April 26, 2023

General microbiome

[PREPRINT]Microbiome diversity: A barrier to the environmental spread of antimicrobial resistance? – Klümper et al. – bioRxiv

Pregnancy and early life

First-Day-of-Life Rectal Swabs Fail To Represent Meconial Microbiota Composition and Underestimate the Presence of Antibiotic Resistance Genes – Graspeuntner et al. – Microbiology Spectrum

Human gut microbiome

Mucin-microbiome signatures shape the tumor microenvironment in gastric cancer – Oosterlinck et al. – Microbiome

[REVIEW]Fecal microbiota transplantation for recurrent C. difficile infection in patients with inflammatory bowel disease: A systematic review and meta-analysis – Porcari et al. – Journal of Autoimmunity

[REVIEW]Alcohol, the gut microbiome, and liver disease – Jew & Hsu – JGH

[REVIEW]Microbial metabolites in colorectal tumorigenesis and cancer therapy – Liu et al. – Gut Microbes

Human biliary microbiome

Neoadjuvant therapy does not impact the biliary microbiome in patients with pancreatic cancer – Behrens et al. – Journal of Surgical Oncology

Animal microbiome (for animals in the wild)

Indirect maternal effects via nest microbiome composition drive gut colonization in altricial chicks – Diez-Mendez et al. – Molecular Ecology

The gut microbiome of solitary bees is mainly affected by pathogen assemblage and partially by land use – de Landa et al. – Environmental Microbiome

Spatial Succession Underlies Microbial Contribution to Food Digestion in the Gut of an Algivorous Sea Urchin – Masasa et al. – Microbiology Spectrum

The microbiota in feces of domestic pigeons in Seoul, Korea – Oh et al. – Heliyon

Plant, root, and soil microbiome

Characterization of the Rhizosphere Bacterial Microbiome and Coffee Bean Fermentation in the Castillo-Tambo and Bourbon Varieties in the Popayán-Colombia Plateau – Solis Pino et al. – BMC Plant Biology

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

Hydrochemical and Seasonally Conditioned Changes of Microbial Communities in the Tufa-Forming Freshwater Network Ecosystem – Cackovic et al. – mSphere


[PREPRINT]ggpicrust2: an R package for PICRUSt2 predicted functional profile analysis and visualization – Yang et al. – arXiv

April 19, 2023

Pregnancy and early life

[REVIEW]The maternal gut microbiome during pregnancy and its role in maternal and infant health – Sinha et al. – Current Opinion in Microbiology

Human oral microbiome

Independent Effects of HIV and Antiretroviral Therapy on the Oral Microbiome Identified by Multivariate Analyses – Beall et al. – mBio

[REVIEW]Oral microbial changes and oral disease management before and after the treatment of hematological malignancies: a narrative review – Lin et al. – Clinical Oral Investigations

Human vaginal microbiome

[REVIEW]Gardnerella Revisited: Species Heterogeneity, Virulence Factors, Mucosal Immune Responses, and Contributions to Bacterial Vaginosis – Shvartsman et al. – Infection and Immunity

Human gut microbiome/virome

[REVIEW]Intrahost evolution of the gut microbiota – Barreta & Gordo – Nature Reviews Microbiology

The gut microbiota contributes to the pathogenesis of anorexia nervosa in humans and mice – Fan et al. – Nature Microbiology

Altered human gut virome in patients undergoing antibiotics therapy for Helicobacter pylori – Wang et al. – Nature Communications

Antibiotic treatment using amoxicillin-clavulanic acid impairs gut mycobiota development through modification of the bacterial ecosystem – Spatz et al. – Microbiome

Metabolic independence drives gut microbial colonization and resilience in health and disease – Watson et al. – Microbiome

Development of the gut microbiota in the first 14 years of life and its relations to internalizing and externalizing difficulties and social anxiety during puberty – Ou et al. – European Child & Adolescent Psychiatry

Reconstructing the landscape of gut microbial species across 29,000 diverse individuals – Segota et al. – NAR

Microbiomic profiles of bile in patients with benign and malignant pancreaticobiliary disease – Poudel et al. – PLOS One

Seasonal variations in gut microbiota and disease course in patients with inflammatory bowel disease – Tani et al. – PLOS One

The convergent application of metabolites from Avena sativa and gut microbiota to ameliorate non-alcoholic fatty liver disease: a network pharmacology study – Oh et al. – Journal of Translational Medicine volume

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

Effects of Extended Cage Component Sanitation Interval on the Microenvironment, Health, and Gastrointestinal Microbiome of Rats (Rattus norvegicus) – Taylor et al. – Journal of the American Association for Laboratory Animal Science

Music-based interventions in the feeding environment on the gut microbiota of mice – Niu et al. – Scientific Reports

Animal microbiome (for animals in the wild)

Characterisation of the koala (Phascolarctos cinereus) pouch microbiota in a captive population reveals a dysbiotic compositional profile associated with neonatal mortality – Maidment et al. – Microbiome

[PREPRINT]Microbiome variability of mosquito lines is consistent over time and across environments – Accoti et al. – bioRxiv

Differences in the luminal and mucosal gut microbiomes and metabolomes of oriental rat snake (Ptyas mucosus) – Wei et al. – Applied Microbiology and Biotechnology


Improved eukaryotic detection compatible with large-scale automated analysis of metagenomes – Bazant et al. – Microbiome


Functional gene-guided enrichment plus in situ microsphere cultivation enables isolation of new crucial ureolytic bacteria from the rumen of cattle – Liu et al. – Microbiome

March 22, 2023

Human gut microbiome

NEMoE: a nutrition aware regularized mixture of experts model to identify heterogeneous diet-microbiome-host health interactions – Xu et al. – Microbiome

The gut microbiome in social anxiety disorder: evidence of altered composition and function – Butler et al. – Translational Psychiatry

Analysis of the fecal metagenome in long-term survivors of pancreas cancer – Kharofa et al. – Cancer

Multiomic signatures of body mass index identify heterogeneous health phenotypes and responses to a lifestyle intervention – Watanabe et al. – Nature Medicine

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

New insights into the impact of microbiome on horizontal and vertical transmission of a tick-borne pathogen – Du et al. – Microbiome

Periodontitis exacerbates atherosclerosis through Fusobacterium nucleatum-promoted hepatic glycolysis and lipogenesis – Zhou et al. – Cardiovascular Research

Gut microbiota in a mouse model of obesity and peripheral neuropathy associated with plasma and nerve lipidomics and nerve transcriptomics – Guo et al. – Microbiome

Characterization of Gut Microbiome Composition in Patients with Triple-Negative Breast Cancer Treated with Neoadjuvant Chemotherapy – Vernaci et al. – The Oncologist

Plant, root, and soil microbiome

Environments and host genetics influence the geographic distribution of plant microbiome structure – Wei & Tan – bioRxiv

Gut feelings: associations of emotions and emotion regulation with the gut microbiome in women – Ke et al. – Psychological Medicine

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

Core species and interactions prominent in fish-associated microbiome dynamics – Yamjima et al. – Microbiome

March 15, 2023

Pregnancy and early life

The impact of prenatal dog keeping on infant gut microbiota development – Panzer et al. – Clinical & Experimental Allergy

Human oral microbiome

Host microbiome interactions in apical periodontitis: the endodontic microbiome in relation to circulatory immunologic markers – Georgiou et al. – International Endodontic Journal

Human gut microbiome

[REVIEW]Microbiota dysbiosis and myasthenia gravis: Do all roads lead to Rome? – Kapoor et al. – Autoimmunity Reviews

Metabolomic interplay between gut microbiome and plasma metabolome in cardiac surgery-associated acute kidney injury – Bai et al. – Rapid Communications in Mass Spectrometry

A non-antibiotic-disrupted gut microbiome is associated with clinical responses to CD19-CAR-T cell cancer immunotherapy – Stein-Thoeringer et al. – Nature Medicine

The gut microbiome modulates the transformation of microglial subtypes – Huang et al. – Molecular Psychiatry

Multi-omics insights into the interplay between gut microbiota and colorectal cancer in the “microworld” age – Wang et al. – Molecular Omics

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

A Longitudinal Characterization of the Seminal Microbiota and Antibiotic Resistance in Yearling Beef Bulls Subjected to Different Rates of Gain – Webb et al. – Microbiology Spectrum

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

Abiotic selection of microbial genome size in the global ocean – Ngugi et al. – Nature Communications


Benchmarking genome assembly methods on metagenomic sequencing data – Zhang et al. – Briefings in Bioinformatics

March 8, 2023

Pregnancy and early life

[PREPRINT]The influence of early life exposures on the infant gut virome – Zhang et al. – bioRxiv

[PREPRINT]Maternal diet and gut microbiome composition modulate early life immune responses – Grant et al. – bioRxiv

Human oral microbiome

Smoking-induced subgingival dysbiosis precedes clinical signs of periodontal disease – Tamashiro et al. – Scientific Reports

Human gut microbiome

Gut microbiota and risk of five common cancers: A univariable and multivariable Mendelian randomization study – Wei et al. – Cancer Medicine

The role of the sex hormone-gut microbiome axis in tumor immunotherapy – Wang et al. – Gut Microbes

[REVIEW]The Influence of the Microbiome on Aggressive Behavior: an Insight into Age Related Aggression – Gulledge, Oyebode & Donaldson – FEMS Microbiology Letters

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

Gnotobiotic mice housing conditions critically influence the phenotype associated with transfer of faecal microbiota in a context of obesity – Daoust et al. – Gut

Animal microbiome (for animals in the wild)

[REVIEW]The coral microbiome: Towards an understanding of the molecular mechanisms of coral-microbiota interactions – Mohamed et al. – FEMS Microbiology Reviews

Comparison of the gut microbiome and resistome in captive African and Asian elephants on the same diet – Feng et al. – Front. Vet. Sci.

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

Core and conditionally rare taxa as indicators of agricultural drainage ditch and stream health and function – Shi et al. – BMC Microbiology

Species invasions shift microbial phenology in a two-decade freshwater time series – Rohwer et al. – PNAS


Controlling taxa abundance improves metatranscriptomics differential analysis – Ji & Ma – BMC Microbiology

coda4microbiome: compositional data analysis for microbiome cross-sectional and longitudinal studies – Luz Calle, Pujolassos & Susin – BMC Bioinformatics

[PREPRINT]You can move, but you can’t hide: identification of mobile genetic elements with geNomad – Camargo et al. – bioRxiv

Assembling the perfect bacterial genome using Oxford Nanopore and Illumina sequencing – Wick, Judd & Holt – PLOS Computational Biology

February 8, 2023

Human gut microbiome

Gut microbiota of Parkinson’s disease in an appendectomy cohort: a preliminary study – Nakahara et al. – Scientific Reports

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

Microbiota-derived acetate enhances host antiviral response via NLRP3 – Niu et al. – Nature Communications

Gut microbiota remodeling improves natural aging-related disorders through Akkermansia muciniphila and its derived acetic acid – Ma et al. – Pharmacological Research

Gut microbiota-derived metabolites mediate the neuroprotective effect of melatonin in cognitive impairment induced by sleep deprivation – Wang et al. – Microbiome

Animal microbiome (for animals in the wild)

[PREPRINT]Impacts of Age on the Gut Microbiota in Captive Giant Pandas – Li, Lui & Zhang – bioRxiv


[PREPRINT]Strain Tracking with Uncertainty Quantification – Kim et al. – bioRxiv

Efficient computation of contributional diversity metrics from microbiome data with FuncDiv – Douglas et al. – Bioinformatics

February 1, 2023

General microbiome

Multi-dimensional experimental and computational exploration of metabolism pinpoints complex probiotic interactions – Zampieri, Efthimiou & Angione – Metabolic Engineering

[REVIEW]Advancing CAR T cell therapy through the use of multidimensional omics data – Yamg et al. – Nature Reviews Clinical Oncology

Pregnancy and early life

[REVIEW]Microbial transmission, colonisation and succession: from pregnancy to infancy – Xiao & Zhai – Gut

Human gut microbiome

Changes in the Gut Microbiome Associated with Intussusception in Patients with Peutz-Jeghers Syndrome – Wang et al. – Microbiology Spectrum

[PREPRINT]Probiotics supplementation to adult human small intestinal stoma microbiota causes dynamic increase in the community resistance to perturbations and nutrient utilization – Jansma et al. – bioRxiv

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

Pathometagenomics reveals susceptibility to intestinal infection by Morganella to be mediated by the blood group-related B4galnt2 gene in wild mice – Vallier et al. – Gut Microbes

Host-microbe co-metabolism via MCAD generates circulating metabolites including hippuric acid – Pruss et al. – Nature Communications

Disruption of the Intestinal Mucosal Barrier Induced by High Fructose and Restraint Stress Is Regulated by the Intestinal Microbiota and Microbiota Metabolites – Yu et al. – Microbiology Spectrum

[PREPRINT]Shift from a Simplified to Complex Gut Microbiota Reduces Adenoma Burden in a Preclinical Rat Model of Colon Cancer – Busi et al. – bioRxiv

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

Viral infection switches the balance between bacterial and eukaryotic recyclers of organic matter during coccolithophore blooms – Vincent et al. – Nature Communications

High-resolution metagenomic reconstruction of the freshwater spring bloom – Kavagutti et al. – Microbiome


[PREPRINT]Accounting for 16S rRNA copy number prediction uncertainty and its implications in microbial diversity analyses – Gao & Wu – bioRxiv


[PREPRINT]Methods for the analysis of skin microbiomes: a comparison of sampling processes and 16S rRNA hypervariable regions – Alyami et al. – bioRxiv

January 25, 2023

Human oral microbiome

Microbiological profile of peri-implantitis: Analyses of microbiome within dental implants – Kensara et al. – Journal of Prosthodontics

Human gut microbiome

Integrated Multi-Cohort Analysis of the Parkinson’s Disease Gut Metagenome – Boktor et al. – Movement Disorders

Gut microbiota and microbiota-derived metabolites promotes endometriosis – Chadchan et al. – Cell Death Discovery

Immune communication between the intestinal microbiota and the cardiovascular system – Ren et al. – Immunology Letters

Animal microbiome

The structure and diversity of microbial communities in Paederus fuscipes (Coleoptera: Staphylinidae): from ecological paradigm to pathobiome – Chamanakar et al. – Microbiome

The gastrointestinal microbiome in dairy cattle is constrained by the deterministic driver of the region and the modified effect of diet – Lin et al. – Microbiome

Fecal Microbiota Was Reshaped in UCP1 Knock-In Pigs via the Adipose-Liver-Gut Axis and Contributed to Less Fat Deposition – Pan et al. – Microbiology Spectrum

Gut microbiota of skywalker hoolock gibbons (Hoolock tianxing) from different habitats and in captivity: Implications for gibbon health – Lan et al. – American Journal of Primatology

Housing temperature plays a critical role in determining gut microbiome composition in research mice: Implications for experimental reproducibility – Hylander et al. – Biochimie

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

The biogeography and co-occurrence network patterns of bacteria and microeukaryotes in the estuarine and coastal waters – Wu et al. – Marine Environmental Research


[PREPRINT]Capturing the dynamics of microbiomes using individual-specific networks – Yousefi et al. – bioRxiv

PhaTYP: predicting the lifestyle for bacteriophages using BERT – Shang, Tang & Sun – Briefings in Bioinformatics

January 18, 2023

Human oral microbiome

[PRIMER]A possible role for taste receptor cells in surveying the oral microbiome – Heisey & McCluskey – PLOS Biology

Type II taste cells participate in mucosal immune surveillance – Qin et al. – PLOS One

Human gut microbiome

[NEWS]How our microbiome is shaped by family, friends and even neighbours – Callaway – Nature

The person-to-person transmission landscape of the gut and oral microbiomes – Valles-Colomer et al. – Nature

[REVIEW]The gut microbiota in obesity and weight management: microbes as friends or foe? – van Hul & Cani – Nature Reviews Endocrinology

Dynamics of the gut microbiome, IgA response, and plasma metabolome in the development of pediatric celiac disease – Girdhar et al. – Microbiome

Multi-omics profiles of the intestinal microbiome in irritable bowel syndrome and its bowel habit subtypes – Jacobs et al. – Microbiome

Microbiome Features Differentiating Unsupervised-Stratification-Based Clusters of Patients with Abnormal Glycometabolism – Xu et al. – mBio

Gut Bacterial Dysbiosis in Irritable Bowel Syndrome: a Case-Control Study and a Cross-Cohort Analysis Using Publicly Available Data Sets – Kim, Lee & Shim – Microbiology Spectrum

Harnessing gut microbes for glycan detection and quantification – Modesto, Pearce & Townsend Il – Nature Communications

The gut-microbiota-brain axis in a Spanish population in the aftermath of the COVID-19 pandemic: microbiota composition linked to anxiety, trauma, and depression profiles – Malan – Müller et al. – Gut Microbes

Animal microbiome

Expanded catalogue of metagenome-assembled genomes reveals resistome characteristics and athletic performance-associated microbes in horse – Li et al. – Microbiome

The bovine foot skin microbiota is associated with host genotype and the development of infectious digital dermatitis lesions – Bay et al. – Microbiome

Plant, root, and soil microbiome

A framework for the targeted recruitment of crop-beneficial soil taxa based on network analysis of metagenomics data – Merihu et al. – Microbiome

Diversity and functional analysis of rumen and fecal microbial communities associated with dietary changes in crossbreed dairy cattle – Kibegwa et al. – PLOS One


Multi-amplicon microbiome data analysis pipelines for mixed orientation sequences using QIIME2: Assessing reference database, variable region and pre-processing bias in classification of mock bacterial community samples – Maki et al. – PLOS One

November 30, 2022

Human respiratory microbiome

Airway microecology in rifampicin-resistant and rifampicin-sensitive pulmonary tuberculosis patients – Cai et al. – BMC Microbiology

Human oral microbiome

Oral Bacteriome and Mycobiome across Stages of Oral Carcinogenesis – Heng et al. – Microbiology Spectrum

Human gut microbiome

[REVIEW]Double-edged sword: impact of fecal microbiome transplants on the gut resistome – Hallowell, Gao & Suez – Current Opinion in Gastroenterology

Targeted suppression of human IBD-associated gut microbiota commensals by phage consortia for treatment of intestinal inflammation – Federici et al. – Cell

Gut microbiome alterations in preclinical Alzheimer’s disease – Jung et al. – PLOS One

[REVIEW]Sex, puberty, and the gut microbiome – Sisk-Hackworth, Kelley & Thackray

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

Lactobacillus reuteri tryptophan metabolism promotes host susceptibility to CNS autoimmunity – Montgomery et al. – Microbiome

Animal microbiome (for animals in the wild)

Genomic and Environmental Factors Shape the Active Gill Bacterial Community of an Amazonian Teleost Holobiont – Sylvain et al. – Microbiology Spectrum

Lack of host phylogenetic structure in the gut bacterial communities of New Zealand cicadas and their interspecific hybrids – Haji et al. – Scientific Reports

Plant, root, and soil microbiome

Unveiling the Wheat Microbiome under Varied Agricultural Field Conditions – Jaiswal et al. – Microbiology Spectrum

Changes of the microbial community in kiwifruit during storage after postharvest application of Wickerhamomyces anomalus – Zhao et al. – Food Chemistry

Food microbiology

[PREPRINT]A dark matter in sake brewing: Origin of microbes producing a Kimoto-style fermentation starter – Ito et al. – bioRxiv