Category Archives: Microbial Ecology

February 12, 2021

Posted on by

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

Posted on by

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 4, 2021

Posted on by

Greetings from a very snowy Pittsburgh!

If you like getting dirty, today’s digest is for you! It includes a review on bat guano, two research articles about compost, four focused on soil research, and a preprint about fertilization with poultry manure.

Happy reading!

Events and jobs

February 1st to 14th: If you’re on twitter, check out #MicrobeValentinesDay! @AnneAMadden is posting 14 days of pink microbes in honor of Valentine’s Day under this hashtag!

Human skin microbiome

Gut microbiome profile in psoriatic patients treated and untreated with biologic therapy – Valentini et al. – The Journal of Dermatology

Human gut microbiome

Preprint – Impact of a human gut microbe on Vibrio cholerae host colonization through biofilm enhancement – Barrasso et al. – bioRxiv

Review: Gut microbiota-mediated pesticide toxicity in humans: methodological issues and challenges in risk assessment of pesticides – Utembe and Kamng’ona – Chemosphere

Animal experiments

Effects of thallium exposure on intestinal microbial community and organ functions in zebrafish (Danio rerio) – Wang et al. – Elementa: Science of the Anthropocene

Is intestinal bacterial diversity enhanced by trans-species spread in the mixed-species flock of hooded crane (Grus monacha) and bean goose (Anser fabalis) wintering in the lower and middle Yangtze river floodplain? – Yang and Zhou – Animals

Animal microbiome

Review: The microbiome of bat guano: for what is this knowledge important? – Dimkić et al. – Applied Microbiology and Biotechnology

Tick microbiomes in neotropical forest fragments are best explained by tick-associated and environmental factors rather than host blood source – Kueneman et al. – Microbial Ecology

Plant, root, and soil microbiome

Survival rates of microbial communities from livestock waste to soils: a comparison between compost and digestate – Akari and Uchida – Applied and Environmental Soil Science

Year, location, and variety impact on grape-, soil-, and leaf-associated fungal microbiota of Arkansas-grown table grapes – Cureau et al. – Microbial Ecology

Preprint: Agricultural fertilization with poultry manure results in persistent environmental contamination with the pathogen Clostridioides difficile – Frentrup et al. – bioRxiv

Impacts of invasive Australian Acacias on soil bacterial community composition, microbial enzymatic activities, and nutrient availability in Fynbos soils – Keet et al. – Microbial Ecology

A novel carboxylesterase derived from a compost metagenome exhibiting high stability and activity towards high salinity – Lu and Daniel – Genes

A two-year field study of nickel-agromining using Odontarrhena chalcidica co-cropped with a legume on an ultramafic soil: temporal variation in plant biomass, nickel yields and taxonomic and bacterial functional diversity – Saad et al. – Plant and Soil

Bacterial response to soil property changes caused by wood ash from wildfire in forest soils around mining areas: Relevance of bacterial community composition, carbon and nitrogen cycling – Zhang et al. – Journal of Hazardous Materials

Water and extremophile microbiome

Microcystis blooms aggravate the diurnal alternation of nitrification and nitrate reduction in the water column in Lake Taihu – Chen et al. – Science of the Total Environment

Temperature and microbial interactions drive the deterministic assembly processes in sediments of hot springs – He et al. – Science of the Total Environment

Cadmium sulfide nanoparticle biomineralization and biofilm formation mediate cadmium resistance of the deep‐sea bacterium Pseudoalteromonas sp. MT33b – Ma and Sun – Environmental Microbiology Reports

Recovery of freshwater microbial communities after extreme rain events is mediated by cyclic succession – Shabarova et al. – Nature Microbiology

Built environment

Preprint: Half-life of biodegradable plastics in the marine environment depends on material, habitat, and climate zone – Lott et al. – bioRxiv

Water flushing irremovable biofilms on support material in dynamic membrane bioreactor: formation, composition, and microbial community – Huang et al. – Chemosphere

Phages and viruses

Preprint: Rampant prophage movement among transient competitors drives rapid adaptation during infection – Marshall et al. – bioRxiv

February 03, 2021

Posted on by

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 26, 2021

Posted on by

Review articles on hygiene hypothesis and COVID, role of microbiome in cancer, different studies on efficacy of probiotics in inflammatory and metabolic diseases, and many more…

General microbiome

The hygiene hypothesis, the COVID pandemic, and consequences for the human microbiome – B. Brett Finlay – PNAS

Exploring the Role of Gut Microbiome in Colon Cancer – Indranil Chattopadhyay – Applied Biochemistry and Biotechnology

Cancer trigger or remedy: two faces of the human microbiome – Anna Grenda – Applied Microbiology and Biotechnology

Human microbiome

Microbiota, Epigenetics and Trained Immunity: Convergent Drivers and Mediators of the Asthma Trajectory from Pregnancy to Childhood – Susan V Lynch – American Journal of Respiratory and Critical Care Medicine

Gut Microbial Signature of Hepatocellular Cancer in Men with Cirrhosis – Somaya Albhaisi – Liver Transplantation

An Evaluation of the Fecal Microbiome in Lynch Syndrome – Adalberto Gonzalez – Journal of Gastrointestinal Cancer

Gut microbiota condition the therapeutic efficacy of trastuzumab in HER2-positive breast cancer – Martina Di Modica – Cancer Research

Recent, mid-, and late-adulthood antibiotic use are associated with subsequent risk of diverticulitis – Long H.Nguyen – Gastroenterology

Animal microbiome

Gestational gut microbial remodeling is impaired in a rat model of preeclampsia superimposed on chronic hypertension – Jeanne A Ishimwe – Physiological Genomics

Diet, habitat environment and lifestyle conversion affect the gut microbiomes of giant pandas – Leijin – Science of the Total Environment

Functional Foods

Probiotic Lactobacillus casei Shirota prevents acute liver injury by reshaping the gut microbiota to alleviate excessive inflammation and metabolic disorders – Ren Yan – Microbial Biotechnology

Functional characterization and immunomodulatory properties of Lactobacillus helveticus strains isolated from Italian hard cheeses – Miriam Zago – PlosOne

The Acid-Dependent and Independent Effects of Lactobacillus acidophilus CL1285, Lacticaseibacillus casei LBC80R, and Lacticaseibacillus rhamnosus CLR2 on Clostridioides difficile R20291 – Sathursha Gunaratnam – Probiotics and Antimicrobial Proteins

Polyphosphate, Derived from Lactobacillus brevis, Modulates the Intestinal Microbiome and Attenuates Acute Pancreatitis – Shuhei Takauji – Digestive Diseases and Sciences

Human Intestinal Barrier: Effects of Stressors, Diet, Prebiotics, and Probiotics – Michael Camilleri – Clinical and Translational Gastroenterology

Plant, root and soil microbiome

Insights into the plant responses to drought and decoding the potential of root associated microbiome for inducing drought tolerance – Piyush Mathur – Physiologia Plantarum

Water microbiome

A genomic view of the microbiome of coral reef demosponges – S. J. Robbins – ISME Journal

Microbes in news

Gut Bacteria Offer Insight into Molecules Protective Against Asthma and COVID-19 – Biospace

January 15, 2021

Posted on by

Today’s digest features a collection of reviews, opinion pieces, discussion on prenatal microbiome, pipeline to extract metabolic models from whole metagenome sequencing data (metaGEM), novel type of colistin resistance genes, mechanisms that shape microbial pangenomes, and more. Check out a list of free web-based microbial seminars. Happy reading/listening!

General microbiome

*Mechanisms That Shape Microbial Pangenomes – Maria Rosa Domingo-Sananes
and James O. McInerney – Trends in Microbiology

Evolution to alternative levels of stable diversity leaves areas of niche space unexplored – Ilan Naftali Rubin – bioRxiv

Prenatal microbiome

*The prenatal in utero microbiome controversy: Microbiome or no microbiome: are we looking at the prenatal environment through the right lens? – W. Florian Fricke and Jacques Ravel – BMC Microbiome

Urinary microbiome

The Urinary Microbiome in Postmenopausal Women with Recurrent Urinary Tract Infections – Monique H. Vaughan – bioRxiv

Alterations in Urobiome in Patients With Bladder Cancer and Implications for Clinical Outcome: A Single-Institution Study – Jiarong Zeng – Frontiers in Cellular and Infection Microbiology

Bare Versus Hair: Do Pubic Hair Grooming Preferences Dictate the Urogenital Microbiome? – Geynisman-Tan J – Female Pelvic Medicine & Reconstructive Surgery

Vaginal microbiome

Amylases in the Human Vagina – Kenetta L. Nunn – mSphere

Gut microbiome

Predicting drug-metagenome interactions: Variation in the microbial β-glucuronidase level in the human gut metagenomes – Moamen M. Elmassry – PlosOne

Microbiome and ischemic stroke: A systematic review – Yee Teng Lee – PlosOne

Antimicrobial resistance

*A novel type of colistin resistance genes selected from random sequence space – Michael Knopp – Plos Genetics

Identifying novel β-lactamase substrate activity through in silico prediction of antimicrobial resistance – Kara K. Tsang – Microbial Genomics

A framework for identifying the recent origins of mobile antibiotic resistance genes – Stefan Ebmeyer – Communications Biology

Minimal biophysical model of combined antibiotic action – Bor Kavčič – Plos Computational Biology

Mobilization of antibiotic resistance genes differ by resistance mechanism – Tue Kjaergaard Nielsen – bioRxiv

Carbapenem and Colistin Resistance in Enterobacter: Determinants and Clones – Zhiyong Zong – Trends in Microbiology

Animal microbiome

Fermented traditional Chinese medicine alters the intestinal microbiota composition of broiler chickens – Peng Huang – Research in Veterinary Science

Plant/root/soil microbiome

Coordination between microbiota and root endodermis supports plant mineral nutrient homeostasis – Isai Salas-González – Science

Food microbiome

Metabolic cooperation and spatiotemporal niche partitioning in a kefir microbial community – Sonja Blasche – Nature Microbiology

Generation of lactose and protease positive probiotic Lacticaseibacillus rhamnosus GG by conjugation with Lactococcus lactis NCDO 712 – Nazar Hussain – Applied and Environmental Microbiology

Phages and Viruses

Engineered Phage Endolysin Eliminates Gardnerella Biofilm without Damaging Beneficial Bacteria in Bacterial Vaginosis Ex Vivo – Christine Landlinger – Pathogens

Bioinformatics

*metaGEM: reconstruction of genome scale metabolic models directly from metagenomes – Francisco Zorrilla – bioRxiv

Whole genome phylogenies reflect the distributions of recombination rates for many bacterial species – Thomas Sakoparnig – eLife

CAFE: a software suite for analysis of paired-sample transposon insertion sequencing data – Anna Abramova – Bioinformatics

Finding orthologous gene blocks in bacteria: the computational hardness of the problem and novel methods to address it – Huy N Nguyen – Bioinformatics

Unraveling city-specific signature and identifying sample origin locations for the data from CAMDA MetaSUB challenge – Runzhi Zhang – Biology Direct

RefSeq: expanding the Prokaryotic Genome Annotation Pipeline reach with protein family model curation – Wenjun Li – Nucleic Acids Research

Techniques

A co-culture microplate for real-time measurement of microbial interactions – Charles Jo – bioRxiv

Webinars

Mind, Mood & Microbes Expert Q&A: From Mechanisms to Clinical Applications – Jane Foster, Mauro Costa-Mattioli, John Cryan, Eldin Jašarević, Aletta D. Kraneveld, Filip Scheperjans, Elaine Hsiao – 21 January

SGBUG (Singapore Bacterial Ultra Group) seminar: Silencing bacterial genes with CRISPR-dCas9: from basic insights to high-throughput screens – David Bikard – 21 January

LoopSeq Solo Webinar: High Resolution Metagenomic Sequencing using DADA2 and LoopSeq Long-Read Sequencing – Benjamin Callahan – 21 January

FEMS Yeast Research Webinar on Genomic Insights into Yeast Diversity and Evolution – FEMS – 28 January

SSB Seminar: Double Trouble: Inappropriate Image Duplications in Biomedical Publications – Elisabeth Bik – 29 January

Geomicrobiology Network Seminar Series – The Mineralogical Society of Great Britain and Ireland

Winter 2021 WESTalks – Weekly seminars related to Water and the Environment with speakers from around the globe – IC-IMPACTS Student Engagement Committee (SEC) and the University of British Columbia’s Future Waters

MicroSeminars 2021 – Free Web-based Microbiology Seminar Series

Conferences &c

1st Microbiome PT Summit – The Portuguese Microbiome Community – 4 February

The 2021 UK Cellular Microbiology Network meeting – The Francis Crick Institute – 1-2 March

The Biology and Physics of Bacterial Chromosomes meeting – 4 March

Symposium Celebrating 100th Birthday and Research Accomplishments of Dr. Evelyn M. Witkin – Waksman Institute of Microbiology – 13 April

Podcast

TWiM 233: Antivirals made by bacteria – Hosts: Vincent Racaniello, Elio Schaechter, Michele Swanson, and Michael Schmidt – This week in microbiology podcast

January 14, 2021

Posted on by

Greetings from Pittsburgh!

Today’s digest contains lots of microbial ecology articles focused on everything from the impacts of sleep on dental biofilm to the response of soil microbiota to high petroleum pollution. Also included are two articles focused on insect-plant interactions, with the first focusing on gall induction in insects and the second on the intestinal microbiota of the pine defoliator C. chuxiongica.

General microbiome

Novel cyanotoxin-producing Synechococcus in tropical lakes – Yew-Hoong et al. – Water Research

Multi-site human microbiome

Impacts of sleep on the characteristics of dental biofilm – Sotozono et al. – Scientific Reports

Animal experiments

Dysbiosis of rat vagina is efficiently rescued by the vaginal microbiota transplantation or probiotic combination: Vaginal microbiota transplantation rescues dysbiosis in rat vagina – Chen et al. – International Journal of Antimicrobial Agents

Are bacterial symbionts associated with gall induction in insects? – Hammer et al. – Arthropod-Plant Interactions

The diversity and function of intestinal microorganisms in four geographic Cephalcia chuxiongica (a pine defoliator) populations – Yu et al. – Journal of Applied Entomology

Animal microbiome

Linking bacterial communities associated with the environment and the ecosystem engineer Orchestia gammarellus at contrasting salt marsh elevations – Hernández et al. – Microbial Ecology

Plant, root, and soil microbiome

Response of bacterial and fungal communities to high petroleum pollution in different soils – Galitskaya et al. – Scientific Reports

Enzyme additives influence bacterial communities of Medicago sativa silage as determined by Illumina sequencing – Hu et al. – AMB Express

First reported quantitative microbiota in different livestock manures used as organic fertilizers in the Northeast of Thailand – Wongsaroj et al. – Scientific Reports

Water and extremophile microbiome

Coastal bacterial community response to glacier melting in the Western Antarctic Peninsula – Alcamán-Arias et al. – Microorganisms

Microbial necromass formation, enzyme activities and community structure in two alpine elevation gradients with different bedrock types – Bhople et al. – Geoderma

Exploring the taxonomical and functional profile of As Burgas hot spring focusing on thermostable β-galactosidases – DeCastro et al. – Scientific Reports

The effect of an adsorbent matrix on recovery of microorganisms from hydrocarbon-contaminated groundwater – Taylor et al. – Microorganisms

Built environment

Electrochemical performance and response of bacterial community during phenanthrene degradation in single-chamber air-cathode microbial fuel cells – Hua et al. – Environmental Science and Pollution Research

Food microbiology

Combination of Flos Sophorae and chili pepper as a nitrite alternative improves the antioxidant, microbial communities and quality traits in Chinese sausages – Tang et al. – Food Research International

December 23, 2020

Posted on by

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 18, 2020

Posted on by

Greetings from cold and snowy Pittsburgh!

As I type this, my housemate (who is an essential healthcare worker) should be getting the first dose of her COVID-19 vaccine! Although I’m not sure what the distribution of COVID-19 vaccines is expected to look like, today’s digest includes an article mapping routine measles vaccination coverage in low- and middle- income countries. I’ve also highlighted a few interesting environmental microbiology preprints, including one on the role of ecosystem engineers in shaping arid soil bacterial communities.

Happy holidays and happy reading!

Events and jobs

Danone North America Gut Microbiome, Yogurt and Probiotics Fellowship Grant – Applications for the 2020-2021 grant are currently open and are due on February 24, 2021.

General microbiome

Mapping routine measles vaccination in low- and middle-income countries – Local Burden of Disease Vaccine Coverage Collaborators – Nature

The functional proteome landscape of Escherichia coli – Mateus et al. – Nature

Preprint: Niche and local geography shape the pangenome of wastewater- and livestock-associated Enterobacteriaceae – Shaw et al. – bioRxiv


Plant, root, and soil microbiome

Preprint: The role of ecosystem engineers in shaping the diversity and function of arid soil bacterial communities – Baubin et al. – bioRxiv

Preprint: Environmental interactions with amoebae as drivers of bacterial-fungal endosymbiosis and pathogenicity – Itabangi et al. – bioRxiv

December 9, 2020

Posted on by

In today’s digest read about the selection and microdiversity in glacier-fed streams, Gardnerella vaginalis contribution to the increased rate of group B Streptococcus vaginal colonization, making F1 hybrids in Escherichia coli using MAE (Mass Allelic Exchange), smORFinder (annotation tool to identify small proteins in microbial genomes and metagenomes), and more.
Check out the new Science Friday podcast episode on microbial interactions in cheese rinds and Svetlana’s pick for happy holidays.
Cheers!

Human microbiome

Effects of Extended Postmortem Interval on Microbial Communities in Organs of the Human Cadaver – Holly Lutz – Frontiers in Microbiology

Gut microbiome

Landscapes of bacterial and metabolic signatures and their interaction in major depressive disorders – Jian Yang – Science Advances

Improved high-molecular-weight DNA extraction, nanopore sequencing and metagenomic assembly from the human gut microbiome – Dylan G. Maghini – Nature Protocols

Elucidation of Gut Microbiota-Associated Lipids Using LC-MS/MS and 16S rRNA Sequence Analyses – Shu Yasuda – iScience

The Healthy Microbiome (What is the definition of a healthy gut microbiome?) – Fergus Shanahan – Gastroenterology

The gut microbiota is associated with immune cell dynamics in humans – Jonas Schluter
– Nature

Utilizing the gut microbiome in decompensated cirrhosis and acute-on-chronic liver failure – Jonel Trebicka – Nature Reviews Gastroenterology & Hepatology

Animal microbiome

Remodeling of the maternal gut microbiome during pregnancy is shaped by parity – Alexander SF Berry – bioRxiv

Animal experiments

*Gardnerella vaginalis promotes group B Streptococcus vaginal colonization, enabling ascending uteroplacental infection in pregnant mice – Nicole M. Gilbert – American Journal of Obstetrics & Gynecology

Akkermansia muciniphila: A potential novel mechanism of nuciferine to improve hyperlipidemia – Yue Yu – Biomedicine & Pharmacotherapy

Gut microbiota modulation by both Lactobacillus fermentum MSK 408 and ketogenic diet in a murine model of pentylenetetrazole-induced acute seizure – Ju Young Eor – Epilepsy Research

Host-age prediction from fecal microbiome composition in laboratory mice – Adrian Low – bioRxiv

Commensal Microbiota Regulates Skin Barrier Function And Repair Via Signaling Through The Aryl Hydrocarbon Receptor – Aayushi Uberoi – bioRxiv

Water microbiome

*Homogeneous selection promotes microdiversity in the glacier-fed stream microbiome – Stilianos Fodelianakis – bioRxiv

Phages and viruses

Long-term persistence of crAss-like phage crAss001 is associated with phase variation in Bacteroides intestinalis – Andrey N. Shkoporov – bioRxiv

Diversity and Distribution of a Novel Genus of Hyperthermophilic Aquificae Viruses Encoding a Proof-Reading Family-A DNA Polymerase – Marike Palmer – Frontiers in Microbiology

Broad Virus Detection and Variant Discovery in Fecal Samples of Hematopoietic Transplant Recipients Using Targeted Sequence Capture Metagenomics – Suze A. Jansen – Frontiers in Microbiology

Antimicrobial Resistance

Review: Multidrug-resistant high-risk Enterococcus faecium clones: can we really define them? – Ana R. Freitas – International Journal of Antimicrobial Agents

Review: Current Trends in Experimental and Computational Approaches to Combat Antimicrobial Resistance – Madangchanok Imchen – Frontiers in Genetics

Predicting clinical resistance prevalence using sewage metagenomic data – Antti Karkman – Communications Biology

Fermented-Food Metagenomics Reveals Substrate-Associated Differences in Taxonomy and Health-Associated and Antibiotic Resistance Determinants – John Leech – mSystems

Uncovering hidden antimicrobial resistance patterns within the hospital microbiome – Bastiaan W. Haak and W. Joost Wiersinga – Nature Medicine

Isolation and characterization of human pathogenic multidrug resistant bacteria associated with plastic litter collected in Zanzibar – Farah N. Rasool – Journal of Hazardous Materials

Integrated metagenomic and metatranscriptomic analyses of ultraviolet disinfection effects on antibiotic resistance genes and bacterial communities during wastewater treatment – Shuyu Jia – Ecotoxicology

A metagenomic glimpse into the gut of wild and domestic animals: Quantification of antimicrobial resistance and more – Magdalena Skarżyńska – Plos One

Techniques

*Mass allelic exchange: enabling sexual genetics in Escherichia coli – Varnica Khetrapal – bioRxiv

Review: Microbial model communities: To understand complexity, harness the power of simplicity – Johan Bengtsson-Palme – Computational and Structural Biotechnology Journal

MALDI-TOF mass spectrometry for sub-typing of Streptococcus pneumoniae – Sivkheng Kann – BMC Microbiology

Bioinformatics

*Automated Prediction and Annotation of Small Open Reading Frames in Microbial Genomes – Matthew G. Durrant and Ami S. Bhatt – Cell Host Microbe

Accurate Microbiome Sequencing with Synthetic Long Read Sequencing – Nico Chung – bioRxiv

Species level resolution of female bladder microbiota from marker gene surveys – Carter Hoffman – bioRxiv

Synthetic Sequencing Standards: A Guide to Database Choice for Rumen Microbiota Amplicon Sequencing Analysis – Paul E. Smith – Frontiers in Microbiology

Events

H3ABioNet Seminars and Webinars – H3ABioNet Pan African Bioinformatics Network

Inspiring the next generation of scientists… online – The Young Microbiologists Symposium (YMS) 2020

MLCB 2020 Day 1 and 2 talks – Machine Learning in Computational Biology meeting

Podcast

Why We’re Giving Thanks To Microbes For Stinky Cheese with Benjamin Wolfe and Casey Cosetta – Katie Feather and Ira Flatow – Science Friday

Svetlana’s pick

Planning Our “Home-mas” this December – MissPond – Emma Pond

Holiday Gift Guide For Microbe Lovers – Justine Dees – Joyful Microbe

The 2020 cookbook giftlist – Fiona Beckett – Matching Food & Wine