulates 16S amplicon results and provides functional insights – Mason R Stothart – Molecular Ecology Resources

SnapShot: The Expobiome Map – Velma T E Aho – Cell Host & Microbe

July 26, 2022

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Highlights!

Microbial determinants of effective donors in faecal microbiota transplantation for UC – Craig Haifer – Gut → Metagenomic and metabolomic data analysis showed that donor microbiota stability and increased species evenness were identified novel markers associated with donor sample therapeutic efficacy in Ulcerative Colitis.

A gut microbial peptide and molecular mimicry in the pathogenesis of type 1 diabetes – Khyati Girdhar – PNAS → A peptide sequence from Parabacteroides distasonis mimics an important insulin epitope, making it susceptible to generating type I diabetes in a mouse model. 

Human and General Microbiome

Gut microbiome changes in anti-N-methyl-D-aspartate receptor encephalitis patients – Jingya Wei – BMC Neurology

Effect of a bacteriocin-producing Streptococcus salivarius on the pathogen Fusobacterium nucleatum in a model of the human distal colon – Garreth W Lawrence – Gut Microbes

Identification of Gut Microbiome Metabolites via Network Pharmacology Analysis in Treating Alcoholic Liver Disease – Ki-Kwang Oh – Current Issues in Molecular Biology

Review: The Gut Microbiota: A Double Edge Sword in Endometriosis – Chandni Talwar – Biology of Reproduction

Non-Model Animal Microbiome

Hair Microbiome Diversity within and across Primate Species – Catherine Kitrinos – mSystems

Seasonal variations in the composition and diversity of gut microbiota in white-lipped deer (Cervus albirostris) – Zhangqiang You – PeerJ

Plant Microbiome

Effects of Domestication on Plant-Microbiome Interactions – Andres Gutierrez – Plant & Cell Physiology

Evaluation of protein extraction methods for metaproteomic analyses of root-associated microbes – Fernanda Salvato – Molecular Plant-Microbe Interactions

Environmental Microbiome

Absence of stress-promoted facilitation coupled with a competition decrease in the microbiome of ephemeral saline lakes – Mateu Menéndez-Serra – Ecology

Insights into the Antimicrobial Activities and Metabolomes of Aquimarina (Flavobacteriaceae, Bacteroidetes) Species from the Rare Marine Biosphere – Sandra Godinho Silva – Marine Drugs

More microbes

Correspondence: International travel, the gut microbiome, and ESBL-E coli carriage – Ye Peng – The Lancet. Microbe

An Engineered λ Phage Enables Enhanced and Strain-Specific Killing of Enterohemorrhagic Escherichia coli – Menglu Jin – Microbiology Spectrum

Bioinformatics and Microbiome Analysis Techniques

MOCHI, a comprehensive cross-platform tool for amplicon-based microbiota analysis – Jun-Jie Zheng – Bioinformatics

July 9, 2022

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Have a nice weekend! 

Human and General Microbiome

Review: Bladder cancer, inflammageing and microbiomes – Austin Martin – Nature Reviews. Urology

Review: Gut associated metabolites and their roles in Clostridioides difficile pathogenesis – Andrea Martinez Aguirre – Gut Microbes

Oral and gut dysbiosis leads to functional alterations in Parkinson’s disease – Sungyang Jo – NPJ Parkinson’s Disease

Transcriptional programming in a Bacteroides consortium – Brian D Huang – Nature Communications

Gut microbiota composition in colorectal cancer patients is genetically regulated – Francesca Colombo – Scientific Reports

Relative contributions of the host genome, microbiome, and environment to the metabolic profile – Kangjin Kim – Genes & Genomics

Beneficial Microbes and Compounds

Effects of probiotic Lactiplantibacillus plantarum IMC 510 supplementation on metabolic factors in otherwise healthy overweight and obese individuals – Maria Magdalena Coman – Journal of Applied Microbiology

Grape seed and skin extract, a potential prebiotic with anti-obesity effect through gut microbiota modulation – Mohamed Mokrani – Gut Pathogens

Lactobacillus acidophilus LA85 ameliorates cyclophosphamide-induced immunosuppression by modulating Notch and TLR4/NF-κB signal pathways and remodeling the gut microbiota – Liangyu Xue – Food & Function

Animal Model Microbiome

Transplantation of bacteriophages from ulcerative colitis patients shifts the gut bacteriome and exacerbates the severity of DSS colitis – Anshul Sinha – Microbiome

Non-Model Animal Microbiome

Rickettsia helvetica infection is associated with microbiome modulation in Ixodes ricinus collected from humans in Serbia – Apolline Maitre – Scientific Reports

Environmental Microbiome

Microplastic exposure across trophic levels: effects on the host-microbiota of freshwater organisms – Javier Edo Varg – Environmental Microbiome

Estuarine plastisphere as an overlooked source of N(2)O production – Xiaoxuan Su – Nature Communications

Uncovering Hidden Members and Functions of the Soil Microbiome Using De Novo Metaproteomics – Joon-Yong Lee – Journal of Proteome Research

Other

Privacy Risks in Microbiome Research: Public Perspectives before and during a Global Pandemic – Andrea Shin – Ethics & Human Research

Bioinformatics and Experimental Microbiome Analysis

Review: Metagenomics Approaches to Investigate the Neonatal Gut Microbiome – Zakia Boudar – Frontiers in Pediatrics

Editorial: Before you go: a packing list for portable DNA sequencing of microbiomes and metagenomes – Arwyn Edwards – Microbiology

A Bayesian method for identifying associations between response variables and bacterial community composition – Adrian Verster – PLoS Computational Biology

GenBank as a Source to Monitor and Analyze Host-Microbiome Data – Vivek Ramanan – Bioinformatics

Phylogenies of the 16S rRNA gene and its hypervariable regions lack concordance with core genome phylogenies – Hayley B Hassler – Microbiome

July 2, 2022

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Have a nice weekend!

Highlights!

Priority effects shape the structure of infant-type Bifidobacterium communities on human milk oligosaccharides – Miriam N. Ojima – The ISME Journal → this paper contributes to the understanding of the configuration of different bifidobacteria in response to human milk oligosaccharides. 

Genomes of six viruses that infect Asgard archaea from deep-sea sediments – Ian M. Rambo – Nature Microbiology →By using metagenomics, authors describe six relatively large viral genomes, capable to infect members of the Asgard superphylum. The paper remarks on the strange features found in those viral genomes.

TLR4 regulates RORγt+ regulatory T-cell responses and susceptibility to colon inflammation through interaction with Akkermansia muciniphila – Yaojiang Liu – Microbiome → This article demonstrates the existence of “a novel protective role of TLR4 against intestinal inflammation, wherein it can modulate A. muciniphila-associated immune responses”. 

Human and General Microbiome

Review: The microbiome and gut homeostasis – Jee-Yon Lee – Science 

Review: The role of microbiome: a novel insight into urolithiasis – Sen-Yuan Hong – Critical Reviews in Microbiology

Review: Symbiosis: the other cells in development – Tyler J Carrier – Development 

Dysbiosis of the Gut Microbiome Is Associated With Histopathology of Lung Cancer – Xiong Qin – Frontiers in Microbiology

Beneficial Microbes and Compounds

Perspective: Leveraging the Gut Microbiota to Predict Personalized Responses to Dietary, Prebiotic, and Probiotic Interventions – Sean M Gibbons – Advances in Nutrition

Akkermansia muciniphila Alters Gut Microbiota and Immune System to Improve Cardiovascular Diseases in Murine Model – Xin He – Frontiers in Microbiology

Impact of probiotics use on clinical outcomes of immune checkpoint inhibitors therapy in cancer patients – Luying Wan – Cancer Medicine

Review: The gut microbiome as possible mediator of the beneficial effects of very low calorie ketogenic diet on type 2 diabetes and obesity: a narrative review – G Defeudis – Eating and Weight Disorders

Animal Microbiome

The coral pathogen Vibrio coralliilyticus kills non-pathogenic holobiont competitors by triggering prophage induction – Weiquan Wang – Nature Ecology & Evolution

Milk microbiomes of three great ape species vary among host species and over time – Sally L Bornbusch – Scientific Reports

Plant Microbiome

Fungal microbiome shifts on avocado fruit associated with a combination of postharvest chemical and physical interventions – Malick Bill – Journal of Applied Microbiology

Environmental Microbiome

Review: Priorities for ocean microbiome research – the Tara Ocean Foundation – Nature Microbiology

Microbiome Analysis Techniques and Tools

Protocol for correlation analysis of the murine gut microbiome and meta-metabolome using 16S rDNA sequencing and UPLC-MS – Xiaoqing Li – STAR Protocols

microbiomeMarker: an R/Bioconductor package for microbiome marker identification and visualization – Yang Cao – Bioinformatics

June 24, 2022

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Today we have a report in Science on bacterium which is 1cm long, a great review of the gut virome in human health, and a meta-analysis of mycobiota signatures in colorectcal cancer among some other great papers.

General microbiology

A centimeter-long bacterium with DNA contained in metabolically active, membrane-bound organelles – Volland et al. – Science

Virome

Filamentous bacteriophage delays healing of Pseudomonas-infected wounds – Bach et al. – Cell Reports Medicine

[REVIEW] The gut virome: A new microbiome component in health and disease – Cao et al. – eBioMedicine

Gut Microbiome

Presence of Blastocystis in gut microbiota is associated with cognitive traits and decreased executive function – Mayneris-Perxachs et al. – ISME

Altered mycobiota signatures and enriched pathogenic Aspergillus rambellii are associated with colorectal cancer based on multi-cohort fecal metagenomic analyses – Lin et al. – Gastroenterology

[REVIEW] Small molecules in the big picture of gut microbiome-host cross-talk – Ma et al. – eBioMedicine

Maternal gut microbiome–induced IgG regulates neonatal gut microbiome and immunity – Sanidad et al. – Science Immunology

Non-Microbiome picks

Time for better time-restricted eating trials to lessen the burden of metabolic diseases – Taub and Panda – Cell Reports Medicine

What SARS-CoV-2 does to our brains – Aschman et al. – Immunity

June 10, 2022

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Several great microbiome papers out today including a review on rethinking healthy eating in Cell Host & Microbe, a large population study on the development of the infant gut microbiome (n=1900) in Science, and two studies showcasing metabolomics predictive value for recurrent CDI and NAFLD.  

Gut Microbiome

[REVIEW] Rethinking healthy eating in light of the gut microbiome – Armet et al. Cell Host & Microbe.

Gut metabolites predict Clostridioides difficile recurrence – Dawkins et al. Microbiome

Robust variation in infant gut microbiome assembly across a spectrum of lifestyles – Olm et al. Science

Risk assessment with gut microbiome and metabolite markers in NAFLD development. Leung et al. Science Translational Medicine.

Profiling Fusobacterium infection at high taxonomic resolution reveals lineage-specific correlations in colorectal cancer – Bi et al. Nature Communications

Impact of a 7-day homogeneous diet on interpersonal variation in human gut microbiomes and metabolomes – Guthrie et al. Cell Host & Microbe

Animal experiments

Nisin probiotic prevents inflammatory bone loss while promoting reparative proliferation and a healthy microbiome – Gao et al. npj Biofilms & Microbiomes

Donor-dependent fecal microbiota transplantation efficacy against necrotizing enterocolitis in preterm pigs – Hui et al. npj Biofilms & Microbiomes

Virome

A catalog of 48,425 nonredundant viruses from oral metagenomes expands the horizon of the human oral virome – Li et al. iScience

Bioinformatics

Phylogeny-guided microbiome OTU-specific association test (POST) – Huang et al. Microbiome