May 16, 2023

Happy Tuesday! Today’s microbiome digest is microbial ecology heavy, with articles focused on the gut microbiome, Antarctic endoliths’, water microbiomes, and more.

Human gut microbiome

Pathobionts in the tumour microbiota predict survival following resection for colorectal cancer – Alexander et al. – Microbiome

Gut microbiome transitions across generations in different ethnicities in an urban setting—the HELIUS study – van der Vossen et al. – Microbiome

Water and extremophile microbiome

Highly diverse and unknown viruses may enhance Antarctic endoliths’ adaptability – Ettinger et al. – Microbiome

Genomic insights into cryptic cycles of microbial hydrocarbon production and degradation in contiguous freshwater and marine microbiomes – Vigneron et al. – Microbiome

preprint: Allochthonous groundwater microorganisms affect coastal seawater microbial abundance, activity and diversity – Yanuka-Golub et al. – bioRxiv

Built environment

preprint: Microbial Diversity on Ancestral Halls with Different Visitor Flow Rates Using Amplicon Sequencing – Liu et al. – bioRxiv


Comparing genomes recovered from time-series metagenomes using long- and short-read sequencing technologies – Orellana et al. – Microbiome

May 12, 2023

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


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


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

May 5, 2023

Today’s microbiome digest is a grab bag that includes ten simple rules for working with other people’s code, an article examining Wolbachia infections in native cockroach populations, and an article examining the role in lactic acid in shaping the human microbiome. Also highlighted is an article focused on human viruses residing within our cells and tissues, which demonstrated a unique virome in nine different human organs through targeted-enrichment viral metagenomics and virus specific qPCRs.

Happy reading!

General microbiome

The structure of prevacuolar compartments in Neurospora crassa as observed with super-resolution microscopy – Bowman – PLOS One

Phylogenetic trees of closely related bacterial species and subspecies based on frequencies of short nucleotide sequences – Nakano et al. – PLOS One

***Unmasking the tissue-resident eukaryotic DNA virome in humans – Pyöriä et al. – Nucleic Acids Research

Predicting partner fitness based on spatial structuring in a light-driven microbial community – Sakkos et al. – PLOS Computational Biology

Multi-site human microbiome

Evaluation of alcohol-free mouthwash for studies of the oral microbiome – Yano et al. – PLOS One

A systematically biosynthetic investigation of lactic acid bacteria reveals diverse antagonistic bacteriocins that potentially shape the human microbiome – Zhang et al. – Microbiome

Human gut microbiome

Positive mood-related gut microbiota in a long-term closed environment: a multiomics study based on the “Lunar Palace 365” experiment – Hao et al. – Microbiome

Animal microbiome

Wolbachia infection in native populations of Blattella germanica and Periplaneta americana – Choubdar et al. – PLOS One

Plant, root, and soil microbiome

Bacterial and fungal community composition and community-level physiological profiles in forest soils – Kunito et al. – PLOS One

Water and extremophile microbiome

Predicting microbial community compositions in wastewater treatment plants using artificial neural networks – Liu et al. – Microbiome

Open ocean and coastal strains of the N2-fixing cyanobacterium UCYN-A have distinct transcriptomes – Muñoz-Marín et al. – PLOS One

Meta-organism gene expression reveals that the impact of nitrate enrichment on coral larvae is mediated by their associated Symbiodiniaceae and prokaryotic assemblages – Tong et al. – Microbiome


Ten simple rules for working with other people’s code – Pilgrim et al. – PLOS Computational Biology

Predicting microbe organisms using data of living micro forms of life and hybrid microbes classifier – Raza et al. – PLOS One

iPHoP: An integrated machine learning framework to maximize host prediction for metagenome-derived viruses of archaea and bacteria – Roux et al. – PLOS Biology

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

April 14, 2023

Today’s reading recommendation includes microbiome from sites with low anthropogenic impact, drinking water microbiome, and more.

If you have only a minute for reading then your must read is this amazing summary thread on how you should be careful with making assumptions ⬇️

See you at #MVIF next week!

Global resistome

Global trends in antimicrobial resistance on organic and conventional farms – Eldon Ager – bioRxiv

*Microbiome diversity: A barrier to the environmental spread of antimicrobial resistance? – Uli Klümper – bioRxiv

Mother-to-infant microbiome

Mother-to-infant microbiota transmission and infant microbiota development across multiple body sites – Debby Bogaert – Cell Host & Microbe

Human gut microbiome

The Local Tumor Microbiome Is Associated with Survival in Late-Stage Colorectal Cancer Patients – Justine W. Debelius – Microbiology Spectrum

Exploring Bifidobacterium species community and functional variations with human gut microbiome structure and health beyond infancy – Ruben Ladeira, Julien Tap, Muriel Derrien – Microbiome Research Reports

Water microbiome

The microbial dark matter and “wanted list” in worldwide wastewater treatment plants – Yulin Zhang – Microbiome

*Microbiome, resistome and mobilome of chlorine-free drinking water treatment systems – David Calderón-Franco – Water Research

Animal experiment

Probiotics of Lacticaseibacillus paracasei SD1 and Lacticaseibacillus rhamnosus SD11 attenuate inflammation and β-cell death in streptozotocin-induced type 1 diabetic mice – Jongdee Nopparat – PlosOne

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

*Experimental Factors Influence Diversity Metrics of the Gut Microbiome in Laboratory Mice – Rikeish R. Muralitharan – bioRxiv

Virome & phages

Expanding known viral diversity in the healthy infant gut – Shiraz A. Shah – Nature Microbiology

Large-scale phage cultivation for commensal human gut bacteria – Juntao Shen – Cell Host & Microbe


Reducing bias in microbiome research: Comparing methods from sample collection to sequencing – Jolanda Kool – Frontiers in Microbiology

In Vitro Modelling of Oral Microbial Invasion in the Human Colon – Lucie Etienne-Mesmin – Microbiology Spectrum


Improved eukaryotic detection compatible with large-scale automated analysis of metagenomes – Wojtek Bazant – Microbiome

April 3, 2023

Human and General Microbiome

Review: Incorporating plasmid biology and metagenomics into a holistic model of the human gut microbiome – Stephen R Stockdale – Current Opinion in Microbiology

No evidence for a common blood microbiome based on a population study of 9,770 healthy humans – Cedric C S Tan – Nature Microbiology

Genetic correlations between Alzheimer’s disease and gut microbiome genera – Davis Cammann – Scientific Reports

Limitations of using 16S rRNA microbiome sequencing to predict oral squamous cell carcinoma – Christopher Delaney – APMIS

Mendelian randomization analyses reveal causal relationships between the human microbiome and longevity – Xiaomin Liu – Scientific Reports

Genomics of Invasive Cutibacterium acnes Isolates from Deep-Seated Infections – Anna Both – Microbiology Spectrum

Vaginal Microbiome Metagenome Inference Accuracy: Differential Measurement Error according to Community Composition – Kayla A Carter – mSystems

Review: Interspecies Interactions within the Host: the Social Network of Group B Streptococcus – Marlyd E Mejia – Infection and Immunity

Beneficial Microbes and Compounds

Review: Kefir as a therapeutic agent in clinical research: a scoping review – Milena Klippel Bessa – Nutrition Research Reviews

Interaction between β-glucans and gut microbiota: a comprehensive review – Reza Karimi – Critical Reviews in Food Science and Nutrition

Combination of vitamin D and probiotics inhibits chemically induced colorectal carcinogenesis in Wistar rats – Carolina S de Oliveira – Life Sciences

Animal Microbiome

Review: Recent advancements in coral health, microbiome interactions and climate change – Nizam Ashraf – The Science of the Total Environment

Detection of specific uncultured bacteriophages by fluorescence in situ hybridisation in pig microbiome – Line Jensen Ostenfeld – PloS One

Microbial Species-Area Relationships on the Skins of Amphibian Hosts – Fan Yang – Microbiology Spectrum

Intestinal microbiota of Nearctic-Neotropical migratory birds vary more over seasons and years than between host species – Heather R Skeen – Molecular Ecology

Food Microbiome

A unique case in which Kimoto-style fermentation was completed with Leuconostoc as the dominant genus without transitioning to Lactobacillus – Kohei Ito – Journal of Bioscience and Bioengineering

Built Environment

Holobiont Urbanism: sampling urban beehives reveals cities’ metagenomes – Elizabeth Hénaff – Environmental Microbiome

Microbiome Analysis: Protocols, Resources, Tools and Techniques

Contamination detection and microbiome exploration with GRIMER – Vitor C Piro – GigaScience

Annotation-free discovery of functional groups in microbial communities – Xiaoyu Shan – Nature Ecology & Evolution

ViroProfiler: a containerized bioinformatics pipeline for viral metagenomic data analysis – Jinlong Ru – Gut Microbes

Sequence-Based Characterization of Microalgal Microbiomes: Impact of DNA Extraction Protocol on Yield and Community Composition – Line Roager – Microbiology Spectrum

Preprint: Identifying keystone species in microbial communities using deep learning – Xu-Wen Wang – bioRxiv

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 20, 2023

Human and General Microbiome

Bacteria require phase separation for fitness in the mammalian gut – Emilia Krypotou – Science

Is there a placental microbiota? A critical review and re-analysis of published placental microbiota datasets – Jonathan J Panzer – BMC Microbiology

Gut-microbiome-expressed 3β-hydroxysteroid dehydrogenase degrades estradiol and is linked to depression in premenopausal females – Di Li – Cell Metabolism

Metagenomic association analysis of cognitive impairment in community-dwelling older adults – Jincheng Li – Neurobiology of Disease

Fusobacterium nucleatum promotes esophageal cancer early occurrence through upregulation of IL-32/PRTN3 expression – Jing Lei – Cancer Science

Review: Postbiotics Implication in the Microbiota-Host Intestinal Epithelial Cells Mutualism – Harpreet Kaur – Probiotics and Antimicrobial Proteins

Review: Microbiota and growth among infants and children in low-income and middle-income settings – James M Njunge – Current Opinion in Clinical Nutrition and Metabolic Care

Review: Cardiometabolic health, diet and the gut microbiome: a meta-omics perspective – Mireia Valles-Colomer – Nature Medicine

Review: Oral polymicrobial communities: Assembly, function, and impact on diseases – George Hajishengallis – Cell Host & Microbe

Review: Gut microbiota: a non-target victim of pesticide-induced toxicity – Tusha Sharma – Gut Microbes

Perspective: Human microbiome research: Growing pains and future promises – Jens Puschhof – PLoS Biology

Beneficial Microbes and Compounds

Versatility of bacterial outer membrane vesicles in regulating intestinal homeostasis – Xinyue Wang – Science Advances

Lactobacillus rhamnosus GG cell-free supernatant as a novel anti-cancer adjuvant – Rossella Salemi – Journal of Translational Medicine

Environmental Microbiome

Community dynamics of microbial eukaryotes in intertidal mudflats in the hypertidal Bay of Fundy – Eke I Kalu – ISME Communications

Other Microbes

Biointerface mineralization generates ultraresistant gut microbes as oral biotherapeutics – Zhongmin Geng – Science Advances

Genomic diversity of non-diarrheagenic fecal Escherichia coli from children in sub-Saharan Africa and south Asia and their relatedness to diarrheagenic E. coli – Tracy H Hazen – Nature Communications

Microbiome Analysis: Tools and Techniques

Spatial profiling of microbial communities by sequential FISH with error-robust encoding – Zhaohui Cao – Nature Communications

sBGC-hm: An atlas of secondary metabolite biosynthetic gene clusters from the human gut microbiome – Huixi Zou – Bioinformatics

Protocol: Bioinformatic and Statistical Analysis of Microbiome Data – Youngchul Kim – Methods in Molecular Biology

Protocol: Multi-omics Data Deconvolution and Integration: New Methods, Insights, and Translational Implications – Xuefeng Wang – Methods in Molecular Biology

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