February 23, 2021

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 9, 2021

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

General microbiome

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

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

Human microbiome

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

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

Animal microbiome

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

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

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

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

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

Functional Foods

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

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

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

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

Water microbiome

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

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

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

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

Techniques

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

Microbes in news

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

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

February 03, 2021

Job market

Postdoctoral Associate in quantitative microbial dynamics in the Clark lab at Duke University

General microbiome

[COMMENT]Microbiome innovations for a sustainable future – D’Hondt et al. – Nature Microbiology

Kin selection explains the evolution of cooperation in the gut microbiota – Simonety & McNally – PNAS

[REVIEW]Crossing Kingdoms: How the Mycobiota and Fungal-Bacterial Interactions Impact Host Health and Disease – Santus, Devlin & Behnsen – Infection and Immunity

Pregnancy and early life

Pregnant women who develop preeclampsia have lower abundance of the butyrate-producer Coprococcus in their gut microbiota – Altemani et al. – Pregnancy Hypertension

Human oral microbiome

Toothbrush microbiomes feature a meeting ground for human oral and environmental microbiota – Blaustein et al. – Microbiome

The role of Saccharibacteria (TM7) in the subginival microbiome as a predictor for secondary cardiovascular events – Schulz et al. – International Journal of Cardiology

Human gut microbiome

The seasonal changes of the gut microbiome of the population living in traditional lifestyles are represented by characteristic species-level and functional-level SNP enrichment patterns – Zhu et al. – BMC Genomics

The pleiotropic effects of prebiotic galacto-oligosaccharides on the aging gut – Arnold et al. – Microbiome

[REVIEW]Priming for Life: Early Life Nutrition and the Microbiota-Gut-Brain Axis – Ratsika et al. – Nutrients

[REVIEW]Gut Microbial Signatures in Sporadic and Hereditary Colorectal Cancer – Mori & Pasca – Int. J. Mol. Sci.

Animal microbiome (for animals in the wild)

[REVIEW]Mechanisms underlying gut microbiota–host interactions in insects – Schmidt & Engel

Plant, root, and soil microbiome

[REVIEW]Plant microbiome structure and benefits for sustainable agriculture – dos Santos & Olivares – Current Plant Biology

A microbial gene catalog of anaerobic digestion from full-scale biogas plants – Ma et al. – GigaScience

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

Microbial intrusion and seasonal dynamics in the groundwater microbiome of a porous basaltic rock aquifer used as municipal water reservoir – Knobloch et al. – FEMS Microbiology Ecology

Bacterial Diversity and Community Composition Distribution in Cold-Desert Habitats of Qinghai–Tibet Plateau, China – Zhang et al. – Microorganisms

Food microbiology

Bacterial community dynamics during different stages of processing of smoked bacon using the 16S rRNA gene amplicon analysis – Li et al. – International Journal of Food Microbiology

Bioinformatics

[PREPRINT]PredicTF: a tool to predict bacterial transcription factors in complex microbial communities – Monteiro et al. – bioRxiv

tidyMicro: a pipeline for microbiome data analysis and visualization using the tidyverse in R – Carpenter et al. – BMC Bioinformatics

Techniques

In vitro infection models to study fungal-host interaction – Last et al. – FEMS Microbiology Reviews

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

Exploring the Relationship Between the Microbiome, Precision Medicine and Cancer – Tom Williams – Technology Networks

January 26, 2021

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 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

December 31, 2020

General microbiome

Review: Brain-gut axis: From the conditioned reflex to the microbiota-gut-brain communication system – Klara Gyires – Integrative Physiology

Human skin microbiome

Microbiological profile of diabetic foot ulcers in Kuwait – Asma Alhubail – PLOS ONE

Human respiratory microbiome

The airways microbiome of individuals with asthma treated with high and low doses of inhaled corticosteroids – Matthew J Martin – PLOS ONE

Human gut microbiome

The beneficial or detrimental fluoride to gut microbiota depends on its dosages – Guijie Chen – Ecotoxicology and Environmental Safety

Review: Synthetic Gut Microbiome: Advances and Challenges – Humphrey A. Mabwi – Computational and Structural Biotechnology Journal

Review: Microbiota-Gut-Brain Axis as a Regulator of Reward Process – Rubén García-Cabrerizo – Journal of Neurochemistry

Review: Modulatory effects of gut microbiome in cancer immunotherapy: A novel paradigm for blockade of immune checkpoint inhibitors – Sama Rezasoltani – Cancer Medicine

Animal experiments

Effects of heat-killed Enterococcus faecalis T-110 supplementation on gut immunity, gut flora, and intestinal infection in naturally aged hamsters – Takio Inatomi – PLOS ONE

Nasal Tissue Extraction Is Essential for Characterization of the Murine Upper Respiratory Tract Microbiota – L Patrick Schenck – mSphere

Animal microbiome

Review: Gut microbiota of animals living in polluted environments are a potential resource of anticancer molecules – Morhanavallee Soopramanien – Journal of Applied Microbiology

Plant, root, and soil microbiome

Metabarcoding on both environmental DNA and RNA highlights differences between fungal communities sampled in different habitats  – Martino Adamo – PLOS ONE

Changes in microbial communities at different soil depths through the first rainy season following severe wildfire in North China artificial Pinus tabulaeformis forest – Qianqian Qin – Journal of Environment Management

Shifts in a Phenanthrene-Degrading Microbial Community are Driven by Carbohydrate Metabolism Selection in a Ryegrass Rhizosphere – Longfei Jiang – ACS

Forest gaps mediate the structure and function of the soil microbial community in a Castanopsis kawakamii forest – Xuelin Wang – Ecological Indicators

Review: Herbicide bioremediation: from strains to bacterial communities – Marcos Pileggi – Heliyon

Spatial scale structure soil bacterial communities across an Arctic landscape – Lucie A Malard – Applied and Environmental Microbiology

Metagenomic Analysis of Rhizosphere Bacteria in Desert Plant Calotropis procera – Ahmed M Ramadan

Water and extremophile microbiome

Archaeal communities of low and high microbial abundance sponges inhabiting the remote western Indian Ocean island of Mayotte – Ana Rita Moura Polónia – Antonie van Leeuwenhoek

Preprint: Novel integrative elements and genomic plasticity in ocean ecosystems – Thomas Hackl – bioRxiv

Food microbiology

The diversity of microbial communities in Chinese milk fan and their effects on volatile organic compound profiles – Chen Chen – Journal of Dairy Science

Characterizing Relationship of Microbial Community in Xiaoqu and Volatiles of Light-aroma-type Xiaoqu Baijiu – Zhe Wang – Food Science and Technology Research

Virus and phages

Acquisition, prevalence and clearance of type-specific human papillomavirus infections in young sexually active Indian women: A community-based multicentric cohort study – Richard Muwonge – PLOS ONE

Techniques

Informed sequential pooling approach to detect SARS-CoV-2 infection – Renato Millioni – PLOS ONE

Thesis: Statistical Methods for Longitudinal Data Analysis and Reproducible Feature Selection in – Lingjing Jiang – UC San Diego Electronic Theses and Dissertations

MicroGMT: A Mutation Tracker for SARS-CoV-2 and Other Microbial Genome Sequences – Yue Xing – Frontiers in Microbiology

Microbes and evolution

Long-term experimental evolution of HIV-1 reveals effects of environment and mutational history – Eva Brons – PLOS BIOLOGY

The role of Ulva fasciata in the evolution of the microbial community and antibiotic resistance genes in maricultural sediments – Yuqin Luo – Marine Pollution Bulletin

Preprint: The Diversity and Evolution of Microbial Dissimilatory Phosphite Oxidation – Sophia D Ewens – bioRxiv

Microbes in the news

Synthetic Biologics Inc. (SYN) Soars 5.43% on December 25 – equities.com

The Brain, Gut and Consciousness: Microbiology of Our Mind – Inquiries Journal

Non-microbiology pick

Preprint: National Institutes of Health Institute and Center Award Rates and Funding Disparities – Michael S Lauer – bioRxiv

Communicating risk in human-wildlife interactions: How stories and images move minds – Sarah K Guenther – PLOS ONE

December 16, 2020

COVID19

Inferring the effectiveness of government interventions against COVID-19 – Brauner et al. – Science

COVID 19 mortality: Probable role of microbiome to explain disparity – Kumar & Chander – Medical Hyptheses

General microbiome

[PREPRINT] Theory of (antimicrobial) relativity: When competitors determine a species’ drug sensitivity. – Reding – bioRxiv

Human respiratory microbiome

Metagenomic Next-Generation Sequencing of Nasopharyngeal Specimens Collected from Confirmed and Suspect COVID-19 Patients – Mostafa et al. – mBio

Human oral microbiome

Variation in oral microbiome is associated with future risk of lung cancer among never-smokers – Hosgood et al. – Lung cancer

Human gut microbiome

Effect of an 8-week Exercise Training on Gut Microbiota in Physically Inactive Older Women – Zhong et al. – Int J Sports Med

Vitamin D metabolites and the gut microbiome in older men – Thomas et al. – Nature Communications

Animal microbiome

[PREPRINT] Longitudinal profiling of the macaque vaginal microbiome reveals similarities to diverse human vaginal communities: implications for use as a pre-clinical model for bacterial vaginosis – Rhoades et al. – bioRxiv

The earthworm microbiome is resilient to exposure to biocidal metal nanoparticles – Swart et al. – Environmental Pollution

Plant, root, and soil microbiome

Environmental microbiome mapping as a strategy to improve quality and safety in the food industry – Filippis et al. – Current Opinion in Food Science

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

Nitrosophilus alvini gen. nov., sp. nov., a hydrogen-oxidizing chemolithoautotroph isolated from a deep-sea hydrothermal vent in the East Pacific Rise, inferred by a genome-based taxonomy of the phylum “Campylobacterota” – Shiotani et al. – PLOS One

Techniques

A rapid approach to profiling diverse fungal communities using the MinION™ nanopore sequencer – Mafune et al. – BioTechniques

[PREPRINT] Microbe-seq: high-throughput, single-microbe genomics with strain resolution, applied to a human gut microbiome – Zheng et al. – bioRxiv

Microbes in the news

Oral Microbiome Diversity and Species Abundance Linked to Lung Cancer in Nonsmokers

November 26, 2020

Greetings from Pittsburgh!

Today’s digest is heavy on environmental microbiology work, especially plant, root, and soil microbiome studies. I also want to highlight a fun research paper (and paired Wired article) on the microbiome of da Vinci’s drawings.

Happy reading! And for all of those in the U.S. who are celebrating the Thanksgiving holiday, please be safe and follow all local COVID precautions.


Multi-site human microbiome

Mycobiome changes in the vitreous of post fever retinitis patients – Arunasri et al. – PLOS ONE

Review: Metabolomics analysis of microbiota-gut-brain axis in neurodegenerative and psychiatric diseases – Konjevod et al. – Journal of Pharmaceutical and Biomedical Analysis

Animal experiments

Cerumen microbial community shifts between healthy and otitis affected dogs – Borriello et al. – PLOS ONE

Plant, root, and soil microbiome

The difference between cellulolytic ‘culturomes’ and microbiomes inhabiting two contrasting soil types – Evdokimova et al. – PLOS ONE

Diversity of bacteria populations associated with different thallus regions of the brown alga Laminaria digitata – Ihua et al. – PLOS ONE

High nitrogen concentration alter microbial community in Allium fistulosum rhizosphere – Zhao et al. – PLOS ONE

Diversity, function and assembly of mangrove root-associated microbial communities at a continuous fine-scale – Zhuang et al. – npj Biofilms and Microbiomes

Water and extremophile microbiome

Shifts in methanogenic archaea communities and methane dynamics along a subtropical estuarine land use gradient – Euler et al. – PLOS ONE

Built environment

**The microbiome of Leonardo da Vinci’s drawings: A bio-archive of their history – Piñar et al. – Frontiers in Microbiology

Microbes in the news

**Meet the microbes living on Da Vinci’s iconic sketches – Simon – Wired

Science, publishing, and career

Postdocs under pressure: ‘Can I even do this any more?’ – Woolston – Nature

November 17, 2020

Multi-site human microbiome

Microbiome diversity predicts surgical success in patients with rectovaginal fistula – Leach et al. – International Urogynecology Journal

Human oral microbiome

[REVIEW]Oral Microbiota and Cancer Development – Tuominen & Rautava – Pathobiology

Human vaginal/pregnancy microbiome

Shotgun sequencing of the vaginal microbiome reveals both a species and functional potential signature of preterm birth – Feehily et al. – npj biofilms and microbiomes

Human gut microbiome

[REVIEW]IBDs and the pediatric age: Their peculiarities and the involvement of the microbiota – Cococcioni et al. – Digestive and Liver Disease

Gut microbiome stability and dynamics in healthy donors and patients with non-gastrointestinal cancers – Byrd et al. – JEM

Species-dependent variation of the gut bacterial communities across Trypanosoma cruzi insect vectors – Arias-Giraldo – PLOS One

Gut Microbiota and Cancer Correlates – Malaviya et al. – Probiotic Research in Therapeutics

Short-Chain Fatty Acids and Lipopolysaccharide as Mediators Between Gut Dysbiosis and Amyloid Pathology in Alzheimer’s Disease – Marizzoni et al. – Journal of Alzheimer’s Disease

Built environment (subways, indoor surfaces)
Unravelling the importance of the eukaryotic and bacterial communities and their relationship with Legionella spp. ecology in cooling towers: a complex network – Paranjape et al. – Microbiome

Techniques
Transductomics: sequencing-based detection and analysis of transduced DNA in pure cultures and microbial communities – Kleiner et al. – Microbiome

[REVIEW]NMR: Unique Strengths That Enhance Modern Metabolomics Research – Edison et al. – Analytical Chemistry

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

Study offers “indisputable” link between Alzheimer’s and gut microbiome – Lavars – New Atlas

October 30, 2020

COVID19
Cancer inpatients with COVID-19: A report from the Brazilian National Cancer Institute – de Melo et al. – PLOS One

Few bacterial co-infections but frequent empiric antibiotic use in the early phase of hospitalized patients with COVID-19: results from a multicentre retrospective cohort study in The Netherlands – Karami – et al. – Infectious Diseases

Infection of dogs with SARS-CoV-2 – Sit et al. – Nature

General microbiome/metabolome

Metabolomics of primary cutaneous melanoma and matched adjacent extratumoral microenvironment – Taylor et al. PLOS One

Human gut microbiome

Microbial signature in IgE-mediated food allergies – Goldberg et al. – Genome Medicine

Gut microbiota profiles of treatment-naïve adult acute myeloid leukemia patients with neutropenic fever during intensive chemotherapy – Rattanathammethee et al. – PLOS One

[Book Chapter]Understanding Polyphenols’ Health Effects Through the Gut Microbiota – Selma et al. – Dietary Polyphenols : Their Metabolism and Health Effects

[REVIEW]Gut Microbiota: Its Potential Roles in Pancreatic Cancer – Li et al. – Front. Cell. Infect. Microbiol.

Plant, root, and soil microbiome

Biological invasions alter environmental microbiomes: A meta-analysis – Malacrino et al. – PLOS One

Phages and viruses

[PREPRINT]VirION2: a short- and long-read sequencing and informatics workflow to study the genomic diversity of viruses in nature – Zablocki et al. – bioRxiv

Mycobiome
[REVIEW]T cell immunity to commensal fungi – Scheffold, Bacher & LeibundGut-Landmann – Current Opinion in Microbiology

Bioinformatics

Prometheus, an omics portal for interkingdom comparative genomic analyses – Ko et al. – PLOS One

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

News in Brie! Scientists discover cheese is so smelly because it helps microbes ‘talk’ to the bacteria that makes it ripe – S. Howes – Daily Mail