May 14, 2021

Today’s digest features Emu for microbial community profiling with expectation-maximization algorithm to generate taxonomic abundance profiles from full-length 16S rRNA reads, glycobiology of UTI, profiling canine fecal microbiome by long-read metagenomics with Nanopore sequencing, spatial-temporal assessment of drinking water microbiome in Puerto Rico, ancient microbial genomes from paleofeces (with 61 previously undescribed species), and more.

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


Today is the last day for #NSURP2021 applications:

The National Summer Undergraduate Research Project – A community-driven initiative to create rewarding remote summer research opportunities for BIPOC and Latinx undergraduate students in the microbial sciences.


Share your experience as an early career researcher with your academic mentor and take part in this important survey on mentorship!

Gut microbiome

Reconstruction of ancient microbial genomes from the human gut – Marsha C. Wibowo – Nature

Human and preclinical studies of the host–gut microbiome co-metabolite hippurate as a marker and mediator of metabolic health – François Brial – Gut Microbiota

Oral microbiome

*Mechanical biofilm disruption causes microbial and immunological shifts in periodontitis patients – William Johnston – Scientific Reports

Vaginal microbiome

Review: The Complex Link between the Female Genital Microbiota, Genital Infections, and Inflammation – Smritee Dabee – Infection and Immunity

Urinary microbiome

*Review: The glycobiology of uropathogenic E. coli infection: the sweet and bitter role of sugars in urinary tract immunity – Federico Lupo – Immunology

The Good and the Bad: Ecological Interaction Measurements Between the Urinary Microbiota and Uropathogens – Laurens E. Zandbergen – Frontiers in Microbiology

Urinary prostaglandin E2 as a biomarker for recurrent UTI in postmenopausal women – Tahmineh Ebrahimzadeh – Life Science Alliance

Impact of Vaginal Estrogen on the Urobiome in Postmenopausal Women With Recurrent Urinary Tract Infection – Carrie E. Jung – Female Pelvic Medicine & Reconstructive Surgery

Animal microbiome

*Long-read metagenomics retrieves complete single-contig bacterial genomes from canine feces – Anna Cuscó – BMC Genomics

Perinatal exposure to tetracycline contributes to lasting developmental effects on offspring – Elizabeth M. Hill – Animal Microbiome

Drinking water microbiome

*Spatial-temporal targeted and non-targeted surveys to assess microbiological composition of drinking water in Puerto Rico following Hurricane Maria – Maria Catalina Sevillano – bioRxiv

Technique

Predicting the presence and abundance of bacterial taxa in environmental communities through flow cytometric fingerprinting – Jasmine Heyse – bioRixv

Sample preservation

Critical evaluation of faecal microbiome preservation using metagenomic analysis – Alena L. Pribyl – ISME Communications

Bioinformatics

*Emu: Species-Level Microbial Community Profiling for Full-Length Nanopore 16S Reads – Kristen D. Curry – bioRxiv

Microbiome differential abundance methods produce disturbingly different results across 38 datasets – Jacob T Nearing – bioRxiv

Improving metagenomic binning results with overlapped bins using assembly graphs – Vijini G. Mallawaarachchi – Algorithms for Molecular Biology

A method for achieving complete microbial genomes and improving bins from metagenomics data – Lauren M. Lui – Plos Computational Biology

Taxonomic annotation of 16S rRNA sequences of pig intestinal samples using MG-RAST and QIIME2 generated different microbiota compositions – J. Lima – Journal of Microbiological Methods

Webinars

EMBARK Spring Webinars – Heike Schmitt “International efforts for One Health surveillance of AMR (WHO Tricycle)” and Etienne Ruppé “On the use of Tricycle in EMBARK” – EMBARK project – May 19
Registration here
More info here

BISMiS Live – GCM 2.0: WDCM 10K Sequencing Project for Type Strains by Juncai Ma – Bergey’s Intl. Society for Microbial Systematics – May 15
Registration here
More info here

Women in Data Science 2021 – Perspectives in Industry and Academia – Bayer AG and de.NBI, Elixir Germany Event – 18 June

PPGSND thesis seminar: The dark side os science: misconduct in biomedical research – Elisabeth Bik – 20 May

mSystems Thinking Series – ASM

Courses

Riffomonas Project – R tutorials and more – PatricK Schloss

Machine learning in Python with scikit-learn – Inria

Introduction to Computer Science and Programming in Python – MIT

Using MOFA for integration of omics data – Ricard Argelaguet – May 25

Data Visualization: Use R, ggplot2, and the principles of graphic design to create beautiful and truthful visualizations of data – Andrew Heiss

Conferences

1st Young AMICI Symposium – Austrian Microbiome Initiative – May 25-26

Microbes, Social Equity, and Rural Health – The Microbes and Social Equity working group and The University of Maine Institute of Medicine – June 14–18

Podcast

Differential gene expression and DESeq2 with Michael Love – The Bioinformatics Chat – Roman Cheplyaka and Jacob Schreiber

The Fake Science Detectives with David Sanders and Elisabeth Bik – Follow the Science – Faye Flam

Research, networking and public perception of science with Linda J Kenney – Microbes and Us – Joseph Shuttleworth

The microbiome: Delicious food and solutions to the climate crisis with Lene Lange – Science Stories – Jens Degett

April 1, 2021

General microbiome

Viral genomic, metagenomic and human transcriptomic characterization and prediction of the clinical forms of COVID-19 – Rodrigez et al. – PLOS Pathogens

A multiomics approach to identify host-microbe alterations associated with infection severity in diabetic foot infections: a pilot study – Radzieta – et al. – NPJ Biofilms and Microbiomes

Pregnancy and early life

Interactions between gut microbiota and metabolites modulate cytokine network imbalances in women with unexplained miscarriage – Liu et al. – NPJ Biofilms and Microbiomes

Developmental trajectory of the healthy human gut microbiota during the first 5 years of life – Roswall et al. – Cell Host & Microbiome

Human gut microbiome

Compositional change of gut microbiome and osteocalcin expressing endothelial progenitor cells in patients with coronary artery disease – Toya et al. – PLOS One

Stool metabolome-microbiota evaluation among children and adolescents with obesity, overweight, and normal-weight using 1H NMR and 16S rRNA gene profiling – Jaimes et al. – PLOS One

Gut dysbiosis and mortality in hemodialysis patients – Lin et al. – NPJ Biofilms and Microbiomes

[REVIEW]The Interplay between Diet, Gut Microbes, and Host Epigenetics in Health and Disease – Shock et al. – The Journal of Nutritional Biochemistry

[REVIEW]Circadian rhythms and the gut microbiome synchronize the host’s metabolic response to diet – Lopez et al. – Cell Metabolism

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

Meta-analysis identifies the effect of dietary multi-enzyme supplementation on gut health of pigs – Ramani et al. – Scientific Reports

Silicon-containing water intake confers antioxidant effect, gastrointestinal protection, and gut microbiota modulation in the rodents – Wu et al. – PLOS One

Animal microbiome (for animals in the wild)

[PREPRINT]16S rRNA Amplicon Sequencing of Bagworm Metisa plana Walker (Lepidoptera: Psychidae) – Ting et al. – bioRxiv

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

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

Geochemical and metagenomics study of a metal-rich, green-turquoise-coloured stream in the southern Swiss Alps – Buetti-Dinh – PLOS One

Phages and viruses

[REVIEW]The human virome: assembly, composition and host interactions – Liang & Bushman – Nature Reviews Microbiology

[PREPRINT]Diverse viruses carrying genes for microbial extremotolerance in the Atacama Desert hyperarid soil – Hwang et al. – bioRxiv

Bioinformatics

MCPdb: The bacterial microcompartment database – Ochoa et al. – PLOS One
[Twitter]97% identity cutoff applied on humans and related species – Matthew Hahn

Techniques

Single strain control of microbial consortia – Fedorec et al. – Nature Communications

Microbes and Art

A Cultural Triumph: Microbiology Student Makes A Petri Dish Masterpiece – McCammon – npr

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 26, 2021

Pregnancy and early life

Multi-kingdom ecological drivers of microbiota assembly in preterm infants – Rao et al. – Nature

Human gut

[PREPRINT]A randomization-based causal inference framework for uncovering environmental exposure effects on human gut microbiota – Sommer et al. – bioRxiv

[PREPRINT]Fiber-associated Lachnospiraceae reduce colon tumorigenesis by modulation of the tumor-immune microenvironment – Almeida et al. – bioRxiv

Animal microbiome/experiments

NLRP6-associated host microbiota composition impacts in the intestinal barrier to systemic dissemination of Brucella abortus – Rungue et al. – PLOS Neglected Tropical Diseases

Effects of sodium butyrate supplementation on inflammation, gut microbiota, and short‐chain fatty acids in Helicobacter pylori‐infected mice – Huang et al. – Helicobacter

The porcine corneal surface bacterial microbiome: A distinctive niche within the ocular surface – Leis et al. – PLOS One

Dysbiosis of fecal microbiota in cats with naturally occurring and experimentally induced Tritrichomonas foetus infection – Bierlein et al. – PLOS One

Hologenome analysis reveals dual symbiosis in the deep-sea hydrothermal vent snail Gigantopelta aegis – Lan et al. – Nature Communications

Plant, root, and soil microbiome

The bacterial communities of Alaskan mosses and their contributions to N2-fixation – Holland-Moritz et al. – Microbiome

Ecosystem engineers drive differing microbial community composition in intertidal estuarine sediments – Wyness et al. – PLOS One

[PREPRINT]Rare genera differentiate urban green space soil bacterial communities in three cities across the world – Mills et al. – bioRxiv

Nitrogen and water addition regulate fungal community and microbial co-occurrence network complexity in the rhizosphere of Alhagi sparsifolia seedlings – Zhang et al. – Applied Soil Ecology

Metabolic profiling and antioxidant activity during flower development in Agastache rugosa – Yeo et al. – Physiology and Molecular Biology of Plants

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

Long-term dynamic changes in attached and planktonic microbial communities in a contaminated aquifer – Mujica-Alarcon, Thornton & Rolfe – Environmental Pollution

Phages and viruses

Virome composition in marine fish revealed by meta-transcriptomics – Geoghegan et al. – Virus Evolution

Bioinformatics

Comparison of beta diversity measures in clustering the high-dimensional microbial data – Chen et al. – PLOS One

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 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

January 29, 2021

Human gut microbiome

Gut microbiome dysbiosis and correlation with blood biomarkers in active-tuberculosis in endemic setting – Khaliq et al. – PLOS One

Gut microbiota profile of Indonesian stunted children and children with normal nutritional status – Surono et al. – PLOS One

[PREPRINT]Infant gut strain persistence is associated with maternal origin, phylogeny, and functional potential including surface adhesion and iron acquisition – Lou et al. – bioRxiv

Human metabolome

Umbilical cord blood metabolome differs in relation to delivery mode, birth order and sex, maternal diet and possibly future allergy development in rural children – Ross et al. – PLOS One

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

Innate gut microbiota predisposes to high alcohol consumption – Ezquer et al. – Addiction Biology

Animal microbiome

Diet-induced changes in bacterial communities in the jejunum and their associations with bile acids in Angus beef cattle – Liu et al. – Animal Microbiome

Plant, root, and soil microbiome

Investigation of the microbiota associated with ungerminated and germinated Norwegian barley cultivars with focus on lactic acid bacteria – Østlie et al. – International Journal of Food Microbiology

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

[PREPRINT]Diversity, activity and abundance of benthic microbes in the southeastern Mediterranean Sea: A baseline for monitoring – Rubin-Blum – bioRxiv

[PREPRINT]Deep-sea plastisphere: long-term colonization by plastic-associated bacterial and archaeal communities in the Southwest Atlantic Ocean – Agostini – bioRxiv

Food microbiology

Systematic assessment of oat β-glucan catabolism during in vitro digestion and fermentation – Bai et al. – Food Chemistry

Bioinformatics

One is not enough: On the effects of reference genome for the mapping and subsequent analyses of short-reads – Valiente-Mullor et al. – PLOS Computational Biology

January 22, 2021

Good morning from New Jersey! A wide range of microbiome research to share with you today. Highlights include fecal microbiota transplantation in horses with colitis and a review on the foggy relationship between microbes and plastics. There are also a couple papers on metabolic modeling and an examination of how much black soldier flies like human food waste (hint: a lot).

Jobs

New postdoctoral positions were just announced at the University of Minnesota for “research at the interface of microbiome + human genomics” in the lab of Dr. Ran Blekhman (disclosure: my Ph.D. advisor).

Human skin microbiome

Potential role of the skin and gut microbiota in premenarchal vulvar lichen sclerosus: A pilot case-control study, Chattopadhyay and Arnold et al., PLOS ONE

Human gut microbiome

Degradation of complex arabinoxylans by human colonic Bacteroidetes, Gabriel V. Pereira et al., Nature Communications

Review – The complexities of the diet-microbiome relationship: advances and perspectives, Emily R. Leeming et al., Genome Medicine

Review – Understanding the host-microbe interactions using metabolic modeling, Jansma and El Aidy, Microbiome

Microbial Species that Initially Colonize the Human Gut at Birth or in Early Childhood Can Stay in Human Body for Lifetime, Li and Nelson, Microbial Ecology

Animal experiments

Preprint – The Predicted Metabolic Function of the Gut Microbiota of Drosophila melanogaster, Nana Ankrah et al, bioRxiv

Animal microbiome

Assessment of clinical and microbiota responses to fecal microbial transplantation in adult horses with diarrhea, Caroline A. McKinney et al., PLOS ONE

Climate change alters the haemolymph microbiome of oysters, Elliot Scanes et al., Marine Pollution Bulletin

Functional screening of a Caatinga goat (Capra hircus) rumen metagenomic library reveals a novel GH3 β-xylosidase, Betulia de Morais Souto et al., PLOS ONE

Built environment

Impact of Processed Food (Canteen and Oil Wastes) on the Development of Black Soldier Fly (Hermetia illucens) Larvae and Their Gut Microbiome Functions, Thomas Klammsteiner et al., Frontiers in Microbiology

Review – Plastics and the microbiome: impacts and solutions, G. Lear et al., Environmental Microbiome

Bioinformatics

Real-time resolution of short-read assembly graph using ONT long reads, Son Hoang Nguyen et al., PLOS Computational Biology

Covariance matrix filtering with bootstrapped hierarchies, Bongiorno and Challet, PLOS ONE

January 19, 2021

Today’s digest includes a full list of the collection of articles looking at the prenatal microbiota that was recently published in Microbiome as well as some excellent articles from Cell Host & Microbe. 

General Microbiome

A microbial metabolite remodels the gut-liver axis following bariatric surgery – Chaudhari et al. Cell Host & Microbe. 

[REVIEW] The microbiota in pneumonia: From protection to predisposition. Thibeault et al. Science Translational Medicine. 

Prenatal Microbiome

BMC Microbiome has published a collection of articles looking at the prenatal microbiome including perspectives, and commentaries from a range of experts.  

A philosophical perspective on the prenatal in utero microbiome debate – Walter and Hornef. Microbiome. 

Batch effects account for the main findings of an in utero human intestinal bacterial colonization study – Goffau et al. Microbiome

Group therapy on in utero colonization: seeking common truths and a way forward. Silverstein and Mysorekar. Microbiome. 

Lessons learned from the prenatal microbiome controversy. Blaser et al. Microbiome. 

Microbiome or no microbiome: are we looking at the prenatal environment through the right lens? – Fricke and Ravel. Microbiome. 

Corroborating evidence refutes batch effect as explanation for fetal bacteria – Rackeiyte et al. Microbiome

Gut microbiome

Role of dietary fiber in the recovery of the human gut microbiome and its metabolome. Tanes et al. Cell Host & Microbe

Biogeography of the Relationship between the Child Gut Microbiome and Innate Immune System – Amenyogbe et al. mSystems

Associations of Genetic Variants Contributing to Gut Microbiota Composition in Immunoglobin A Nephropathy – He et al. mSystems

Traditional Human Populations and Nonhuman Primates Show Parallel Gut Microbiome Adaptations to Analogous Ecological Conditions – Sharma et al. mSystems

Animal microbiome

Heritable Gut Microbiome Associated with Salmonella enterica Serovar Pullorum Infection in Chickens –  Ding et al. mSystems 

Probiotics

Bifidobacterium bifidum strains synergize with immune checkpoint inhibitors to reduce tumour burden in mice – Lee et al. Nature Microbiology. 

January 12, 2021

Good morning, today we have a quite divers selection of studies. Of special note are the results of the PREDICT 1 study, published in Nature Medicine (Asnicar et al.). Furthermore, we cover among others virome in pregnant women, gut microbiome and PD, some animal microbiome studies, water microbiome, and bioinformatic tools.

General microbiome

[Meeting Report]Microbiome for Mars: surveying microbiome connections to healthcare with implications for long-duration human spaceflight, virtual workshop, July 13, 2020 – LaPelusa et al. – Microbiome

Identifying background microbiomes in an evidence recovery laboratory: A preliminary study – Neckovic et al. – Science & Justice

Human vaginal microbiome/virome

Comparison of viromes in vaginal secretion from pregnant women with and without vaginitis – Zhang et al. – Virology Journal

Human gut microbiome

Microbiome connections with host metabolism and habitual diet from 1,098 deeply phenotyped individuals – Asnicar et al. – Nature Medicine

Gut Microbiota Dysbiosis Is Associated with Elevated Bile Acids in Parkinson’s Disease – Li et al. – Metabolites

Animal microbiome

The Combined Effects of Magnesium Oxide and Inulin on Intestinal Microbiota and Cecal Short-Chain Fatty Acids – Omori et al. – Nutrients

Effect of host breeds on gut microbiome and serum metabolome in meat rabbits – Ye et al. – BMC Veterinary Research

Differential response of digesta- and mucosa-associated intestinal microbiota to dietary insect meal during the seawater phase of Atlantic salmon – Li et al. – Animal Microbiome

Plant, root, and soil microbiome

Diversity and composition of the Panax ginseng rhizosphere microbiome in various cultivation modesand ages – Tong et al. – BMC Microbiology

Water microbiome

Eukaryotic community diversity and pathogenic eukaryotes in a full-scale drinking water treatment plant determined by 18S rRNA and metagenomic sequencing – Li et al. – Environmental Science and Pollution Research

Microbial community structure in aquifers associated with arsenic: analysis of 16S rRNA and arsenite oxidase genes – Sonthiphand et al. – PeerJ

Fungi Present in Antarctic Deep-Sea Sediments Assessed Using DNA Metabarcoding – Ogaki et al. – Environmental Microbiology

Built environment

Comparative analysis of impact of human occupancy on indoor microbiomes – Cao et al. – Frontiers of Environmental Science & Engineering

Bioinformatics

Re-purposing software for functional characterization of the microbiome – Gardiner et al. – Microbiome

[PREPRINT]Mining underutilized whole-genome sequencing projects to improve 16S rRNA databases – Nolan et al. – bioRxiv

Meta-Apo improves accuracy of 16S-amplicon-based prediction of microbiome function – Jing et al. – BMC Genomics

Techniques

Exploring protocol bias in airway microbiome studies: one versus two PCR steps and 16S rRNA gene region V3 V4 versus V4 – Drengenes et al. – BMC Genomics

Quantitative image analysis of microbial communities with BiofilmQ – Hartmann et al. – Nature Microbiology

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

Do the bugs in our guts make us sick, sad and obese? – Sismondo – Toronto Star

New microbiome research finds associations between microbes, diet, and metabolic health – Krawiec – Nutritional outlook