April 07, 2021

General microbiome

Primate phageomes are structured by superhost phylogeny and environment – Gogarten et al. – PNAS

Fungal‐induced glycolysis in macrophages promotes colon cancer by enhancing innate lymphoid cell secretion of IL‐22 – Zhu et al. – The EMBO Journal

A method for detection of SARS-CoV-2 RNA in healthy human stool: a validation study – Coryell et al. – The Lancet Microbe

The Ocular Microbiome and Microbiota and their Effects on Ocular Surface Pathophysiology and Disorders – Aragona et al. – Survey of Ophthalmology

Human oral microbiome

Multi-dimensional study of the oral microbiome, metabolite, and immunologic environment in peanut allergy – Ho et al. – Journal of Allergy and Clinical Immunology

Human skin microbiome

Temporal Variation in Staphylococcus aureus Protein A Genotypes from Nose and Skin in Atopic Dermatitis Patients – van Mierlo et al. – Dermatology

Sex‐Based Differences in Fecal Short‐Chain Fatty Acid and Gut Microbiota in Irritable Bowel Syndrome Patients – Sun et al. – Journal of Digestive Diseases

Human gut microbiome

[REVIEW]Ecological and evolutionary responses to antibiotic treatment in the human gut microbiota – Pennycook & Scanlan – FEMS Microbiology Reviews

Animal microbiome (for animals in the wild)

The Fecal and Serum Metabolomics of Giant Pandas Based on Untargeted Metabolomics – Yang et al. – Zoological Scienc

Microbes in space

Astrobiology of life on Earth – Hallsworth et al. – Environmental Microbiology
Mars’ surface is not universally biocidal – Hallsworth – Environmental Microbiology

Bioinformatics

Draft Genome Sequences and Antimicrobial Profiles of Three Staphylococcus epidermidis Strains from Neonatal Blood Samples – Afeke et al. – Microbiology Resource Announcements

CoCoNet: An Efficient Deep Learning Tool for Viral Metagenome Binning – Arisdakessian et al. – Bioinformatics

Techniques

Rank normalization empowers a t-test for microbiome differential abundance analysis while controlling for false discoveries – Davis, Huang & Wang – Briefings in Bioinformatics

Discovering multiple types of DNA methylation from bacteria and microbiome using nanopore sequencing – Tourancheau et al. – Nature Methods

March 16, 2021

Human gut microbiome

Strain-level functional variation in the human gut microbiota based on bacterial binding to artificial food particles – Patnode et al. Cell Host & Microbe. 

Debaryomyces is enriched in Crohn’s disease intestinal tissue and impairs healing in mice – Jain et al. Science.

Dysbiosis in Metabolic Genes of the Gut Microbiomes of Patients with an Ileo-anal Pouch Resembles That Observed in Crohn’s Disease – Dubinsky et al. mSystems

Human-associated microbiota suppress invading bacteria even under disruption by antibiotics – Letten et al. ISME

Early life 

Key bacterial taxa and metabolic pathways affecting gut short-chain fatty acid profiles in early life – Tsukuda et al. ISME

Human oral microbiome

Tonsillar Microbiota: a Cross-Sectional Study of Patients with Chronic Tonsillitis or Tonsillar Hypertrophy – Wu et al. mSystems

Animal experiments 

Long-term evolution and short-term adaptation of microbiota strains and sub-strains in mice – Yilmaz et al. Cell Host & Microbe

Bioinformatics

ContigExtender: a new approach to improving de novo sequence assembly for viral metagenomics data – Deng & Delart. BMC Bioinformatics

March 12, 2021

Today’s digest is HUGE.

Read about the healthy urogenital microbiome profiling by culturomics, gutSMASH (Specialized Primary Metabolite Analysis From Anaerobic Bacteria), (sub)strains evolution in mice, and AMPSphere (a comprehensive catalog of antimicrobial peptides).

There are interesting results of a new metaanalysis of the neonatal microbiome, maternal strain inheritance, and persistence into adolescence, evaluation of the effect of long-term freezing storage temperature on fecal samples, and estimation of the bioinformatic carbon footprint using the freely available Green Algorithms calculator. Find out more about statistics & challenges in molecular microbiology (with a reproducible research appendix!).

NEWS: The Transbiome project is a community driven research program using crowdfunding and co-creation to discover the diversity of the neo-vaginal microbiome. You can support the project here.

Check out a list of awesome webinars, courses and podcasts. Happy Friday!

Gut microbiome

*A systematic analysis of metabolic pathways in the human gut microbiota – Victòria Pascal Andreu – bioRxiv

*Strain inheritance and neonatal gut microbiota development: A meta-analysis – Daniel Podlesny and W. Florian Fricke – International Journal of Medical Microbiology

Adaptive ecological processes and metabolic independence drive microbial colonization and resilience in the human gut – Andrea R. Watson – bioRixv

Effect of fecal microbiota transplantation on neurological restoration in a spinal cord injury mouse model: involvement of brain-gut axis – Yingli Jing – Microbiome

Review: Association between antibiotics and gut microbiome dysbiosis in children: systematic review and meta-analysis – Lucy McDonnell – Gut Microbes

Review: Salmonella versus the Microbiome – Andrew W. L. Rogers – Microbiology and Molecular Biology Reviews

Respiratory microbiome

Strain-Resolved Dynamics of the Lung Microbiome in Patients with Cystic Fibrosis – Marija Dmitrijeva – mBio

Oral microbiome

Review: Resilience of the oral microbiome – William G. Wade – Periodontology 2000

Skin microbiome

Skin microbiota and clinical associations in Netherton sindrome – Veera Sillanpää – JID Innovations

Urogenital microbiome

*Long-term stability of the urogenital microbiota of asymptomatic European women – Magdalena Ksiezarek – BMC Microbiology

Limosilactobacillus urinaemulieris sp. nov. and Limosilactobacillus portuensis sp. nov. isolated from urine of healthy women – Magdalena Ksiezarek – International Journal of Systematic and Evolutionary Microbiology

Vaginal microbiome

The structure and diversity of strain-level variation in vaginal bacteria – Brett A. Tortelli – Microbial Genomics

Obesity is associated with lower bacterial vaginosis prevalence in menopausal but not pre-menopausal women in a retrospective analysis of the Women’s Interagency HIV Study – Elizabeth Daubert – PlosOne

Bacterial biofilm formation on vaginal ring pessaries used for pelvic organ prolapse – Felicity G. Gould – International Urogynecology Journal

Animal microbiome

*Long-term storage of feces at −80 °C versus −20 °C is negligible for 16S rRNA amplicon profiling of the equine bacterial microbiome – Stefan Gavriliuc – PeerJ

Differences in the gut microbiomes of dogs and wolves: roles of antibiotics and starch – Yuting Liu – BMC Veterinary Research

An Expanded Gene Catalog of Mouse Gut Metagenomes – Jiahui Zhu – mSphere

Animal experiments

*Long-term evolution and short-term adaptation of microbiota strains and sub-strains in mice – Bahtiyar Yilmaz – Cell Host & Microbe

The gut mycobiome of healthy mice is shaped by the environment and correlates with metabolic outcomes in response to diet – Tahliyah S. Mims – Communications Biology

Functional genetics of human gut commensal Bacteroides thetaiotaomicron reveals metabolic requirements for growth across environments – Hualan Liu – Cell Reports

Tea polyphenols regulate gut microbiota dysbiosis induced by antibiotic in mice – Jie Li – Food Research International

Plant microbiome

Designing a home for beneficial plant microbiomes – Chunxu Song – Current Opinion in Plant Biology

Food

Review: Polymicrobial interaction between Lactobacillus and Saccharomyces cerevisiae: coexistence-relevant mechanisms – Zhenbo Xu – Critical Reviews in Microbiology

Viruses and phages

Viromes outperform total metagenomes in revealing the spatiotemporal patterns of agricultural soil viral communities – Christian Santos-Medellin – The ISME Journal

Review: Biases in Viral Metagenomics-Based Detection, Cataloguing and Quantification of Bacteriophage Genomes in Human Faeces, a Review – Julie Callanan – Microorganisms

Techniques

High molecular weight DNA extraction strategies for long-read sequencing of complex metagenomes – Florian Trigodet – bioRxiv

Bioinformatics

*AMPSphere: the worldwide survey of prokaryotic antimicrobial peptides – Célio Dias Santos-Júnior – Zenodo

*A Statistical Perspective on the Challenges in Molecular Microbial Biology – Pratheepa Jeganathan and Susan P. Holmes – arXiv

*The carbon footprint of bioinformatics – Jason Grealey – bioRxiv

*Make Interactive Complex Heatmaps in R – Zuguang Gu and Daniel Huebschmann – bioRxiv

Machine learning applications in microbial ecology, human microbiome studies, and environmental monitoring – Ryan B.Ghannam and Stephen M.Techtmann – Computational and Structural Biotechnology Journal

Tutorial: assessing metagenomics software with the CAMI benchmarking toolkit – Fernando Meyer – Nature Protocols

STATegra: Multi-Omics Data Integration – A Conceptual Scheme With a Bioinformatics Pipeline – Nuria Planell – Frontiers in Genetics

Exploring bacterial diversity via a curated and searchable snapshot of archived DNA sequences – Grace A. Blackwell – bioRxiv

clinker & clustermap.js: automatic generation of gene cluster comparison figures – Cameron L M Gilchrist & Yit-Heng Chooi – Bioinformatics

gapseq: informed prediction of bacterial metabolic pathways and reconstruction of accurate metabolic models – Johannes Zimmermann – Genome Biology

Webinars

mSystems Thinking Series: Diversity, Equity, and Inclusion in Microbiology – ASM – March 26

The Microbiome Centers Consortium Seminar Series – weekly seminars featuring early career researchers – Thursdays

Americas Webinar: Mother’s Milk & Baby’s Bacteria: Discoveries from the CHILD Cohort Study – Meghan Azad – April 14

Courses & Workshops

Get R Done: R Tutorials video series – Chad C. Williams

Machine Learning in Genomics: Tools, Resources, Clinical Applications and Ethics – the NHGRI Genomic Data Science Working Group of the National Advisory Council for Human Genome Research – April 13-14

Podcast

February 2021 Pod: Global Chang‪e‬ – Bengtsson-Palme Lab – Microbiology Lab Pod

Enhancers with Molly Gasperini – Jacob Schreiber – The Bioinformatics Chat

Matthew Schechter: Metagenomics History Part 1 and 2 – Leo Elworth – The Bioinformatics and Beyond Podcast

Ep. 33 Oyster Microbiome with Dr. Rachel Diner – Julie Laurin – Planet B612

Art

UMich Microbial Masterpieces – Community for microbe enthusiasts and artists – Erica Gardner, Anna Urso, Bruna Iunes Sanches
*Check out their giant Winogradsky Panel in the Duderstadt Center gallery

February 25, 2021

General microbiome
The evolution of coexistence from competition in experimental co-cultures of Escherichia coli and Saccharomyces cerevisiae – Jake N. Barber – ISME Journal

Human microbiome
Quantifying the effects of antibiotic treatment on the extracellular polymer network of antimicrobial resistant and sensitive biofilms using multiple particle tracking – Lydia C. Powell – npj Biofilms and Microbiomes

Biofilms harbour Clostridioides difficile, serving as a reservoir for recurrent infection – Charmaine Normington – npj Biofilms and Microbiomes

Gut microbiome
REVIEW: The contribution of gut bacterial metabolites in the human immune signaling pathway of non-communicable diseases – F. Hosseinkhani – Gut Microbes

The effect of acute moderate-intensity exercise on the serum and fecal metabolomes and the gut microbiota of cross-country endurance athletes – Mariangela Tabone – Scientific Reports

Oral microbiome
Candida albicans promotes tooth decay by inducing oral microbial dysbiosis – Qian Du – ISME Journal

Characterization of oral virome and microbiome revealed distinctive microbiome disruptions in paediatric patients with hand, foot and mouth disease – Si Xian Ho – npj Biofilms and Microbiomes

Skin microbiome
Characterization of the human skin resistome and identification of two microbiota cutotypes – Zhiming Li – Microbiome

Animal experiment
A gene co-association network regulating gut microbial communities in a Duroc pig population – Antonio Reverter – Microbiome

Modulating gut microbiota in a mouse model of Graves’ orbitopathy and its impact on induced disease – Sajad Moshkelgosha – Microbiome

Multi-compartment metabolomics and metagenomics reveal major hepatic and intestinal disturbances in cancer cachectic mice – Sarah A. Pötgens – Journal of Cachexia, Sarcopenia and Muscle

Expanded catalog of microbial genes and metagenome-assembled genomes from the pig gut microbiome – Congying Chen – Nature Communications

Mining zebrafish microbiota reveals key community-level resistance against fish pathogen infection – Franziska A. Stressmann – ISME Journal

Plant, root, and soil microbiome
REVIEW: From exploration to remediation: A microbial perspective for innovation in mining – Alan Levett – Earth-Science Reviews

Food microbiology
A Combined Metagenomics and Metatranscriptomics Approach to Unravel Costa Rican Cocoa Box Fermentation Processes Reveals Yet Unreported Microbial Species and Functionalities – Marko Verce – Frontiers in Microbiology

Water and extremophile microbiome
Mechanistic strategies of microbial communities regulating lignocellulose deconstruction in a UK salt marsh – Daniel R. Leadbeater – Microbiome

Taxonomic and functional analyses of intact microbial communities thriving in extreme, astrobiology-relevant, anoxic sites – Alexandra Kristin Bashir – Microbiome

Genomic evidence for sulfur intermediates as new biogeochemical hubs in a model aquatic microbial ecosystem – Adrien Vigneron – Microbiome

REVIEW: The Seagrass Holobiont: What We Know and What We Still Need to Disclose for Its Possible Use as an Ecological Indicator – Chiara Conte – Water

Spatiotemporal variations and relationships of phosphorus, phosphomonoesterases, and bacterial communities in sediments from two Chilean rivers – Marco Camposa – Science of The Total Environment

Resource partitioning of phytoplankton metabolites that support bacterial heterotrophy – Frank Xavier Ferrer-González – ISME Journal

Phages and virues
Next-generation diagnostics: virus capture facilitates a sensitive viral diagnosis for epizootic and zoonotic pathogens including SARS-CoV-2 – Claudia Wylezich – Microbiome

Preliminary Assessment of Viral Metagenome from Cancer Tissue and Blood from Patients with Lung Adenocarcinoma – Hua‐Zhong Cai – Journal of Medical Virology

Bioinformatics
PathoFact: a pipeline for the prediction of virulence factors and antimicrobial resistance genes in metagenomic data – Laura de Nies – Microbiome

CANTARE: finding and visualizing network-based multi-omic predictive models – Janet C. Siebert – BMC Bioinformatics

kLDM: Inferring Multiple Metagenomic Association Networks based on the Variation of Environmental Factors – Yuqing Yang – Genomics, Proteomics & Bioinformatics

Methods
REVIEW: Cross-species RNA-seq for deciphering host–microbe interactions – Alexander J. Westermann – Nature Review Genetics

A community resource for paired genomic and metabolomic data mining – Michelle A. Schorn – Nature Chemical Biology

Pre-prints
Cross-sectional analysis of the microbiota of the human gut and their direct environment (exposome) in a household cohort in northern Vietnam – Bich Vu Thi Ngoc – bioRxiv

HumGut: A comprehensive Human Gut prokaryotic genomes collection filtered by metagenome data – Pranvera Hiseni – bioRxiv

Comparative analysis of 16S rRNA gene and metagenome sequencing in pediatric gut microbiomes – Danielle Peterson – bioRxiv

Unifying the known and unknown microbial coding sequence space – Chiara Vanni – bioRxiv

February 24, 2021

Today’s digest is about functional analyses of microbial community in anoxic sites, microbial life in billions of years old fluid inclusions, development and use of human skin commensal, expanded pig metagenome catalogue and a brilliant review on advances in RNAseq technologies to decipher host-microbiota interactions. Happy reading!

General microbiome

Taxonomic and functional analyses of intact microbial communities thriving in extreme, astrobiology-relevant, anoxic sites – Alexandra Kristin Bashir – Microbiome

Pseudomonas kielensis sp. nov. and Pseudomonas baltica sp. nov., isolated from raw milk in Germany – Stefanie Gieschler – International Journal of Systematic and Evolutionary Microbiology

Human microbiome

Development of a human skin commensal microbe for bacteriotherapy of atopic dermatitis and use in a phase 1 randomized clinical trial – Teruaki Nakatsuji – Nature Medicine

Gut microbiome diversity is an independent predictor of survival in cervical cancer patients receiving chemoradiation – Travis T. Sims – Communications Biology

Characterization of the human skin resistome and identification of two microbiota cutotypes – Zhiming Li – Microbiome

Microbial analyses of blood spot surfaces collected from a laboratory and the bathroom of a female single-person household under different environmental conditions – Hee Sang You – FEMS Microbiology Letters

Animal microbiome

Antidepressants fluoxetine and amitriptyline induce alterations in intestinal microbiota and gut microbiome function in rats exposed to chronic unpredictable mild stress – Weijie Zhang – Translational Psychiatry

Ginsenoside Rk3 Ameliorates Obesity-Induced Colitis by Regulating of Intestinal Flora and the TLR4/NF-κB Signaling Pathway in C57BL/6 Mice – Hongwei Chen – Journal of Agricultural and Food Chemistry

Dietary anthocyanin-rich extract of açai protects from diet-induced obesity, liver steatosis, and insulin resistance with modulation of gut microbiota in mice – Haizhao Song – Nutrition

Effects of supplementing sow diets during late gestation with Pennisetum purpureum on antioxidant indices, immune parameters and faecal microbiota – Peng‐Fei Huang – veterinary Medicine and Science

Alterations in the gut microbiome and metabolic profile in rats acclimated to high environmental temperature – Yang Cao – Microbial Biotechnology

The pelvic flexure separates distinct microbial communities in the equine hindgut – Kailee J. Reed – Scientific Reports

Effects of urolithins on obesity-associated gut dysbiosis in rats fed on a high-fat diet – Abdulrasheed O. Abdulrahman – International Journal of Food Sciences and Nutrition

Functional Foods

Prebiotic Lactulose Ameliorates the Cognitive Deficit in Alzheimer’s Disease Mouse Model through Macroautophagy and Chaperone-Mediated Autophagy Pathways – Yan-Suan Lee – Journal of Agricultural and Food Chemistry

Water microbiome

Ingredients for microbial life preserved in 3.5 billion-year-old fluid inclusions – Helge Mißbach – Nature Communications

Techniques

Expanded catalog of microbial genes and metagenome-assembled genomes from the pig gut microbiome – Congying Chen – Nature Communications

Cross-species RNA-seq for deciphering host–microbe interactions – Alexander J. Westermann – Nature Reviews Genetics

Computational modeling of the gut microbiota reveals putative metabolic mechanisms of recurrent Clostridioides difficile infection – Michael A. Henson – Plos Computational Biology

An ambient-temperature storage and stabilization device performs comparably to flash-frozen collection for stool metabolomics in infants – Sivapriya Ramamoorthy – BMC Microbiology

Ecological rules for the assembly of microbiome communities – Katharine Z. Coyte – Plos Biology

February 16th, 2021

Good afternoon from sunny Adelaide, Australia. Today’s digest highlights a range of interesting microbiome research, an article in Science modelling the future of SARS-CoV2, and a commentary in Cell on data sharing.

COVID-19

Immunological characteristics govern the transition of COVID-19 to endemicity – Lavine et al. Science.

Human gut microbiome

Can we modulate the breastfed infant gut microbiota through maternal diet? – Sindi et al. FEMS Microbiology Reviews. 

Impact of synbiotics on gut microbiota during early life: a randomized, double-blind study – Phavichitr et al. Scientific Reports

Adaptation of the small intestine to microbial enteropathogens in Zambian children with stunting – Amadi et al. Nature Microbiology

Genomic aberrations after short-term exposure to colibactin-producing E. coli transform primary colon epithelial cells – Iftekhar et al. Nature Communications

Animal experiments 

Human Milk-Fed Piglets Have a Distinct Small Intestine and Circulatory Metabolome Profile Relative to That of Milk Formula-Fed Piglets –  Rosa et al. – mSystems

Human oral microbiome

Impact of the repurposed drug thonzonium bromide on host oral-gut microbiomes – Simon-Soro et al. npj biofilms and microbiomes

Marine  microbiome 

Deciphering a Marine Bone-Degrading Microbiome Reveals a Complex Community Effort – Borchest et al. – mSystems

Phages and viruses

Balance between promiscuity and specificity in phage λ host range – Andrews and Fields – ISME

Bioinformatics

Resolving cryptic species complexes in marine protists: phylogenetic haplotype networks meet global DNA metabarcoding datasets – Luca et al – ISME

A “data sharing trust” model for rapid, collaborative science – Chan et al. –  Cell

A 16S rRNA Gene and Draft Genome Database for the Murine Oral Bacterial Community – Joseph et al. – mSystems 

February 03, 2021

Job market

Postdoctoral Associate in quantitative microbial dynamics in the Clark lab at Duke University

General microbiome

[COMMENT]Microbiome innovations for a sustainable future – D’Hondt et al. – Nature Microbiology

Kin selection explains the evolution of cooperation in the gut microbiota – Simonety & McNally – PNAS

[REVIEW]Crossing Kingdoms: How the Mycobiota and Fungal-Bacterial Interactions Impact Host Health and Disease – Santus, Devlin & Behnsen – Infection and Immunity

Pregnancy and early life

Pregnant women who develop preeclampsia have lower abundance of the butyrate-producer Coprococcus in their gut microbiota – Altemani et al. – Pregnancy Hypertension

Human oral microbiome

Toothbrush microbiomes feature a meeting ground for human oral and environmental microbiota – Blaustein et al. – Microbiome

The role of Saccharibacteria (TM7) in the subginival microbiome as a predictor for secondary cardiovascular events – Schulz et al. – International Journal of Cardiology

Human gut microbiome

The seasonal changes of the gut microbiome of the population living in traditional lifestyles are represented by characteristic species-level and functional-level SNP enrichment patterns – Zhu et al. – BMC Genomics

The pleiotropic effects of prebiotic galacto-oligosaccharides on the aging gut – Arnold et al. – Microbiome

[REVIEW]Priming for Life: Early Life Nutrition and the Microbiota-Gut-Brain Axis – Ratsika et al. – Nutrients

[REVIEW]Gut Microbial Signatures in Sporadic and Hereditary Colorectal Cancer – Mori & Pasca – Int. J. Mol. Sci.

Animal microbiome (for animals in the wild)

[REVIEW]Mechanisms underlying gut microbiota–host interactions in insects – Schmidt & Engel

Plant, root, and soil microbiome

[REVIEW]Plant microbiome structure and benefits for sustainable agriculture – dos Santos & Olivares – Current Plant Biology

A microbial gene catalog of anaerobic digestion from full-scale biogas plants – Ma et al. – GigaScience

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

Microbial intrusion and seasonal dynamics in the groundwater microbiome of a porous basaltic rock aquifer used as municipal water reservoir – Knobloch et al. – FEMS Microbiology Ecology

Bacterial Diversity and Community Composition Distribution in Cold-Desert Habitats of Qinghai–Tibet Plateau, China – Zhang et al. – Microorganisms

Food microbiology

Bacterial community dynamics during different stages of processing of smoked bacon using the 16S rRNA gene amplicon analysis – Li et al. – International Journal of Food Microbiology

Bioinformatics

[PREPRINT]PredicTF: a tool to predict bacterial transcription factors in complex microbial communities – Monteiro et al. – bioRxiv

tidyMicro: a pipeline for microbiome data analysis and visualization using the tidyverse in R – Carpenter et al. – BMC Bioinformatics

Techniques

In vitro infection models to study fungal-host interaction – Last et al. – FEMS Microbiology Reviews

Microbes in the news (popular press, EurekAlert, ScienceDaily, Youtube, NPR, etc)

Exploring the Relationship Between the Microbiome, Precision Medicine and Cancer – Tom Williams – Technology Networks

January 21, 2021

Today’s post include review article on gut-liver axis, research articles on diet-microbiota interaction in Chinese adults, association between microbiome and type1 diabetes, and new metagenomic profiling method using phylogenetic markers.

General microbiome

Bacterial and eukaryotic extracellular vesicles and non-alcoholic fatty liver disease: new players in the gut-liver axis? – Alexandre Villard – American Joural of Physiology Gastrointestinal and Liver Physiology

Potential Contribution of the Intestinal Microbiome to Phenethylamine-Induced Hyperthermia – Aburahma A. – Brain, Behavior and Evolution

Human microbiome

Long-term diet quality is associated with gut microbiome diversity and composition among urban Chinese adults – Danxia Yu – American Journal of Clinical Nutrition

Long-term dietary intake from infancy to late adolescence is associated with gut microbiota composition in young adulthood – Kolade Oluwagbemigun – American Journal of Clinical Nutrition

The gut microbiota metabolite propionate ameliorates intestinal epithelial barrier dysfunction-mediated Parkinson’s disease via the AKT signaling pathway – Tingting Huang – Neuroreport

Fecal and mucosal microbiota profiling in pediatric inflammatory bowel diseases – Lorenza Putignani – European Journal of Gastroenterology and Hepatology

Associations between diet, the gut microbiome and short chain fatty acids in youth with islet autoimmunity and type 1 diabetes – Jessica E. Harbison – Pediatric Diabetes

Reproducing the scalp microbiota community: co‐colonization of a 3D reconstructed human epidermis with C. acnes and M. restricta – Marisa Melon – International Journal of Cosmetic Science

Hepatic steatosis relates to gastrointestinal microbiota changes in obese girls with polycystic ovary syndrome – Beza Jobira – PlosOne

Animal microbiome

Infection trains the host for microbiota-enhanced resistance to pathogens – Apollo Stacy – Cell

Changes of Gut Microbiota and Its Correlation With Short Chain Fatty Acids and Bioamine in Piglets at the Early Growth Stage – Renli Qi – Frontiers in Veterinary Science

Functional Foods

Prospecting Human Milk Oligosaccharides as a Defense Against Viral Infections – Rebecca E Moore- ACS Infectious Diseases

Techniques

TIPP2: metagenomic taxonomic profiling using phylogenetic markers – Nidhi Shah – Bioinformatics

Precision long-read metagenomics sequencing for food safety by detection and assembly of Shiga toxin-producing Escherichia coli in irrigation water – Meghan Maguire – PlosOne

Microbes in news

Your Microbiome Isn’t Shaped Just By What You Feed It – Discover

Taurine Enhances the Microbiome’s Resistance to Future Pathogens – Genetic Engineering and Biotech News

December 23, 2020

Good morning from Northern Germany! It is almost Xmas. Today’s microbiome digest is rather long and comprises some interesting findings about c-section and the gut microbiome in early life, human breast milk, chronic pain, antimicrobial resistance, imbalance of the gut microbiome in relation to Parkinon’s disease and COVID19, diet, honey bees (two pre-prints), roundup, and last but not least some bioinformatic papers. Additionally, we select some interesting reviews. Of specific interest is a study about showing reveals poor correlations in microbial taxonomic abundance between humans and mice after gnotobiotic transfer.

General microbiome

Sequence variant analysis reveals poor correlations in microbial taxonomic abundance between humans and mice after gnotobiotic transfer – Fouladi et al. – The ISME Journal

Application of ecological and evolutionary theory to microbiome community dynamics across systems – McDonald, Marchesi & Koskella – Proceedings of the Royal Society B

[BOOK CHAPTER]Salivary and Urinary Metabolome in Pediatric Obesity and Metabolic Syndrome – Troisi et al. – Obesity and Diabetes

Human early life microbiome

Cesarean delivery is associated with decreased beneficial gut microbes and increased pathobionts and butyrate excretion: a longitudinal study over the first year of life. – Mueller et al – BJOG

Human oral microbiome

[OPINION]Future directions for studying resilience of the oral ecosystem – Zemouri et al. – British Dental Journal

Human milk microbiome

Maternal diet alters human milk oligosaccharide composition with implications for the milk metagenome – Seferovic et al. – Scientific Reports

Mapping the Human Milk Microbiome: Impetus for a Long-Awaited Renaissance in Maternal and Infant Nutrition Research? – McGuire & McGuire – The Journal of Nutrition

[PREVIEW]Breast Milk Modulates Transgenerational Immune Inheritance – Zimmermann & Macpherson – Cell

An Immunologic Mode of Multigenerational Transmission Governs a Gut Treg Setpoint – Ramanan et al. – Cell

Human respiratory/lung microbiome

[REVIEW]The Lung Microbiome and Pneumonia – Pettigrew, Tanner & Harris

[REVIEW]Microbiome: A Supportive or a Leading Actor in Lung Cancer? – Martins, Mendes & Schmitt – Pathobiology

Human skin microbiome

[REVIEW]Skin and Gut Microbiome in Psoriasis: Gaining Insight Into the Pathophysiology of It and Finding Novel Therapeutic Strategies – Chen et al. – Frontiers in Microbiology

Human gut microbiome

An association between chronic widespread pain and the gut microbiome – Freidin et al. – Rheumatology

The Gut Microbiome as a Reservoir for Antimicrobial Resistance – Anthony et al. – The Journal of Infectious Diseases

[REVIEW]Dietary modification of gut microbial metabolism protects the kidney – Carney – Nature Reviews Nephrology

Gut Microbiome Imbalance and Neuroinflammation: Impact of COVID‐19 on Parkinson’s Disease – Follmer – Movement Disorders

US nativity and dietary acculturation impact the gut microbiome in a diverse US population – Peters et al. – The ISME Journal

[REVIEW]Gut Microbiota Status in COVID-19: An Unrecognized Player? – Zeppa et al. – Front. Cell. Infect. Microbiol.

Animal microbiome

[PREPRINT]Honeybee gut microbiota modulates host behaviors and neurological processes – Zhang et al. – bioaRxiv

[PREPRINT]Honeybee genetics shape the strain-level structure of gut microbiota in social transmission – Wu et al. – bioRxiv

Description of the microbiota in epidermal mucus and skin of sharks (Ginglymostoma cirratum and Negaprion brevirostris) and one stingray (Hypanus americanus) – Caballero et al. – PeerJ

Roundup causes embryonic development failure and alters metabolic pathways and gut microbiota functionality in non-target species – Microbiome – Suppa et al. – Microbiome

Plant, root, and soil microbiome

Influence of vintage, geographic location and cultivar on the structure of microbial communities associated with the grapevine rhizosphere in vineyards of San Juan Province, Argentina – Aguilar et al. – PLOS One

[REVIEW]Restoring degraded microbiome function with self-assembled communities – Gutierrez et al. – FEMS Microbiology Ecology

Combining whole-genome shotgun sequencing and rRNA gene amplicon analyses to improve detection of microbe–microbe interaction networks in plant leaves – Regalado et al. – The ISME Journal

Bioinformatics/Data analysis

A joint modeling approach for longitudinal microbiome data improves ability to detect microbiome associations with disease – PLOS Computation Biology – Luna, Mansbach & Shaw

Predicting Nash equilibria for microbial metabolic interactions – Cai, Tan & Chan – Bioinformatics

microeco: An R package for data mining in microbial community ecology – Liu et al. – FEMS Microbiology Ecology

[REVIEW]Multi-omics data integration considerations and study design for biological systems and disease – Graw et al. – Molecular Omics

Techniques

[PREPRINT]Improved microbial community characterization of 16S rRNA via metagenome hybridization capture enrichment – Beaudry et al. – bioRxiv

December 17, 2020

Bonjour from Paris, France ! In today’s digest, readers interested in viromes will find a nice selection of papers looking at the viral populations associated to deep lake waters, birds, star fish and human gut! I also recommend anyone interested in this topic to take a look at a preprint from Amgarten and collaborators presenting a new computational tool called “vHULK”, allowing an in-silico bacteriophage host prediction!

Readers may also be interested in taking a look at the announcement of a new web interface allowing the exploration of the Human Microbiome Project (HMP). The ressource, called HMPDACC, provides a unified data repository for the two phases of the HMP, allows to search samples on a multitude of metadata, and provides analysis pipelines and standardized protocols to facilitate community use of HMP dataset.

Finally, today’s non-microbiology digest is a paper taking a look at the avalanche of papers and preprints published this year around the COVID-19 pandemic. Impressively, 84,180 indexed publications were relevant to COVID-19 written by 322,279 unique authors from all scientific subfields (except for Automobile Design & Engineering scientists!)

Have a great Saturday!


General microbiome

Preprint: Trait Evolution in Microbial Communities – Zhao et al. – BioRXiv

Human gut microbiome

The Pre‐treatment Gut Microbiome is Associated with Lack of Response to Methotrexate in New Onset Rheumatoid Arthritis – Artacho et al. – Arthitis and Rheumatology

Chapter: Oral Microbes: A Hidden Yet Powerful Evidence for Futuristic Forensic Investigation – Patel and Ganguly Soni – In: Shrivastava P., et al. (eds) Forensic DNA Typing: Principles, Applications and Advancements. Springer.

Microbiome Analysis from Paired Mucosal and Fecal Samples of a Colorectal Cancer Biobank – Wirth et al. – Cancers


Animal microbiome

Not That Close to Mommy: Horizontal Transmission Seeds the Microbiome Associated with the Marine Sponge Plakina cyanorosea – Oliveira et al. – mircoorganisms


Phages and viruses

Comparative Metagenomics of Palearctic and Neotropical Avian Cloacal Viromes Reveal Geographic Bias in Virus Discovery – Truchado et al. – microorganisms

Virome Analysis of Near-Bottom Coastal Water of Lake Baikal – Butina et al. – Microbiology ressource announcements

Virome Variation during Sea Star Wasting Disease Progression in Pisaster ochraceus (Asteroidea, Echinodermata) – Hewson et al. – Viruses

Gut eukaryotic virome in colorectal carcinogenesis: Is that a trigger? – Massimino et al. – Computational and structural biotechnology journal

Bioinformatics

Preprint: vHULK, a new tool for bacteriophage host prediction based on annotated genomic features and deep neural networks – Amgarten et al. – BioRXiv

HMPDACC: a Human Microbiome Project Multi-omic data resource – Huot Creasy et al. Nucleic Acids Research

Review: Literature on Applied Machine Learning in Metagenomic Classification: A Scoping Review – Tonkovic et al. – biology


My non-microbiology picks

Preprint: The rapid, massive infection of the scientific literature and authors by COVID-19 – Ioannidis et al. – BioRXiv