February 27th, 2021

Hyvää Päivää from Helsinki, Finland ! Today’s digest contains quite a lot of different topics. If you are interested in gut microbiomes, I recomment taking a look at the preprint by Weiss and collaborator. In this study, they explore bacteria-bacteria interactions, bacterial growth and metabolic interactions in a synthetic bacterial community: the Oligo-Mouse-Microbiota, which is increasingly used as model system in gut microbiome research.

Additionally, anyone interested in microbiome-based forensic tools should read the study from Sang You and collaborators.  They compared the composition of microbial communities in blood spot surfaces placed in different environments sampled across seasons and time points, in order to evaluate the environmental factors leading to variation in these microbial communities.

Today’s non-microbiology pick is a fascinating study looking at the prevalence of COVID-19 related misinformation among the Yemeni population and its association with vaccine acceptance and perceptions. From this study, the authors recommend the deployment of awareness campaigns to decrease misinformation before initiating any mass vaccination in Yemen.

Have a great Weekend!


Human gut microbiome

Review: The Multiomics Analyses of Fecal Matrix and Its Significance to Coeliac Disease Gut Profiling – Gangadoo et al. – International Journal of Molecular Sciences

Preprint: Exploring the interaction network of a synthetic gut bacterial community – Weiss et al. – BioRxiV


Animal experiments

Environmental concentrations of antibiotics alter the zebrafish gut microbiome structure and potential functions – Rehman Kayani et al. – Environmental Pollution

Fish farm effluents as a source of antibiotic resistance gene dissemination on Jeju Island, South Korea – Jo et al. – Environmental Pollution

Influence of environmental factors and bacterial community diversity in pond water on health of Chinese perch through Gut Microbiota change – Li et al. – Aquaculture Reports

Preprint: The diversity, composition, and metabolic pathways of archaea in pigs – Deng et al. – Preprints

Animal microbiome

Preprint: Stony Coral Tissue Loss Disease biomarker bacteria identified in corals and overlying waters using a rapid field-based sequencing approach – Becker et al. – bioRxiV

Built environment

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


Phages and viruses

Opinion paper: Rapid emergence of virus–host mutualism under stress – Dolja – PNAS

Patterns of virus growth across the diversity of life – Jin and Yin – Integrative biology

Techniques

Standard Bacteriophage Purification Procedures Cause Loss in Numbers and Activity – Carroll-Portillo et al. – Viruses


My non-microbiology picks

Preprint: Misinformation, Perceptions Towards COVID-19 and Willingness to be Vaccinated: A Population-Based Survey in Yemen – Naoras Bitar et al. – BioRxiV

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 12, 2021

Today’s quite diverse digest features: the role of gut commensal fungi mycobiota in shaping the human protective IgG antibody repertoire, Mouse Microbial Genome Collection, gut microbiome – lymphocytes – diet link, competition between Gardnerella species, microbiota-derived bile acids pool as a mediator of host–microbiota interactions, multiscale variation in genome graphs, and a list of awesome webinars, courses and podcasts. Check out two cool science and art projects, Bacterial Alphabet and Microbe Crayon. Happy Friday!

Gut microbiome

*Human gut mycobiota tune immunity via CARD9-dependent induction of anti-fungal IgG antibodies – Itai Doron – Cell

*Functional and taxonomic comparison of mouse and human gut microbiotas using extensive culturing and metagenomics – Benjamin S. Beresford-Jones – bioRxiv

*High intake of vegetables is linked to lower white blood cell profile and the effect is mediated by the gut microbiome – Cristina Menni – BMC Medicine

The Reactobiome Unravels a New Paradigm in Human Gut Microbiome Metabolism – Gholamreza Bidkhori – bioRxiv

Spatial analysis of gut microbiome reveals a distinct ecological niche associated with the mucus layer – Kellyanne Duncan – Gut Microbes

Review: Diversity and dynamism of IgA−microbiota interactions – Kelsey E. Huus – Nature Reviews Immunology

Antibiotic-associated dysbiosis affects the ability of the gut microbiota to control intestinal inflammation upon fecal microbiota transplantation in experimental colitis models – Francesco Strati – Microbiome

Adherent-invasive E. coli metabolism of propanediol in Crohn’s disease regulates phagocytes to drive intestinal inflammation – Monica Viladomiu – Cell Host & Microbe

Adults with Prader–Willi syndrome exhibit a unique microbiota profile – Wendy J. Dahl – BMC Research Notes

Vaginal microbiome

*Population density affects the outcome of competition in co-cultures of Gardnerella species isolated from the human vaginal microbiome – Salahuddin Khan and Janet E. Hill – bioRxiv

Review: Lactic acid-containing products for bacterial vaginosis and their impact on the vaginal microbiota: A systematic review – Erica L. Plummer – PlosOne

Urinary microbiome

Functional and Taxonomic Dysbiosis of the Gut, Urine, and Semen Microbiomes in Male Infertility – Scott D. Lundy – European Urology

Review: The microbiome and host mucosal interactions in urinary tract diseases – Bernadette Jones-Freeman – Mucosal Immunology

Epidemiology of urinary tract infections in children: Causative bacteria and antimicrobial therapy – Yuhei Tanaka – Paediatrics International

Human milk microbiome

Repeatability and reproducibility assessment in a large-scale population-based microbiota study: case study on human milk microbiota – Shirin Moossavi – Microbiome

Respiratory microbiome

Review: Respiratory microbiome in mechanically ventilated patients: a narrative review – Mélanie Fromentin – Intensive Care Medicine

Animal microbiome

Genomic and functional analyses of fungal and bacterial consortia that enable lignocellulose breakdown in goat gut microbiomes – Xuefeng Peng – Nature Microbiology

Metagenomics of antimicrobial and heavy metal resistance in the cecal microbiome of fattening pigs raised without antibiotics – Paiboon Tunsagool – Applied and Environmental Microbiology

Unravelling the Role of Rumen Microbial Communities, Genes, and Activities on Milk Fatty Acid Profile Using a Combination of Omics Approaches – Sokratis Stergiadis – Frontiers in Microbiology

Evaluation of the ocular surface mycobiota in clinically normal horses – Mary L. Walsh – PlosOne

Animal experiments

Colonization at birth with human CST IV cervicovaginal microbiota alters development and increases neonatal mortality in mice – Eldin Jašarević – bioRxiv

Novel gut pathobionts confound results in a widely used mouse model of human inflammatory disease – Samuel C Forster – bioRxiv

Low-dose exposure of glyphosate-based herbicides disrupt the urine metabolome and its interaction with gut microbiota – Jianzhong Hu – Scientific Reports

Microbiota control of maternal behavior regulates early postnatal growth of offspring – Yujung Michelle Lee – Science Advances

Probiotics

Minireview: Lactic acid bacteria as probiotics for the nose? – Ilke De Boeck – Microbial Biotechnology

*Lactobacillus bile salt hydrolase substrate specificity governs bacterial fitness and host colonization – Matthew H. Foley – PNAS

Probiotic nasal spray development by spray drying – Katarina Jokicevic – European Journal of Pharmaceutics and Biopharmaceutics

Water microbiome

Microbiota analysis of rural and urban surface waters and sediments in Bangladesh identifies human waste as driver of antibiotic resistance – Ross S. McInnes – bioRxiv

Depth-discrete metagenomics reveals the roles of microbes in biogeochemical cycling in the tropical freshwater Lake Tanganyika – Patricia Q. Tran – The ISME Journal

Soil microbiome

Trace gas oxidizers are widespread and active members of soil microbial communities – Sean K. Bay – Nature Microbiology

Bacterial communities regulate temporal variations of the antibiotic resistome in soil following manure amendment – Jianhua Cheng – Environmental Science and Pollution Research

Techniques

Quantifying Variation in Bacterial Reproductive Fitness: a High-Throughput Method – Pascal M. Frey – mSystems

Bioinformatics

*Enabling multiscale variation analysis with genome graphs – Brice Letcher – bioRxiv

HMD-ARG: hierarchical multi-task deep learning for annotating antibiotic resistance genes – Yu Li – Microbiome

BAGET 2.0: an updated web tool for the effortless retrieval of prokaryotic gene context and sequence – Benjamin Hepp – Bioinformatics

Metagenomics workflow for hybrid assembly, differential coverage binning, metatranscriptomics and pathway analysis (MUFFIN) – Renaud Van Damme – Plos Computational Biology

PATO: Pangenome Analysis Toolkit – Miguel D. Fernández-de-Bobadilla – bioRxiv

Struo2: efficient metagenome profiling database construction for ever-expanding microbial genome datasets – Nicholas D. Youngblut and Ruth E. Ley – bioRxiv

Webinars

UCC Science Society STEMinar: The Gut Microbiome, Health & Disease. You truly are what you eat – Paul O’Toole – 15 February

SGBUG (Singapore Bacterial Ultra Group) seminar: Human Gut Bacteria, Bile Acids, and Host Physiology – Sloan Devlin – 18 February

MicroSeminars 2021 – Free Web-based Microbiology Seminar Series

Biofilm Baithak – An India-specific Meetup – India Biofilms Society- 20-27 February 2021.

Klebsiella Virtual Seminar Series 2021 #KlebClub2021 – Department of Microbiology and Immunology, University of Michigan

Courses

Bioinformatics for Biologists: An Introduction to Linux, Bash Scripting, and R – The Wellcome Genome Campus

Next Generation Sequencing Bioinformatics course – Wellcome Genome Campus Advanced Courses & Scientific Conferences – H3Abionet

Biobanking – Institut Pasteur

Podcasts

Season 2, Ep. 2: Building Biomes with Jack Gilbert – Ruairi Robertson – Biomes

Reverse mentoring with Martin Dougherty – Alice Matimba – Your Digital Mentor

Episode 17: Post-docs Part 2: Hiring – Stephanie Hicks and John Muschelli – The Corresponding Author

Episode 235: Green algae and fatty acids – Vincent Racaniello, Elio Schaechter, Michele Swanson, and Michael Schmidt – This week in microbiology podcast

Dr. Heer Mehta: Antibiotic Resistance and Experimental Evolution – Leo Elworth – The Bioinformatics and Beyond Podcast

Science and Art

Microbe Crayon Project – Anne A. Madden

Drawing the #BacterialAlphabet – Noémie Matthey

February 9, 2021

Today’s updates in microbiome – iron homeostasis in host and gut bacteria, flavonol catabolism in gut bacteria, protocol for characterization of pulmonary microbiota, how single bacterial strain prevents GVHD and many more… happy reading!

General microbiome

Iron homeostasis in host and gut bacteria – a complex interrelationship – Yohannes Seyoum – Gut Microbes

α1-3Gal antigen in gut microbiota, a potential new environmental factor in multiple sclerosis – LéoBoussamet – Clinical Immunology

Human microbiome

Alterations in the gut bacterial microbiome in people with type 2 diabetes mellitus and diabetic retinopathy – Taraprasad Das – Scientific Reports

Discovery of an ene-reductase for initiating flavone and flavonol catabolism in gut bacteria – Gaohua Yang – Nature Communications

Animal microbiome

A single strain of Bacteroides fragilis protects gut integrity and reduces GVHD – M. Hanief Sofi – JCI Insight

Social behavior of musk deer during the mating season potentially influences the diversity of their gut microbiome – Jianmei Li​ – PeerJ

Low-dose exposure of glyphosate-based herbicides disrupt the urine metabolome and its interaction with gut microbiota – Jianzhong Hu – Scientific Reports

Cross-Feeding of a Toxic Metabolite in a Synthetic Lignocellulose-Degrading Microbial Community – Jessica A. Lee – Microorganisms

Dietary sphinganine is selectively assimilated by members of the mammalian gut microbiome – LeeMin-Ting – Journal of Lipid Research

Functional Foods

Shaping the Future of Probiotics and Prebiotics – Marla Cunningham – Trends in Microbiology

Utilizing the Food–Pathogen Metabolome to Putatively Identify Biomarkers for the Detection of Shiga Toxin-Producing E. coli (STEC) from Spinach – Snehal R. Jadhav – Metabolites

Clinical effects and gut microbiota changes of using probiotics, prebiotics or synbiotics in inflammatory bowel disease: a systematic review and meta-analysis – Xiao-Feng Zhang – European Journal of Nutrition

Diabetes-induced cardiomyopathy is ameliorated by heat-killed Lactobacillus reuteri GMNL-263 in diabetic rats via the repression of the toll-like receptor 4 pathway – Chung-Jen Chiang – European Journal of Nutrition

Water microbiome

Understanding structure/function relationships in nitrifying microbial communities after cross-transfer between freshwater and seawater – Blanca M. Gonzalez-Silva – Scientific Reports

The microbial dimension of submarine groundwater discharge:current challenges and future directions – Clara Ruiz-González- FEMS Microbiology Reviews

Estrogen induces shift in abundances of specific groups of the coral microbiome – Caren L. S. Vilela – Scientific Reports

Metabolic fingerprinting of the Antarctic cyanolichen Leptogium puberulum–associated bacterial community (Western Shore of Admiralty Bay, King George Island, Maritime Antarctica) – Jakub Grzesiak – Microbial Ecology

Techniques

Development of a robust protocol for the characterization of the pulmonary microbiota – Nathan Dumont-Leblond – Nature Communications

Microbes in news

Eating fat-rich foods as a child causes long-lasting changes in gut microbiome: Study – First post

Human Microbiome Market Set to Register Healthy CAGR During to 2026 – KSU The Sentinel Newspaper

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 28, 2021

Happy almost Friday from the US’s west coast, everybody! I recently finished reading “Braiding Sweetgrass: Indigenous Wisdom, Scientific Knowledge, and the Teachings of Plants” by Robin Wall Kimmerer and plants have been on my mind so today’s Digest is heavy on the plant microbiome research. Two plant papers I found especially fascinating applied different experimental designs to study the same issue: one looks at how the mono-cropping of maize negatively impacts soil microbial communities and the other found that sugarcane/peanut intercropping enriches for beneficial microbes that promote nitrogen and phosphate release from the soil. There are also several papers looking at the relationship between microbes and the host immune system and an eLife paper in which the popular shelter-in-place hobby of making sourdough and our beloved microbiome field collide. Happy reading!

Pregnancy and Early Life
Fecal Microbiota Nutrient Utilization Potential Suggests Mucins as Drivers for Initial Gut Colonization of Mother-Child Shared Bacteria. – Nilsen, M. et al., Applied and Environmental Microbiology.

Metagenomic insights of the infant microbiome community structure and function across multiple sites in the United States. – Casaburi, G. et al., Scientific Reports.

Human Gut Microbiome
Gut bacteria-derived 5-hydroxyindole is a potent stimulant of intestinal motility via its action on L-type calcium channels. – Waclawiková, B. et al., PLoS Biology.

Animal Experiments
Gut CD4+ T cell phenotypes are a continuum molded by microbes, not by TH archetypes. – Kiner, E. et al., Nature Immunology.

Regulation of Gut Microbiota Disrupts the Glucocorticoid Receptor Pathway and Inflammation-related Pathways in the Mouse Hippocampus. – Rao, X. et al., Experimental Neurobiology.

Decreased Ecological Resistance of the Gut Microbiota in Response to Clindamycin Challenge in Mice Colonized with the Fungus Candida albicans. – Markey, L. et al., mSphere.

Gut Commensal Segmented Filamentous Bacteria Fine-Tune T Follicular Regulatory Cells to Modify the Severity of Systemic Autoimmune Arthritis. – Bates, N.A. et al., Journal of Immunology.

Microbial metabolism of L-tyrosine protects against allergic airway inflammation. – Wypych, T.P. et al., Nature Immunology.

Animal Microbiome
Host development overwhelms environmental dispersal in governing the ecological succession of zebrafish gut microbiota. – Xiao, F. et al., npj Biofilms and Microbiomes.

Quantifying fluorescent glycan uptake to elucidate strain-level variability in foraging behaviors of rumen bacteria. – Klassen, L. et al., Microbiome.

Plant, Root, and Soil Microbiome
Complementary Roles of Wood-Inhabiting Fungi and Bacteria Facilitate Deadwood Decomposition. – Tláskal, V. et al., mSystems.

Natural Bacterial Assemblages in Arabidopsis thaliana Tissues Become More Distinguishable and Diverse during Host Development. – Beilsmith, K. et al., mBio.

Colonization of naïve roots from Populus tremula x alba involves successive waves of fungi and bacteria with different trophic abilities. – Fracchia, F. et al., Applied and Environmental Microbiology.

The role of host promiscuity in the invasion process of a seaweed holobiont. – Bonthond, G. et al., The ISME Journal.

Sugarcane/peanut intercropping system improves the soil quality and increases the abundance of beneficial microbes. – Tang, X. et al., Journal of Basic Microbiology.

Variation of rhizosphere microbial community in continuous mono-maize seed production. – Zhao, Y. et al., Scientific Reports.

Food Microbiology
The diversity and function of sourdough starter microbiomes. – Landis, E.A. et al., eLife.

Probiotics
Optimization of probiotic therapeutics using machine learning in an artificial human gastrointestinal tract. – Westfall, S. et al., Scientific Reports.

Metagenomics
How reliably do metagenome-assembled genomes (MAGs) represent natural populations? Insights from comparing MAGs against isolate genomes derived from the same fecal sample. – Meziti, A. et al., Applied and Environmental Microbiology.

Techniques
Precision modification of the human gut microbiota targeting surface-associated proteins. – Marcos-Fernández, R. et al., Scientific Reports.

High-throughput cultivation and identification of bacteria from the plant root microbiota. – Zhang, J. et al., Nature Protocols.

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

January 20, 2021

Good morning readers! Today we have two very interesting studies published in Nature Genetics. One focuses on host factors influencing human gut microbiome composition, the other shows the influence of ABO histo-blood groups on gut microbiome.

Human gut microbiome

Large-scale association analyses identify host factors influencing human gut microbiome composition – Kurilshikov et al. – Nature Genetics

Genome-wide association study in 8,956 German individuals identifies influence of ABO histo-blood groups on gut microbiome – Rühlemann et al. – Nature Genetics

Fecal microbiome and metabolome differ in healthy and food-allergic twins – Bao et al. – JCI

Hepatic steatosis relates to gastrointestinal microbiota changes in obese girls with polycystic ovary syndrome – Jobira et al. – PLOS One

Animal microbiome

Microbiota modulates gut immunity and promotes baculovirus infection in Helicoverpa armigera – Yuan et al. – Insect Science

Immunological design of commensal communities to treat intestinal infection and inflammation – Brown et al. – PLOS Pathogens

Ticks Resist Skin Commensals with Immune Factor of Bacterial Origin – Hayes et al. – Cell

Techniques

The effect of taxonomic classification by full-length 16S rRNA sequencing with a synthetic long-read technology – Jeong et al. – Scientific Reports