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 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 8, 2022

Greetings from Pittsburgh, PA!

It’s election day here, which means I have low grade nausea and am looking for a distraction. If you’re in the same boat, check out today’s awesome articles on a holobiont deep sea shrimp, plant-microbiome assemblies of poplar trees, and viral community-wide auxiliary metabolic genes. I also included a few interesting preprints, my favorite of which is noted below and uses a microbiome public dataset to compare different normalization and transformation methods.

Animal microbiome

A novel and dual digestive symbiosis scales up the nutrition and immune system of the holobiont Rimicaris exoculata – Aubé et al. – Microbiome

Plant, root, and soil microbiome

Plant sex affects plant-microbiome assemblies of dioecious Populus cathayana trees under different soil nitrogen conditions – Guo et al. – Microbiome

Phages and viruses

Viral community-wide auxiliary metabolic genes differ by lifestyles, habitats, and hosts – Luo et al. – Microbiome


*Preprint: Alpha and beta-diversities performance comparison between different normalization methods and centered log-ratio transformation in a microbiome public dataset – Bars-Cortina – bioRxiv

Preprint: Noise reduction strategies in metagenomic chromosome confirmation capture to link antibiotic resistance genes to microbial hosts – McCallum et al. – bioRxiv

Preprint: Targeted metagenomics using probe capture detects a larger diversity of nitrogen and methane cycling genes in complex microbial communities than traditional metagenomics – Siljanen et al. – bioRxiv

November 7, 2022

Human and General Microbiome

Immunomodulatory fecal metabolites are associated with mortality in COVID-19 patients with respiratory failure – Matthew R Stutz – Nature Communications

Taxonomic Abundance in Primary and Secondary Root Canal Infections – Ronald Ordinola-Zapata – International Endodontic Journal

Review: The intestinal barrier in disorders of the central nervous system – Carolina Pellegrini – The Lancet. Gastroenterology & Hepatology

Review: Resistance is futile? Mucosal immune mechanisms in the context of microbial ecology and evolution – Emma Slack – Mucosal Immunology

Correspondence: A critical analysis of eating disorders and the gut microbiome – Sydney M Terry – Journal of Eating Disorders

Beneficial Microbes and Compounds

Bifidobacterial carbohydrate/nucleoside metabolism enhances oxidative phosphorylation in white adipose tissue to protect against diet-induced obesity – Gihyeon Kim – Microbiome

Lactobacillus rhamnosus GG supernatant promotes intestinal mucin production through regulating 5-HT4R and gut microbiota – Yu Gu – Food & Function

Animal Model Microbiome

Genetic and environmental circadian disruption induce weight gain through changes in the gut microbiome – Baraa Altaha – Molecular Metabolism

Strains producing different short-chain fatty acids alleviate DSS-induced ulcerative colitis by regulating intestinal microecology – Shuo Yang – Food & Function

Non-Model Animal Microbiome

Microbiome assembly and maintenance across the lifespan of bumble bee workers – Tobin J Hammer – Molecular Ecology

The gut microbiome reflects ancestry despite dietary shifts across a hybrid zone – Danny P Nielsen – Ecology Letters

Characterization of the core gut microbiota of Nile tilapia (Oreochromis niloticus): indication of a putative novel Cetobacterium species and analysis of its potential function on nutrition – Ziyue Zhang – Archives of Microbiology

Forensic Microbiome

Sampling from four geographically divergent young female populations demonstrates forensic geolocation potential in microbiomes – Thomas Clarke – Scientific Reports

Plant Microbiome

Insights into the potential for mutualistic and harmful host-microbe interactions affecting brown alga freshwater acclimation – Hetty KleinJan – Molecular Ecology

Built Environment Microbiome

Review: Microplastics in urban waters and its effects on microbial communities: a critical review – Saber Entezari – Environmental Science and Pollution Research International

Microbiome Analysis and Techniques

Assessing the Dark Field of Metaproteome – Haonan Duan – Analytical Chemistry

November 4, 2022

Today’s digest features a 30-color colorblind friendly color palette and functions for mapping color to hierarchical/nested data, ecosystem-specific reference databases, stoma samples for a very effective way of small intestinal microbiome characterization, and a reminder that 16S rRNA gene sequencing is NOT metagenomics. Happy Friday!

Join the next #MVIF when Sarah Lebeer will talk about citizen science and vaginal microbiome!!

Global resistome

Sharing of Antimicrobial Resistance Genes between Humans and Food Animals – Huiluo Cao – mSystems

Gut microbiome

Host-microbiome interactions: Gut-Liver axis and its connection with other organs – Swadha Anand & Sharmila S. Mande – npj Biofilms and Microbiomes

Gut microbiota bacterial strain richness is species specific and limits therapeutic engraftment – Alice Chen-Liaw – bioRxiv

Effects of different amoxicillin treatment durations on microbiome diversity and composition in the gut – Katrine Lekang – Plos One

The microbiota promotes social behavior by modulating microglial remodeling of forebrain neurons – Joseph J. Bruckner – Plos Biology

Strain-specific impacts of probiotics are a significant driver of gut microbiome development in very preterm infants – Lauren C. Beck – Nature Microbiology

*Plasticity of the adult human small intestinal stoma microbiota – Bahtiyar Yilmaz – Cell Host & Microbe


MIDAS2: Metagenomic Intra-species Diversity Analysis System – Chunyu Zhao – Bioinformatics

Automated identification of sequence-tailored Cas9 proteins using massive metagenomic data – Matteo Ciciani – Nature Communications

*microshades: An R Package for Improving Color Accessibility and Organization of Microbiome Data – Erin M. Dahl – Microbiology Resource Announcements

*Application of ecosystem-specific reference databases for increased taxonomic resolution in soil microbial profiling – Christina Karmisholt Overgaard – Frontiers in Microbiology

November 02, 2022

General microbiome

[RETRACTION]Metagenomic analysis exploring taxonomic and functional diversity of bacterial communities of a Himalayan urban fresh water lake – Ahmad et al. – PLOS One

Pregnancy and early life

A distinct clade of Bifidobacterium longum in the gut of Bangladeshi children thrives during weaning – Vatanen et al. – Clee

Multi-site human microbiome

[REVIEW]Recent advances in systemic lupus erythematosus and microbiota: from bench to bedside – Zhan et al. –

Human vaginal microbiome

Identification of shared bacterial strains in the vaginal microbiota of related and unrelated reproductive-age mothers and daughters using genome-resolved metagenomics – France et al. – PLOS One

Human gut microbiome

Gut microbiome dysbiosis in antibiotic-treated COVID-19 patients is associated with microbial translocation and bacteremia – Bernard-Raichon et al. – Nature Communications

Gut microbiota and myocardial fibrosis – Xu, Yang & Bao – European Journal of Pharmacology

Assessing the relationship between physical activity and the gut microbiome in a large, population-based sample of Wisconsin adults – Holzhausen et al. – PLOS One

Challenges and costs of donor screening for fecal microbiota transplantations – Bernard et al. – PLOS One

Animal microbiome

Gut colonization by Proteobacteria alters host metabolism and modulates cocaine neurobehavioral responses – Cuesta et al. – Cell Host & Microbe

Enriching captivity conditions with natural elements does not prevent the loss of wild-like gut microbiota but shapes its compositional variation in two small mammals – Koziol et al. – Microbiology Open

Understanding the Dynamic of POMS Infection and the Role of Microbiota Composition in the Survival of Pacific Oysters, Crassostrea gigas – Delisle et al. – Microbiology Spectrum

Changes in Gut Microbiota Structure: A Potential Pathway for Silver Nanoparticles to Affect the Host Metabolism – Wang et al. – ACS Nano

Skin microbiota of oxazolone-induced contact hypersensitivity mouse model – Mäenpää et al. – PLOS One

Effects of a farm-specific fecal microbial transplant (FMT) product on clinical outcomes and fecal microbiome composition in preweaned dairy calves – Slanzon et al. – PLOS One

Multiomics Characterization of the Canada Goose Fecal Microbiome Reveals Selective Efficacy of Simulated Metagenomes – Gil & Hird – Microbiology Spectrum

Uropygial gland microbiota differ between free-living and captive songbirds – Grieves et al. – Scientific Reports

Plant, root, and soil microbiome

Crop management shapes the diversity and activity of DNA and RNA viruses in the rhizosphere – Muscatt et al. – Microbiome


CRAMdb: a comprehensive database for composition and roles of microbiome in animals – Lei et al. – NAR


DNA extraction bias is more pronounced for microbial eukaryotes than for prokaryotes – Brauer & Bengtsson – Microbiology Open

synDNA—a Synthetic DNA Spike-in Method for Absolute Quantification of Shotgun Metagenomic Sequencing – Zaramela et al. – mSystems

October 26, 2022

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


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


[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

October 12, 2022

General microbiome

Global airborne bacterial community—interactions with Earth’s microbiomes and anthropogenic activities – Zhao et al. – PNAS

Tumor microbiome links cellular programs and immunity in pancreatic cancer – Cancer Cell – Ghaddar et al. – Cancer Cell

Human wound microbiome

The Wound Microbiome – White & Grice – Cold Spring Harbor Perspectives in Biology

Human gut microbiome

Pivotal interplays between fecal metabolome and gut microbiome reveal functional signatures in cerebral ischemic stroke – Zhou et al. – Journal of Translational Medicine volume

Gut-Testis Axis: Microbiota Prime Metabolome To Increase Sperm Quality in Young Type 2 Diabetes – Yan et al. – Microbiology Spectrum

Multi-angle meta-analysis of the gut microbiome in Autism Spectrum Disorder: a step toward understanding patient subgroups – West et al. – Scientific Reports

[REVIEW]The role of the gut microbiota in health and cardiovascular diseases – Wang et al. – Molecular Biomedicine

Animal microbiome

Airborne polystyrene microplastics and nanoplastics induce nasal and lung microbial dysbiosis in mice – Zha et al. – Chemosphere

Effects of urban particulate matter on gut microbiome and partial schizophrenia-like symptoms in mice: Evidence from shotgun metagenomic and metabolomic profiling – Yi et al. – Science of The Total Environment

Lactococcus lactis’ Effect on the Intestinal Microbiota of Streptococcus agalactiae-Infected Zebrafish (Danio rerio) – Tan et al. – Microbiology Spectrum

Exploring AI-2-mediated interspecies communications within rumen microbial communities – Liu et al. – Microbiome

Microbiome-driven breeding strategy potentially improves beef fatty acid profile benefiting human health and reduces methane emissions – Martinez-Alvaro et al. – Microbiome

Chicken intestinal microbiota modulation of resistance to nephropathogenic infectious bronchitis virus infection through IFN-I – Yin et al. – Microbiome

Plant, root, and soil microbiome

[CORRESONDENCE]Functionally-explicit sampling can answer key questions about the specificity of plant–microbe interactions – Fleishman et al. – Environmental Microbiome

Dissecting the cotranscriptome landscape of plants and their microbiota – Nobori et al. – EMBO Reports


MiMeDB: the Human Microbial Metabolome Database – Wishart et al. – NAR

gutMDisorder v2.0: a comprehensive database for dysbiosis of gut microbiota in phenotypes and interventions – Qi et al. – NAR