March 4, 2021

Happy Thursday from San Francisco! Today’s Microbiome Digest includes: a paper by Marbouty et al. in which a large number of phages and their interacting bacteria were identified in the healthy human gut; a thorough examination by Zhu et al. of the composition and metabolic potential of cave-dwelling bacteria, including sequencing of 14 new bacterial species; and a study by Mu et al. which found that the maternally-derived microbe Lactobacillus reuteri promotes immunoglobulin A production in the neonatal gut.

There is also a study by Serrano-Villar et al. which examined the use of fecal microbiota transplantation (FMTs) in HIV patients. The authors observed that FMT led to engraftment of two bacterial families–Lachnospiraceae and Ruminococcaceae–typically depleted in HIV-infected subjects and decreased levels of a plasma biomarker of intestinal permeability. While the findings are interesting, I remain skeptical of the appropriateness of FMTs in this context. Instead of an FMT–which requires donors and screening of their stool to ensure quality and safety–why not use a probiotic cocktail of Lachnospiraceae and Ruminococcaceae family members and perhaps include prebiotic factors to try to promote engraftment?

Additionally, there is a great article by Ras et al. discussing the results of a pilot study that successfully implemented microbiome-related bioinformatics courses across 11 African countries.

Pregnancy and Early Life
Distinct Changes Occur in the Human Breast Milk Microbiome Between Early and Established Lactation in Breastfeeding Guatemalan Mothers. – Gonzales, E. et al., Frontiers in Microbiology.

Human Skin Microbiome
Spermidine-induced recovery of human dermal structure and barrier function by skin microbiome. – Kim, G. et al. Communications Biology.

Human Vaginal Microbiome
Influence of dapivirine vaginal ring use on cervicovaginal immunity and functional microbiome in adolescent girls. – Farr Zuend, C. et al., AIDS.

Mapping the entire functionally active endometrial microbiota. – Sola-Leyva, A. et al., Human Reproduction.

Genomic relatedness and clinical significance of Streptococcus mitis strains isolated from the urogenital tract of sexual partners. – Mores, C.R. et al., Microbial Genomics.

Human Gut Microbiome
Identification of an N-acetylneuraminic acid-presenting bacteria isolated from a human microbiome. – Han, Z. et al., Scientific Reports.

Fecal microbiota transplantation in HIV: A pilot placebo-controlled study. – Serrano-Villar, S. et al., Nature Communications.

Gastrointestinal microbiota composition predicts peripheral inflammatory state during treatment of human tuberculosis. – Wipperman, M.F. et al., Nature Communications.

Animal Experiments
Regulation of neonatal IgA production by the maternal microbiota. – Mu, Q. et al., PNAS.

Lysates of Methylococcus capsulatus Bath induce a lean-like microbiota, intestinal FoxP3+RORγt+IL-17+ Tregs and improve metabolism. – Jensen, B.A.H., et al., Nature Communications.

Sex-dependent modulation of immune development by secretory IgA–coated Lactobacillus reuteri isolated from breast milk. – Qi, C. et al., Journal of Dairy Science.

Oral berberine improves brain dopa/dopamine levels to ameliorate Parkinson’s disease by regulating gut microbiota. – Wang, Y. et al., Signal Transduction and Targeted Therapy.

Animal Microbiome
Lactobacillus reuteri-derived extracellular vesicles maintain intestinal immune homeostasis against lipopolysaccharide-induced inflammatory responses in broilers. – Hu, R. et al., Journal of Animal Science and Biotechnology.

Plant, Root, and Soil Microbiome
Dicer-like proteins influence Arabidopsis root microbiota independent of RNA-directed DNA methylation. – Kaushal, R. et al., Microbiome.

Succession of the Resident Soil Microbial Community in Response to Periodic Inoculations. – Wang, Z. et al., Applied and Environmental Microbiology.

Climate change alters temporal dynamics of alpine soil microbial functioning and biogeochemical cycling via earlier snowmelt. – Broadbent, A.A.D. et al., ISME Journal.

Water and Extremophile Microbiome
Microbial Community Structure Driven by a Volcanic Gradient in Glaciers of the Antarctic Archipelago South Shetland. – García-Lopez, E. et al., Microorganisms.

Effect of polymer type on the colonization of plastic pellets by marine bacteria. – Hansen, J. et al., FEMS Microbiology Letters.

Lifestyle of sponge symbiont phages by host prediction and correlative microscopy. – Jahn, M.T. et al., ISME Journal.

Bacteria and Metabolic Potential in Karst Caves Revealed by Intensive Bacterial Cultivation and Genome Assembly. – Zhue, H-Z et al., Applied and Environmental Microbiology.

Phages and Viruses
MetaHiC phage-bacteria infection network reveals active cycling phages of the healthy human gut. – Marbouty, M. et al., Elife.

Bioinformatics
On the evolutionary origins of host–microbe associations. – Sieber, M. et al., PNAS.

Ecology-guided prediction of cross-feeding interactions in the human gut microbiome. – Goyal, A. et al., Nature Communications.

Using a multiple-delivery-mode training approach to develop local capacity and infrastructure for advanced bioinformatics in Africa. – Ras, V. et al., PLoS Computational Biology.

Techniques
Amplicon-based skin microbiome profiles collected by tape stripping with different adhesive film dressings: a comparative study. – Ogai, K. et al., BMC Microbiology.

High-Resolution Differentiation of Enteric Bacteria in Premature Infant Fecal Microbiomes Using a Novel rRNA Amplicon. – Graf, J. et al., mBio.

February 19, 2021

Good morning from New Jersey! There’s an amazing batch of microbiome papers to share with you today, including studies that use skin microbes to fight cancer, gut microbes to fight rotavirus, and evidence that the bird microbiome may harbor a mechanism that protects them from malaria. There’s also a fun story about dogs training a computer to detect prostate cancer.

General microbiome

Feasibility of integrating canine olfaction with chemical and microbial profiling of urine to detect lethal prostate cancer, Guest, Harris and Sfanos et al., PLOS ONE

Human skin microbiome

Preprint: Eliciting a potent antitumor immune response by expressing tumor antigens in a skin commensal, Yiyin Erin Chen et al., bioRxiv

Human nearly-sterile sites

Preprint: Fetal gut colonization: meconium does not have a detectable microbiota before birth, Katherine M. Kennedy et al., bioRxiv

Human gut microbiome

The gut microbiome modulates the protective association between a Mediterranean diet and cardiometabolic disease risk, Dong D. Wang et al., Nature Medicine

Gut microbiome pattern reflects healthy ageing and predicts survival in humans, Tomasz Wilmanski et al., Nature Metabolism

The composition of the gut microbiome differs among community dwelling older people with good and poor appetite, Cox and Bowyer et al., Journal of Cachexia, Sarcopenia and Muscle

Animal microbiome

The uropygial gland microbiome of house sparrows with malaria infection, Elin Videvall et al., Journal of Avian Biology

The amphibian microbiome exhibits poor resilience following pathogen-induced disturbance, Andrea J. Jani et al., The ISME Journal

Plant, root and soil microbiome

Carbon Fluxes and Microbial Activities from Boreal Peatlands Experiencing Permafrost Thaw, M.P. Waldrop et al., JGR Biogeosciences

Probiotics/prebiotics

Escherichia coli Nissle 1917 administered as a dextranomar microsphere biofilm enhances immune responses against human rotavirus in a neonatal malnourished pig model colonized with human infant fecal microbiota, Husheem Michael et al., PLOS ONE

Impact of Probiotic B. infantis EVC001 Feeding in Premature Infants on the Gut Microbiome, Nosocomially Acquired Antibiotic Resistance, and Enteric Inflammation, Marielle Nguyen et al., Frontiers in Pediatrics

February 17, 2021

General microbiome

Microbial diversity in homes and the risk of allergic rhinitis and inhalant atopy in two European birth cohorts – Hyytiäinen et al. – Environmental Research

Pregnancy and early life

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

Human respiratory microbiome

The nasal microbiome, nasal transcriptome, and pet sensitization – Chun et al. – Journal of Allergy and Clinical Immunology

Human gut microbiome

The Effects of Genetic Relatedness on the Preterm Infant Gut Microbiota – Lim et al. – Microorganisms

[REVIEW]Inflammatory bowel disease: tri-directional relationship between microbiota, immune system and intestinal epithelium – Ahlawat et al. – Critical Reviews in Microbiology

Fecal Microbiota Transplantation Is a Promising Method to Restore Gut Microbiota Dysbiosis and Relieve Neurological Deficits after Traumatic Brain Injury – Du et al. – Oxidative Medicine and Cellular Longevity

The baseline gut microbiota directs dieting-induced weight loss trajectories – Jie et al. – Gastroenterology

Animal microbiome (for animals in the wild)

Bacterial microbiota similarity between predators and prey in a blue tit trophic network – Dion-Phenix et al. The ISME Journal

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

Landscape Setting Drives the Microbial Eukaryotic Community Structure in Four Swedish Mountain Lakes over the Holocene – Capo et al. – Microorganisms

Profiling of Microbial Communities in the Sediments of Jinsha River Watershed Exposed to Different Levels of Impacts by the Vanadium Industry, Panzhihua, China – He et al. – Environmental Microbiology

Bioinformatics

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

ASaiM-MT: a validated and optimized ASaiM workflow for metatranscriptomics analysis within Galaxy framework – Mehta et al. – f1000

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 10, 2021

Hello from snowy Lübeck,
today we have selected, among others, some papers about soil microbiota, associations of bacteria in healthy humans across different populations (in gut) and a couple of bioinformatic papers. Happy reading!

General microbiome

[REVIEW]Blautia—a new functional genus with potential probiotic properties? – Liu et al. – Gut Microbes

The sum is greater than the parts: exploiting microbial communities to achieve complex functions – Zaramela et al. – Current Opinion in Biotechnology

Pregnancy and early life

Influence of Lactobacillus crispatus, Lactobacillus iners and Gardnerella vaginalis on bacterial vaginal composition in pregnant women – Witkin et al. – Archives of Gynecology and Obstetrics

Human gut microbiome

The faecal metabolome in COVID-19 patients is altered and associated with clinical features and gut microbes – Lv et al. – Analytica Chimica Acta

Bacterial associations in the healthy human gut microbiome across populations – Loftus, Hassouneh & Yooseph – Scientific Reports

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

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

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

Black Current Anthocyanins Improve Lipid Metabolism and Modulate Gut Microbiota in High‐Fat Diet‐Induced Obese Mice – Song et al. – Molecular Nutrition & Food Research

Animal microbiome (for animals in the wild)

Japanese quail (Coturnix japonica) as a novel model to study the relationship between the avian microbiome and microbial endocrinology-based host-microbe interactions – Lyte et al. – Microbiome

Plant, root, and soil microbiome

Impacts of earthworm introduction and cadmium on microbial communities composition and function in soil – Ren et al. – Environmental Toxicology and Pharmacology

Tree‐induced alterations to soil properties and rhizoplane‐associated bacteria following 23 years in a common garden – Yates et al. – Plant and Soil

Influence of imidacloprid on bacterial community diversity of mango orchard soil assessed through 16S rRNA sequencing-based metagenomic analysis – Garg et al. – Environmental Monitoring and Assessment

Bioinformatics

[PREPRINT]Multi-Block Sparse Functional Principal Components Analysis for Longitudinal Microbiome Multi-Omics Data – Jiang et al. – arXiv.org

Model-based microbiome data ordination: A variational approximation approach – Zeng, Zhao & Wang – Journal of Computational and Graphical Statistics

VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses – Guo et al. – Microbiome

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 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 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 15, 2021

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