Category Archives: Metagenomics & Bioinformatics

February 23, 2021

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Greetings from Pittsburgh!

Today’s digest is heavy on plant and soil-associated research. It includes a review on the use of metagenomics in soil ecology research, original research focused on the microbiome of plants growing in a Sandhills ecosystem, as well as articles focused on the soil-associated microorganisms Marinobacter caseinilyticus sp. and Dickeya sp. This digest also features several articles focused on extremophiles found in permafrost, the South Pole, and a Mars-like environment! Finally, I also wanted to highlight an Q&A with Dr. Kizzmekia Corbett, an immunologist at the National Institute of Health and one of the designers of the Moderna COVID-19 vaccine.

Events and jobs

Black in Microbiology is now also the Black Microbiologists Association. If you’re interested in joining or learning more information, check out their webpage for details!

General microbiome

Biochemical characterization of a low salt-adapted extracellular protease from the extremely halophilic archaeon Halococcus salifodinae – Hou et al. – International Journal of Biological Macromolecules

Identification and characterization of a metal-resistant Acidithiobacillus ferrooxidans as important potential application for bioleaching – Tavakoli et al. – Biologia

Human vaginal microbiome

Review: Lactic acid-containing products for bacterial vaginosis and their impact on the vaginal microbiota: A systematic review — Plummer et al. – PLOS One

Human gut microbiome

Effects of colon-targeted vitamins on the composition and metabolic activity of the human gut microbiome– a pilot study – Pham et al. – Gut Microbes

Animal experiments

Co-infecting pathogen lineages have additive effects on host bacterial communities – Medina et al. – FEMS Microbiology Ecology

Plant, root, and soil microbiome

Aggregate-related changes in living microbial biomass and microbial necromass associated with different fertilization patterns of greenhouse vegetable soils – Luan et al. – European Journal of Soil Biology

Alkaline soil pH affects bulk soil, rhizosphere and root endosphere microbiomes of plants growing in a Sandhills ecosystem – Lopes et al. – FEMS Microbiology Ecology

Marinobacter caseinilyticus sp. nov., isolated from saline soil – Nie et al. – Current Microbiology

Genomic diversity and organization of complex polysaccharide biosynthesis clusters in the genus Dickeya – Ranjan et al. – PLOS One

Review: Metabarcoding and Metagenomics in Soil Ecology Research: Achievements, Challenges, and Prospects – Semenov – Biology Bulletin Reviews

A DNA metabarcoding approach for recovering plankton communities from archived samples fixed in formalin – Shiozaki et al. – PLOS One

Water and extremophile microbiome

Are permafrost microorganisms as old as permafrost? – Abramov et al. – FEMS Microbiology Ecology

Cultivation and characterization of snowbound microorganisms from the South Pole – Hayward et al. – Extremophiles

Survival of desert algae Chlorella exposed to Mars-like near space environment – Wang et al. – Life Sciences in Space Research

Microbes in the news

This COVID-vaccine designer is tackling vaccine hesitancy — in churches and on Twitter – Subbaraman – Nature

February 17, 2021

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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

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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

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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 9, 2021

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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

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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

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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

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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

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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 27, 2021

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General microbiome

[REVIEW]The complexities of the diet-microbiome relationship: advances and perspectives – Leeming et al. – Genome Medicine

Human skin microbiome

A mixed community of skin microbiome representatives influences cutaneous processes more than individual members – Loomis et al. – Microbiome

Analysis of the Composition and Functions of the Microbiome in Diabetic Foot Osteomyelitis Based on 16S rRNA and Metagenome Sequencing Technology – Zou et al. – Diabetes

Human gut microbiome

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

[REVIEW]Role of the gut microbiota in type 2 diabetes and related diseases – Yang et al. – Metabolism

Animal microbiome (for animals in the wild)

Seasonal shifts in the gut microbiome indicate plastic responses to diet in wild geladas – Baniel et al. – Microbiome

Taxonomic and functional adaption of the gastrointestinal microbiome of goats kept at high altitude (4800 m) under intensive or extensive rearing conditions – Zhang et al. – FEMS Microbiology Ecology

Shifts in bacterial communities and antibiotic resistance genes in surface water and gut microbiota of guppies (Poecilia reticulata) in the upper Rio Uberabinha, Brazil – Jia et al. – Ecotoxicology and Environmental Safety

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

Microdiversity and phylogeographic diversification of bacterioplankton in pelagic freshwater systems revealed through long-read amplicon sequencing – Okazaki et al. – Microbiome

Microbiota entrapped in recently-formed ice: Paradana Ice Cave, Slovenia – Mulec et al. – Scientific Reports

Sea‐ice microbial communities in the Central Arctic Ocean: Limited responses to short‐term pCO2 perturbations – Torstensson et al. – Limnology and Oceanography

Built environment (subways, indoor surfaces)

Bacterial community assemblages in classroom floor dust of 50 public schools in a large city: characterization using 16S rRNA sequences and associations with environmental factors – Park et al. – Microbiome

[REVIEW]Plastics and the microbiome: impacts and solutions – Lear et al. – Environmental Microbiome

Bioinformatics

[REVIEW]Understanding the host-microbe interactions using metabolic modeling – Jansma & El Aidy – Microbiome