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 4th, 2023

Bonjour from Paris, France !

In today’s digest you will find a wide variety of interesting preprints and published research papers encompassing very interesting microbiome such as Yak calves rumen, compost, wineyard soil and lichen symbionth microbiota!

If you are interested in virome, I recommend looking at the fascinating preprint from Ha and collaborators investigating the biogeography of giant viruses from the phylum Nucleocytoviricota. They leveraged the bioGEOTRACES metagenomic dataset collected across the Atlantic and Pacific Oceans to recovered novel genomes from these viruses and identified geographical patterns of distribution.

If you are working on human microbiomes, I recommend checking out a really interesting preprint, comparing the biases and strengths of four commercially available DNA extraction kits frequently used for whole genome shotgun analysis of the human microbiome.

Have a great Saturday!

Events and jobs

Event: Cell Symposia: Infection biology in the age of the microbiome. Paris, France June 7-9

Event: 55th Annual Meeting of the European Society for Paediatric Gastroenterology, Hepatology and Nutrition. Vienna, Austria 17-20 May

Pregnancy and early life

Insufficient Evidence of a Breastmilk Microbiota at Six-Weeks Postpartum: A Pilot Study – Leech et al. – Nutrients

Effects of Perinatal Antibiotic Exposure and Neonatal Gut Microbiota – Morreale et al. – Antibiotics

Necrotizing Enterocolitis: The Role of Hypoxia, Gut Microbiome, and Microbial Metabolites – Kaplina et al. – International Journal of Molecular sciences

Human gut microbiome

Preprint: Functional assignment of gut-specific archaeal proteins in the human gut microbiome – Novikova et al. – BioRxiv

Animal microbiome

Combining vertebrate mitochondrial 12S rRNA gene sequencing and shotgun metagenomic sequencing to investigate the diet of the leopard cat (Prionailurus bengalensis) in Korea – Woo et al. – PLOS ONE

The association between gingivitis and oral spirochetes in young cats and dogs – Yamaki et al. – PLOS ONE

Maternal rumen and milk microbiota shapes the establishment of early-life rumen microbiota in grazing yak calves – Guo et al. – Journal of Dairy Science

Plant, root, and soil microbiome

Preprint: Fundamentals of biofilm formation in soil: From functionalized self-assembled monolayers to rewilding – Hendiani et al. – BioRxiv

Local conditions matter: Minimal and variable effects of soil disturbance on microbial communities and functions in European vineyards – Steiner et al. – PLOS ONE

Preprint: Evidence for a core set of microbial lichen symbionts from a global survey of metagenomes – Tagirdzhanova et al. – BioRxiv

Water and extremophile microbiome

Preprint: Assessing the biogeography of marine giant viruses in four oceanic transects – Ha et al. – BioRxiv

Preprint: Cross-domain interactions induce community stability to benthic biofilms in proglacial streams – Busi et al. – BioRxiv

Opinion: Viral infection in the ocean—A journey across scales – Vincent and Vardi – PLOS biology


Preprint: Identifying and tracking mobile elements in evolving compost communities yields insights into the nanobiome – Van Dijk et al – BioRxiv


Preprint: Comparison of commercial DNA extraction kits for whole metagenome sequencing of human oral, vaginal, and rectal microbiome samples – Wright 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 13, 2023

The very first 2023 digest features HMOs, antimicrobials and the neonatal gut microbiota, cheese community, cow rumen microbiome, SemiBin2, and more. Happy Friday and see you next week at #MVIF!

Food microbiome

*Longitudinal, Multi-Platform Metagenomics Yields a High-Quality Genomic Catalog and Guides an In Vitro Model for Cheese Communities – Christina C. Saak – mSystems

Gut microbiome

*Human milk oligosaccharides, antimicrobial drugs, and the gut microbiota of term neonates: observations from the KOALA birth cohort study – D.J.M Barnett – Gut microbes

The gut microbiota in multiple sclerosis varies with disease activity – Florence Thirion – Genome Medicine

Review: Intestinal gas production by the gut microbiota: A review – Erasme Mutuyemungu – Journal of Functional Foods

Gestational diabetes is driven by microbiota-induced inflammation months before diagnosis – Yishay Pinto – Gut

Review: The gut microbiota is an emerging target for improving brain health during ageing – Marcus Boehme – Gut microbiome

Vaginal microbiome

Commensal Lactobacilli Metabolically Contribute to Cervical Epithelial Homeostasis in a Species-Specific Manner – Nicole R. Jimenez – mSphere

Preterm birth is associated with xenobiotics and predicted by the vaginal metabolome – William F. Kindschuh – Nature Microbiology

Animal experiment

Gut microbiota of the young ameliorates physical fitness of the aged in mice – Kwang H. Kim – Microbiome

Catheterization of mice triggers resurgent urinary tract infection seeded by a bladder reservoir of Acinetobacter baumannii – Jennie E. Hazen – Science Translational Medicine

Prebiotic intervention with HAMSAB in untreated essential hypertensive patients assessed in a phase II randomized trial – Hamdi A. Jama – Nature Cardiovascular Research

Akkermansia muciniphila protects mice against an emerging tick-borne viral pathogen – Jinyan Xie – Nature Microbiology

Animal microbiome

Beehives possess their own distinct microbiomes – Lorenzo A. Santorelli – Environmental Microbiome

*Differential carbon utilization enables co-existence of recently speciated Campylobacteraceae in the cow rumen epithelial microbiome – Cameron R. Strachan – Nature Microbiology


Ecological landscapes guide the assembly of optimal microbial communities – Ashish B. George and Kirill S. Korolev – Plos Computational Biology

Over-optimism in unsupervised microbiome analysis: Insights from network learning and clustering – Theresa Ullmann – Plos Computational Biology

Ten simple rules for using public biological data for your research – Vishal H. Oza – Plos Computational Biology

*SemiBin2: self-supervised contrastive learning leads to better MAGs for short- and long-read sequencing – Shaojun Pan – bioRxiv

December 12, 2022

Today’s digest has the kind of articles I like best–they are all focused on the unique relationship between microbial communities and their niche environments. These environments span everything from rice seeds to the Mariana Trench to the gut microbiome and even Appalachian coalbeds. Happy reading!

Human gut microbiome

Gut microbiome of helminth-infected indigenous Malaysians is context dependent – Tee et al. – Microbiome

Animal experiments

Taurine metabolism is modulated in Vibrio-infected Penaeus vannamei to shape shrimp antibacterial response and survival – Wang et al. – Microbiome

Plant, root, and soil microbiome

Multi-genome metabolic modeling predicts functional inter-dependencies in the Arabidopsis root microbiome – Mataigne et al. – Microbiome

Dynamics of rice microbiomes reveal core vertically transmitted seed endophytes – Zhang et al. – Microbiome

Water and extremophile microbiome

Comparison of prokaryotes between Mount Everest and the Mariana Trench – Liu et al. – Microbiome

Built environment

Predominance of Methanomicrobiales and diverse hydrocarbon-degrading taxa in the Appalachian coalbed biosphere revealed through metagenomics and genome-resolved metabolisms – Ross et al. – Environmental Microbiology

Evaluation of the Microbial Community and Geochemistry in Produced Waters Collected from CO2 EOR in the Niagaran Pinnacle Reef – Stemple et al. – ACS Earth Space Chem

December 9, 2022

Today’s digest features global antimicrobial resistance, comammox and anammox bacteria in wastewater treatment, mOTUs3, and more. Check out Elisa Granato & Christoph Ziegenhain’s story about postdoc life. Happy Friday and see you next week at #MVIF!

Global microbiome & resistome

Experimental temperatures shape host microbiome diversity and composition – Jingdi Li – Global Change Biology

Global biogeography and projection of soil antibiotic resistance genes – Zheng et al. – Science Advances

*Genomic analysis of sewage from 101 countries reveals global landscape of antimicrobial resistance – Patrick Munk – Nature Communications

Blood microbiome

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

Gut microbiome

Effects of dog ownership on the gut microbiota of elderly owners – Chaona Jiang – Plos One

Prokaryotic and viral genomes recovered from 787 Japanese gut metagenomes revealed microbial features linked to diets, populations, and diseases – Yoshihiko Tomofuji – Cell Genomics

Gut microbiome-wide association study of depressive symptoms – Djawad Radjabzadeh – Nature Communications

Development of non-alcoholic steatohepatitis is associated with gut microbiota but not oxysterol synthesis – Jacqueline Wyss – bioRxiv

The microbiome’s fiber degradation profile and its relationship with the host diet – Yotam Cohen & Elhanan Borenstein – BMC Biology

Animal microbiome

Lactobacillus reuteri improves the development and maturation of fecal microbiota in piglets through mother-to-infant microbe and metabolite vertical transmission – Gang Wang – Microbiome

Live biotherapeutics

Development of a live biotherapeutic throat spray with lactobacilli targeting respiratory viral infections – Irina Spacova – Microbial Biotechnology

Soil/root/plant microbiome

Differential microbial assembly processes and co-occurrence networks in the soil-root continuum along an environmental gradient – Yangquanwei Zhong – iMeta

Water microbiome

*Co-occurrence and cooperation between comammox and anammox bacteria in a full-scale attached growth municipal wastewater treatment process – Katherine J Vilardi – bioRxiv

Full-scale activated sludge transplantation reveals a highly resilient community structure – Giulia Dottorini – Water Research


Towards complete representation of bacterial contents in metagenomic samples – Xiaowen Feng, Heng Li – arXiv

*Cultivation-independent genomes greatly expand taxonomic-profiling capabilities of mOTUs across various environments – Hans-Joachim Ruscheweyh – Microbiome

Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2023 – CNCB-NGDC Members and Partners – Nucleic Acids Research

Nanopore long-read-only metagenomics enables complete and high-quality genome reconstruction from mock and complex metagenomes – Lei Liu – Microbiome

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

November 23, 2022

General microbiome

[PREPRINT]Patterns and determinants of the global herbivorous mycobiome – Meili et al. – bioRxiv

[EDITORIAL]Helicobacter pylori: Have potential benefits been overlooked? – Schubert et al. – JGH Open

Pregnancy and early life

Mechanisms affecting the gut of preterm infants in enteral feeding trials: a nested cohort within a randomised controlled trial of lactoferrin – Young et al. – Arch Dis Child Fetal Neonatal Ed

Human oral microbiome

Ancient oral microbiomes support gradual Neolithic dietary shifts towards agriculture – Quagliariello et al. – Nature Communications

Human vaginal microbiome

[PREPRINT]Longitudinal dynamics of the human vaginal ecosystem across the reproductive cycle – Costello et al. – bioRxiv

Human gut microbiome

[REVIEW]Maternal obesity and resistance to breast cancer treatments among offspring: Link to gut dysbiosis – Andrade, Verma & Hilakivi-Clark

Atypical enteropathogenic E. coli are associated with disease activity in ulcerative colitis – Baumgartner et al. – Gut Microbes

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

Impact of antibiotic perturbation on fecal viral communities in mice – Anderson et al. – G3

Animal microbiome (for animals in the wild)

Assessing Fungal Diversity and Abundance in the Black Soldier Fly and its Environment – Vitenberg & Opatovsky – Journal of Insect Science

Plant, root, and soil microbiome

Bacterial communities vary across populations and tissue type in red mangroves (Rhizophora mangle, Rhizophoraceae) along an expanding front – Scherer, Mason & Rast – FEMS Microbiology Ecology


proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes – Fullam et al. – NAR

[PREPRINT]Sparsification of Large Ultrametric Matrices: Insights into the Microbial Tree of Life – Gorman & Lladser


[PREPRINT]Soil metatranscriptomics: An improved RNA extraction method toward functional analysis using nanopore direct RNA sequencing – Poursalavati et al. – bioRxix

November 16, 2022

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


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


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

November 14, 2022

Human and General Microbiome

Genetic regulation of serum IgA levels and susceptibility to common immune, infectious, kidney, and cardio-metabolic traits – Lili Liu – Nature Communications

Kidney microbiota dysbiosis contributes to the development of hypertension – Xin-Yu Liu – Gut Microbes

Gut mycobiota dysbiosis in drug-naïve, first-episode schizophrenia – Xiuxia Yuan – Schizophrenia Research

Transcriptomic analysis reveals an association of FCGBP with Parkinson’s disease – Pilar Gómez-Garre – NPJ Parkinson’s Disease

Integration of stool microbiota, proteome and amino acid profiles to discriminate patients with adenomas and colorectal cancer – Sofie Bosch – Gut Microbes

Human gut homeostasis and regeneration: the role of the gut microbiota and its metabolites – Claudia Marcela Arenas-Gómez – Critical Reviews in Microbiology

Colibactin possessing E. coli isolates in association with colorectal cancer and their genetic diversity among Pakistani population – Habiba Tariq – PloS one

Intestinal toxicity to CTLA-4 blockade driven by IL-6 and myeloid infiltration – Yifan Zhou – The Journal of Experimental Medicine

Genome-microbiome interplay provides insight into the determinants of the human blood metabolome – Christian Diener – Nature Metabolism

Vaginal microbiota in women with spontaneous preterm labor versus those with term labor in Kenya: a case control study – Edgar Gulavi – BMC Microbiology

Characteristics of oral microbiome of healthcare workers in different clinical scenarios: a cross-sectional analysis – Zhixia Zhang – BMC Oral Health

Multi-kingdom gut microbiota analyses define COVID-19 severity and post-acute COVID-19 syndrome – Qin Liu – Nature Communications

Characterization of antibiotic-resistance traits in Akkermansia muciniphila strains of human origin – Rossella Filardi – Scientific Reports

Food Microbiome

Causality Verification for the Correlation between the Presence of Nonstarter Bacteria and Flavor Characteristics in Soft-Type Ripened Cheeses – Ryosuke Unno – Microbiology Spectrum

Animal Microbiome

Microbiota of healthy and bleached corals of the species Siderastrea stellata in response to river influx and seasonality in Brazilian northeast – Gustavo Vasconcelos Bastos Paulino – Environmental Science and Pollution Research International

Environmental Microbiome

Exploring structure, microbiota, and metagenome functions of epigean and hypogean black deposits by microscopic, molecular and bioinformatic approaches – Beatrice Farda – Scientific Reports

Plant Microbiome

High throughput method of 16S rRNA gene sequencing library preparation for plant root microbial community profiling – Kie Kumaishi – Scientific Reports

Sugarcane cultivation practices modulate rhizosphere microbial community composition and structure – Ana Paula Corrêa Moneda – Scientific Reports

Effects of Two Bacillus velezensis Microbial Inoculants on the Growth and Rhizosphere Soil Environment of Prunus davidiana – Huimin Shi – International Journal of Molecular Sciences

Review: Climate change and plant pathogens – Muhammad M Raza – Current Opinion in Microbiology

Bioinformatics and Microbiome Analysis

Faecal microbiome-based machine learning for multi-class disease diagnosis – Qi Su – Nature Communications

Wochenende – modular and flexible alignment-based shotgun metagenome analysis – Ilona Rosenboom – BMC Genomics

De novo identification of microbial contaminants in low microbial biomass microbiomes with Squeegee – Yunxi Liu – Nature Communications