Category Archives: Built Environment Microbiology

April 19, 2020

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Hello from the Sonoran Desert! It is a lovely morning here in Tucson, Az. I am excited to send my first contribution to Microbiome Digest! There is a lot of diversity in today’s digest, but if microbes thriving in all kinds of strange, extreme conditions are your area of interest, you’ll be interested in the book compiling the latest studies on extremophiles. Each chapter focuses on a particular environment, ranging from deserts to deep-sea hydrothermal vents, and explores the mechanisms allowing microbes to survive these incredible conditions.

If like me, you are a computational biology enthusiast and a machine learning addict, you should enjoy reading the last entry, a short perspective paper examining how machine learning algorithms can help predict antibiotic resistance!

Have a great Sunday!

General microbiology

Preprint: Interspecies interactions in bacterial colonies are determined by physiological traits and the environment – Booth – BioRxiv

Human gut and mouth microbiome

Bacterial colonization reprograms the neonatal gut metabolome – Bittinger – Nature microbiology

Salivary Factors that Maintain the Normal Oral Commensal Microflora – Carpenter – Journal of dental research

Preprint: Metagenomic Next-Generation Sequencing of Rectal Swabs for the Surveillance of Antimicrobial Resistant Organisms on the Illumina Miseq and Oxford MinION Platforms – Yee – bioRxiv

Animal microbiome

Preprint: Mortality of native and invasive ladybirds co-infected by ectoparasitic and entomopathogenic fungi – Haelewaters – bioRxiv

Built environment

Preprint: The Microbes Found in the Honey of New York City Beehives – Weiss – BioRxiv

Correlation between autochthonous microbial communities and key odorants during the fermentation of red pepper (Capsicum annuum L.) – Xu – Food Microbiology

Water and extremophile microbiome

Book: Microbial Versatility in Varied Environments: Microbes in Sensitive Environments – collective – Springer Nature

The seasonal variation of microbial communities in drinking water sources in Shanghai – Guo – Journal of Cleaner Production

Plant, root and soil microbiome

LDPE microplastics significantly alter the temporal turnover of soil microbial communities –  Wang – Science of the total environment

High abundance of Ralstonia solanacearum changed tomato rhizosphere microbiome and metabolome – Wen – BMC Plant Biology

Phages and viruses

Preprint : First evidence of virus-like particles in the bacterial symbionts of Bryozoa – Vishnyakov – BioRxiv

Microbial community development on model particles in the deep sulfidic waters of the Black Sea – Suominen – Environmental microbiology

The stepwise assembly of the neonatal virome is modulated by breastfeeding – Liang – Nature

Bioinformatics

Preprint: Bayesian classification, anomaly detection, and survival analysis using network inputs with application to the microbiome – Josephs – arXiv

Techniques

Preprint: Expanding the diversity of bacterioplankton isolates and modeling isolation efficacy with large scale dilution-to-extinction cultivation – Henson – bioRxiv

Catalyzing rapid discovery of gold-precipitating bacterial lineages with university students – Riley – PeerJ

COVID-19 and career

Science-ing from home – Powell – Nature

My non-microbiology pick

Perspective: Lean, mean, learning machines – Wheeler – Nature review microbiology

April 11, 2020

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Happy Saturday morning, y’all! I’m excited for my first contribution to the digest, and hope you enjoy my picks over a luxurious weekend meal. Today’s digest starts with some preprints about COVID including research on a drug that may inhibit viral replication. Other research highlights include an examination of the relationship between the vaginal microbiome and pre-term birth, a preprint on the oral microbiome in space, and a potential new technique for low cost, high-throughput metagenome profiling. Scroll all the way to the end for information about a fun project by a University of Wyoming student called The Microbestiary.

COVID-19
Preprint: Genomic determinants of pathogenicity in SARS-CoV-2 and other human coronaviruses. Auslander, N. et al.

Preprint: Nelfinavir inhibits replication of severe acute respiratory syndrome coronavirus 2 in vitro. Yamamoto, N. et al.

Preprint: Understanding the B and T cells epitopes of spike protein of severe respiratory syndrome coronavirus-2: A computational way to predict the immunogens. Vashi, Y. et al.

General Microbiome
Preprint: From iron to antibiotics: Identification of conserved bacterial-fungal interactions across diverse partners. Pierce, EC. et al.

Human Gut Microbiome
Review: Unraveling Host-Gut Microbiota Dialogue and Its Impact on Cholesterol Levels. Villette R. et al. Frontiers in Pharmacology.

Metagenomics analysis reveals features unique to Indian distal gut microbiota. Kaur, K. et al. PLOS ONE.

Gut Microbiota Modulate CD8 T Cell Responses to Influence Colitis-Associated Tumorigenesis. Yu, A.I. et al. Cell Reports.

Human Oral Microbiome
Preprint: Characterization of the oral microbiome of medically controlled type-2 diabetes patients. Santos, A. et al.

Human Vaginal Microbiome
Cervicovaginal microbiome and natural history of HPV in a longitudinal study. Usyk, M. et al. PLOS Pathogens.

Meta-Analysis of Vaginal Microbiome Data Provides New Insights Into Preterm Birth. Kosti, I. et al. Frontiers in Microbiology.

Water and Extremophile Microbiome
Microbiota characterization of Exaiptasia diaphana from the Great Barrier Reef. Hartman, L.M. et al. Animal Microbiome.

Microbial Diversity and Metabolic Potential in the Stratified Sansha Yongle Blue Hole in the South China Sea. He, P. et al. Scientific Reports.

Metabolic versatility of freshwater sedimentary archaea feeding on different organic carbon sources. Compte-Port, S. et al. PLOS ONE.

Animal Experiments and Animal Microbiome
The skin microbiome facilitates adaptive tetrodotoxin production in poisonous newts. Vaelli, P.M. et al. eLife.

Metatranscriptomic virome assessment of Rhipicephalus microplus from Colombia. Gomez, G.F. et al. Ticks and Tick-borne Diseases.

Preprint: Metabolic differences between symbiont subpopulations in the deep-sea tubeworm Riftia pachyptila. Hinzke, T. et al.

Preprint: Similar gut bacterial microbiota in two fruit-feeding moth pests collected from different host species and locations. Gong, Q et al.

Plant, Root, and Soil Microbiome
The preceding root system drives the composition and function of the rhizosphere microbiome. Zhou, Y. et al. Genome Biology.

Microbial Co-Occurrence in Floral Nectar Affects Metabolites and Attractiveness to a Generalist Pollinator. Rering, C.C. et al. Journal of Chemical Ecology.

Impact of phages on soil bacterial communities and nitrogen availability under different assembly scenarios. Braga, L.P.P. et al. Microbiome.

A predatory myxobacterium controls cucumber Fusarium wilt by regulating the soil microbial community. Ye, X. et al. Microbiome.

A plant genetic network for preventing dysbiosis in the phyllosphere. Chen, T. et al. Nature.

Fungal communities differentially respond to warming and drought in tropical grassland soil. de Oliveira, T.B. et al. Molecular Ecology.

Built Environment
An in-depth survey of the microbial landscape of the walls of a neonatal operating room. Derilus, D. et al. PLOS ONE.

Microbes in Space
Preprint: Defining the resilience of the human salivary microbiota by a 520 days longitudinal study in confined environment: the Mars500 mission. Bacci, G. et al.

Phages and Viruses
Phage cocktail containing Podoviridae and Myoviridae bacteriophages inhibits the growth of Pectobacterium spp. under in vitro and in vivo conditions. Zaczek-Moczydłowska, M.A. et al. PLOS ONE.

Dynamic genome evolution and complex virocell metabolism of globally-distributed giant viruses. Moniruzzaman M., et al. Nature Communications.

Preprint: Infection with novel Bacteroides phage BV01 alters host transcriptome and bile acid metabolism in a common human gut microbe. Campbell, D.E. et al.

Bioinformatics
Preprint: Integrative and Conjugative Elements (ICE) and Associated Cargo Genes within and across Hundreds of Bacterial Genera. Kaufman, J. et al.

Techniques
A restriction enzyme reduced representation sequencing approach for low-cost, high-throughput metagenome profiling. Hess, M.K. et al. PLOS ONE.

Industrial Microbiome
Open microbiome dominated by Clostridium and Eubacterium converts methanol into i-butyrate and n-butyrate. Huang, S. et al. Applied Microbiology and Biotechnology.

Fun with Microbes
University of Wyoming masters student Erin Bentley was selected for an Arctic Circle Expedition in 2021 where she will characterize microbes and share her discoveries on The Microbestiary.
“The Microbestiary strives to show the public, in welcoming and memorable ways, that the microbial world is populated by strange and beautiful characters,” says Bentley in an article published on the UW website.

March 5, 2020

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Today’s Digest is heavy, so you might want to pace yourself. It’s hard to pick the highlights, but I’m biased towards fungal research, so first about a wake-up call to look at the fungi seriously. The insects might provide for remedy against antibiotic resistance and is the dust settled on the sparse fetal intestinal microbiota? Stay healthy and keep reading.

Event

Call for papers – Global Outbreaks and Responses – BMC Medicine

General microbiology

** Viewpoints: Fungal diseases as neglected pathogens: A wake-up call to public health officials – Marcio L. Rodrigues & Joshua D. Nosanchuk – PLoS NTD

Inducible cell-to-cell signaling for tunable dynamics in microbial communities – Arianna Miano et al. – Nature Communications

Antimicrobial resistance

** The insect antimicrobial peptide cecropin A disrupts uropathogenic Escherichia coli biofilms – Miriam Kalsy et al. – npj Biofilms and Microbiomes

Using comparative genomics to understand molecular features of carbapenem-resistant Acinetobacter baumannii from South Korea causing invasive infections and their clinical implications – Min Hyung Kim – PLoS One

Factors associated with sufficient knowledge of antibiotics and antimicrobial resistance in the Japanese general population – Shinya Tsuzuki et al. – Scientific Reports

Faeces and vaccines could be the key to tackling antimicrobial resistance – Elisabeth Mahase – BMJ

A survey of extended-spectrum beta-lactamase-producing Enterobacteriaceae in urban wetlands in southwestern Nigeria as a step towards generating prevalence maps of antimicrobial resistance – Olawale Olufemi Adelowo et al. – PLoS One

Pregnancy and early life

** Viable bacterial colonization is highly limited in the human intestine in utero – E. Rackaityte et al. – Nature Medicine

Perinatal Antibiotic Exposure Affects the Transmission between Maternal and Neonatal Microbiota and Is Associated with Early-Onset Sepsis – Ping Zhou et al. – mSphere

Combined analysis of microbial metagenomic and metatranscriptomic sequencing data to assess in situ physiological conditions in the premature infant gut – Yonatan Sher et al. – PLoS One

Human skin microbiome

A microbiome and metabolomic signature of phases of cutaneous healing identified by profiling sequential acute wounds of human skin: An exploratory study – Mohammed Ashrafi et al. – PLoS One

Human oral microbiome

Review: Single-Cell Genomics and the Oral Microbiome – M. Balachandran et al. – Journal of Dental Research

Insights Obtained by Culturing Saccharibacteria With Their Bacterial Hosts – B. Bor et al. – Journal of Dental Research

Electronic Cigarette Aerosol Modulates the Oral Microbiome and Increases Risk of Infection – Smruti Pushalkar et al. – iScience

Press: Oral Microbiome Changes Implicated in Gum Inflammation in E-Cigarette Users – GenomeWeb

In vitro: A salivary metabolite signature that reflects gingival host-microbe interactions: instability predicts gingivitis susceptibility – Marcela M. Fernandez-Gutierrez et al. – Scientific Reports

Human respiratory microbiome

Review: The Role of Lung and Gut Microbiota in the Pathology of Asthma – Weronika Barcik et al. – Immunity

Cancer and microbiome

Endogenous murine microbiota member Faecalibaculum rodentium and its human homologue protect from intestinal tumour growth – Elena Zagato et al. – Nature Microbiology

Escherichia coli adhesion portion FimH functions as an adjuvant for cancer immunotherapy – Wei Zhang et al. – Nature Communications

Temporal changes in gut microbiota profile in children with acute lymphoblastic leukemia prior to commencement-, during-, and post-cessation of chemotherapy – Ling Ling Chua et al. – BMC Cancer

Review: Interplay between Dietary Polyphenols and Oral and Gut Microbiota in the Development of Colorectal Cancer – Carolina Cueva & Mariana Silva – Nutrients

Human gut microbiome

In vitro: Short-term supplementation of celecoxib-shifted butyrate production on a simulated model of the gut microbial ecosystem and ameliorated in vitro inflammation – Emma Hernandez-Sanabria et al. – npj Biofilms and Microbiomes

Review: Crosstalk Between Gut Microbiota and Innate Immunity and Its Implication in Autoimmune Diseases – Yuhao Jiao et al. – Frontiers in Immunology

An empirically derived method for measuring human gut microbiome alpha diversity: Demonstrated utility in predicting health-related outcomes among a human clinical sample – Sarah L. Hagerty et al. – PLoS One

Proof-of-concept study of the efficacy of a microbiota-directed complementary food formulation (MDCF) for treating moderate acute malnutrition – Ishita Mostafa et al. – BMC Public Health

Microbiota as Predictor of Mortality in Allogeneic Hematopoietic-Cell Transplantation – Jonathan U. Peled et al. – New England Journal of Medicine

Human multi-site microbiome

Age-Related Variation of Bacterial and Fungal Communities in Different Body Habitats across the Young, Elderly, and Centenarians in Sardinia – Lu Wu et al. – mSphere

Response of the human gut and saliva microbiome to urbanization in Cameroon – Ana Lokmer et al. – Scientific Reports

The gut-microbiota-brain axis

Therapeutic Effects of the In Vitro Cultured Human Gut Microbiota as Transplants on Altering Gut Microbiota and Improving Symptoms Associated with Autism Spectrum Disorder – Kainan Chen et al. – Microbial Ecology

Built environment microbiome

A preliminary study on the potential of Nanopore MinION and Illumina MiSeq 16S rRNA gene sequencing to characterize building-dust microbiomes – Anders B. Nygaard et al. – Scientific Reports

Metabolomics

Spatial metabolomics of in situ host–microbe interactions at the micrometre scale – Benedikt Geier et al. – Nature Microbiology

Global chemical effects of the microbiome include new bile-acid conjugations – Robert A. Quinn et al. – Nature

Animal experiments

PM2.5 exposure perturbs lung microbiome and its metabolic profile in mice – Jingli Li et al. – Science of the Total Environment

Growth hormone deficiency and excess alter the gut microbiome in adult male mice – Elizabeth A Jensen et al. – Endocrinology

Dissociation of Adaptive Thermogenesis from Glucose Homeostasis in Microbiome-Deficient Mice – Tibor L. Krisko et al. – Cell Metabolism

Fecal IgA Levels Are Determined by Strain-Level Differences in Bacteroides ovatus and Are Modifiable by Gut Microbiota Manipulation – Chao Yang et al. – Cell Host & Microbe

Animal microbiome

Can rumen bacteria communicate to each other? – Mi-Young Won et al. – Microbiome

Entomopathogenic nematode-associated microbiota: from monoxenic paradigm to pathobiome – Jean-Claude Ogier et al. – Microbiome

The canine oral microbiome: variation in bacterial populations across different niches – Avika Ruparell et al. – BMC Microbiology

Evolutionary analysis of Mycobacterium bovis genotypes across Africa suggests co-evolution with livestock and humans – Osvaldo Frederico Inlamea et al. – PLoS NTD

Nanopore sequencing of microbial communities reveals the potential role of sea lice as a reservoir for fish pathogens – Ana Teresa Gonçalves et al. – Scientific Reports

Plant, root and soil microbiome

Insights on aquatic microbiome of the Indian Sundarbans mangrove areas – Paltu Kumar Dhal et al. – PLoS One

Ganoderma lucidum cultivation affect microbial community structure of soil, wood segments and tree roots – Fei Ren et al. – Scientific Reports

Effect of long-term destocking on soil fungal functional groups and interactions with plants – Jie Wang et al. – Plant and Soil

Comparative Analysis of Root Microbiomes of Rice Cultivars with High and Low Methane Emissions Reveals Differences in Abundance of Methanogenic Archaea and Putative Upstream Fermenters – Zachary Liechty et al. – mSystems

Fungal diversity and community composition of wheat rhizosphere and non-rhizosphere soils from three different agricultural production regions of South Africa – Magalane Pheladi Gqozo et al. – Applied Soil Ecology

Microbial and volatile profiling of soils suppressive to Fusarium culmorum of wheat – Adam Ossowicki & Vittorio Tracanna et al. – Proceedings of the Royal Society B

Industrial development as a key factor explaining variances in soil and grass phyllosphere microbiomes in urban green spaces – Zhen-Zhen Yan et al. – Environmental Pollution

Plant communities mediate the interactive effects of invasion and drought on soil microbial communities – Catherine Fahey et al. – The ISME Journal

Water and extremophile microbiome

Methyl t-butyl ether-degrading bacteria for bioremediation and biocontrol purposes – Giada d’Errico et al. – PLoS One

Uncovering microbial responses to sharp geochemical gradients in a terrace contaminated by acid mine drainage – Rui Xu et al. – Environmental Pollution

Snapshot: Microbial Extremophiles – Amy K. Schmid et al. – Cell

Denitrification performance and microbial communities of solid-phase denitrifying reactors using poly (butylene succinate)/bamboo powder composite – Wanhe Qi et al. – Bioresource Technology

Meta-omics Provides Insights into the Impact of Hydrocarbon Contamination on Microbial Mat Functioning – Johanne Aubé et al. – Microbial Ecology

Role of microbial diversity for sustainable pyrite oxidation control in acid and metalliferous drainage prevention – Omy T. Ogbughalu et al. – Journal of Hazardous Materials

Phages and viruses

** Coronavirus research highlights – BMC

Fecal Viral Community Responses to High-Fat Diet in Mice – Anjelique Schulfer et al. – mSphere

Technology

Rapid MinION profiling of preterm microbiota and antimicrobial-resistant pathogens – Richard M. Leggett et al. – Nature Microbiology

Assembly-free single-molecule sequencing recovers complete virus genomes from natural microbial communities – John Beaulaurier et al. – Genome Research

Bioinformatics

Rapid inference of antibiotic resistance and susceptibility by genomic neighbour typing – Karel Břinda et al. – Nature Microbiology

Microbes in the news

Tough microbe’s DNA could be a lasting archive – Steve Nadis – Science

How Bacteria Can ‘Sculpt The Gut’ – Maya Trabulsi – KPBS

The bee microbiome can fight back against fungi that cause Colony Collapse Disorder – Lauren Sara McKee – Massive Science

Ancient gut microbiomes shed light on human evolution – Newswise

Launch of the Marine Microbiome Roadmap – NIOZ

Understanding Microbiome Resilience on a Changing Planet – Michigan State University

Adaptations in gut microbes helped our ancestors thrive in new geographical territories: Study – New Kerala

Scientists Announce VIRGO, First Comprehensive Gene Catalog To Decode the Vaginal Microbiome – PR Newswire

Metabolomics Reveals Connection Between Gut Microbiome and Blood – Metabolon

Study shows universally positive effect of cover crops on soil microbiome – Phys.org

New Center of Microbiome Science is in the works at Ohio State – Emily Caldwell – Ohio State University News

Common diseases may be communicable through microbiome, says UBC researcher – Stephanie Blain – The Ubyssey

The microbes in your mouth, and a reminder to floss and go to the dentist – Science Daily

For Your Microbiome, How You Eat Could Be As Important As What You Eat – Technology Networks

Study: Infectious gut bacteria may predict UTI risk – Sue Treiman – Cornell Chronicle

The Best Way to Avoid Getting Sick Is to Wash Your Hands — But You’re Probably Doing It Wrong – Bojana Galic – Live Strong

Microbes on the market

DuPont carries on microbiome momentum with metabolic disease collaboration – Will Chu – Nutraingredients

Non-microbiology picks

Invest 5% of research funds in ensuring data are reusable – Barend Mons – Nature

 

February 1, 2020

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Today’s Digest brings you an Outlook collection on human gut microbiome by Nature, a Hi-C investigation of the evolution of the gut microbiota, and be careful with the dust, there’s transferrable antimicrobial genes within!

Events

Reshaping the Microbiome through Nutrition – Nature Conference – San Diego, CA

General microbiology

Commensal Bacteroidetes protect against Klebsiella pneumoniae colonization and transmission through IL-36 signalling – Richard P. Sequeira et al. – Nature Microbiology

** The gut microbiome – Nature Outlook

Antimicrobial resistance

The negative cofactor 2 complex is a key regulator of drug resistance in Aspergillus fumigatus – Takanori Furukawa et al. – Nature Communications

Plasmid-mediated metronidazole resistance in Clostridioides difficile – Ilse M. Boekhoud et al. – Nature Communications

A Common Practice of Widespread Antimicrobial Use in Horse Production Promotes Multi-Drug Resistance – S. Álvarez–Narváez et al. – Scientific Reports

Surveys of knowledge and awareness of antibiotic use and antimicrobial resistance in general population: A systematic review – PLoS One

Antimicrobial resistance patterns and molecular resistance markers of Campylobacter jejuni isolates from human diarrheal cases – Mohamed Elhadidy et al. – PLoS One

Review: Antibiotic resistance: turning evolutionary principles into clinical reality – Dan I Andersson et al. – FEMS Microbiology Reviews

Antibiotic resistome associated with microbial communities in an integrated wastewater reclamation system – Kaifeng Yu et al. – Water Research

Human gut microbiome

** Tracking microbial evolution in the human gut using Hi-C reveals extensive horizontal gene transfer, persistence and adaptation – Eitan Yaffe & David A. Relman – Nature Microbiology

Growth effects of N-acylethanolamines on gut bacteria reflect altered bacterial abundances in inflammatory bowel disease – Nadine Fornelos et al. – Nature Microbiology

Human cancer microbiome

The Influence of Lung Microbiota on Lung Carcinogenesis, Immunity, and Immunotherapy – Ariel G. Ramírez-Labrada et al. – Trends in Cancer

Built environment microbiome

** Mobilizable antibiotic resistance genes are present in dust microbial communities – Sarah Ben Maamar et al. – PLoS Pathogens

Indoor and outdoor airborne bacterial and fungal air quality in kindergartens: seasonal distribution, genera, levels, and factors influencing their concentration – Farhad Mirkhond Chegini et al. – Building and Environment

Metabolomics

Targeted metabolomics of pellicle and saliva in children with different caries activity – Annika Schulz et al. – Scientific Reports

Animal experiments

Review: The role of the microbiota in sedentary life style disorders and ageing: Lessons from the animal kingdom – P.W. O’Toole & P.G. Shiels – Journal of Internal Medicine

Animal microbiome

Dietary effects on gut microbiota of the mesquite lizard Sceloporus grammicus (Wiegmann, 1828) across different altitudes – Nina Montoya-Ciriaco et al. – Microbiome

Late weaning is associated with increased microbial diversity and Faecalibacterium prausnitzii abundance in the fecal microbiota of piglets – Francesca Romana Massacci et al. – Animal Microbiome

Plant, root and soil microbiome

Effects of soil chemical properties and fractions of Pb, Cd, and Zn on bacterial and fungal communities – Xiaomei Pan et al. – Science of the Total Environment

Resilience of the microbial communities of semiarid agricultural soils during natural climatic variability events – Lumarie Pérez-Guzmán et al. – Applied Soil Ecology

Effects of microbial inoculants on the fermentation characteristics and microbial communities of sweet sorghum bagasse silage – Miaoyin Dong et al. – Scientific Reports

Water and extremophile microbiome

Diversity of Bacterial Community in the Oxygen Minimum Zones of Arabian Sea and Bay of Bengal as Deduced by Illumina Sequencing – Genevieve L. Fernandes et al. – Frontiers in Microbiology

Ionic Liquid Enriches the Antibiotic Resistome, Especially Efflux Pump Genes, Before Significantly Affecting Microbial Community Structure – Xiaolong Wang et al. – Environmental Science & Technology

Methane yield enhancement of mesophilic and thermophilic anaerobic co-digestion of algal biomass and food waste using algal biochar: Semi-continuous operation and microbial community analysis – Le Zhang et al. – Bioresource Technology

Characterization and co-occurrence of microbial community in epiphytic biofilms and surface sediments of wetlands with submersed macrophytes – Yuansi Liu et al. – Science of the Total Environment

Phages and viruses

** Giant virus diversity and host interactions through global metagenomics – Frederik Schulz et al. – Nature

Reassortment and adaptive mutations of an emerging avian influenza virus H7N4 subtype in China – Bingqian Qu et al. – PLoS One

Outbreak of Pneumonia of Unknown Etiology in Wuhan China: the Mystery and the Miracle – Hongzhou Lu et al. – Journal of Medical Virology

Bioinformatics

Comparing bioinformatic pipelines for microbial 16S rRNA amplicon sequencing – Andrei Prodan et al. – PLoS One

Microbes in the news

Walnuts May Benefit Gut Bacteria and Improve Heart Health – Karina Lichtenstein – Medicine Net

How to create living art with microbes – Eugenia Angulo – BBVA OpenMind

December 27, 2019

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Today’s Digest brings you a report linking gut microbiota and metabolites, a study on dishwasher rubber as a bacterial reservoir, a news piece for your guide to probiotics, and many more. If we don’t see you again in 2019, Happy New Year! May 2020 bring much success and happiness!

General microbiology

Preprint: The Microbe Directory v2.0: An Expanded Database of Ecological and Phenotypical Features of Microbes – Maria A. Sierra et al. – bioRxiv

A novel graph theoretical approach for modeling microbiomes and inferring microbial ecological relationships – Suyeon Kim et al. – BMC Genomics

Antimicrobial resistance

Preprint: Longitudinal linked read sequencing reveals ecological and evolutionary responses of a human gut microbiome during antibiotic treatment – Morteza Roodgar et al. – bioRxiv

Human oral microbiome

Re-initiation of Oral Food Intake Following Enteral Nutrition Alters Oral and Gut Microbiota Communities – Sayaka Katagiri et al. – Frontiers in Cellular and Infection Microbiology

Human respiratory microbiome

Microbiome in Chronic Obstructive Pulmonary Disease: Role of Natural Products Against Microbial Pathogens – Alessia Santoro et al. – Current Medicinal Chemistry

Human gut microbiome

Comparison of Japanese and Indian intestinal microbiota shows diet-dependent interaction between bacteria and fungi – Siddhika Pareek et al. – npj Biofilms and Microbiomes

Review: The influence of dietary patterns on gut microbiome and its consequences for nonalcoholic fatty liver disease – Qing-Song Zhang et al. – Trends in Food Science and Technology

** Relationship between gut microbiota and circulating metabolites in population-based cohorts – Dina Vojinovic et al. – Nature Communications

Human gut microbiota is associated with HIV-reactive immunoglobulin at baseline and following HIV vaccination – Jacob A. Cram et al. – PLoS One

Preprint: The interplay between host genetics and the gut microbiome reveals common and distinct microbiome features for human complex diseases – Fengzhe Xu & Yuanqing Fu et al. – bioRxiv

Effect of Helicobacter pylori on gastrointestinal microbiota: a population-based study in Linqu, a high-risk area of gastric cancer – Yang Guo et al. – Gut

Human gut-microbiome-brain axis

The relationship between the gut microbiome and mild cognitive impairment in patients without dementia: a cross-sectional study conducted in Japan – Naoki Saji et al. – Scientific Reports

Synergistic effects of APOE and sex on the gut microbiome of young EFAD transgenic mice – Juan Maldonado Weng et al. – Molecular Neurodegeneration

Metabolomics

Tech Note: Boost that metabolomic confidence – Vivien Marx – Nature Methods

The total microbiome functions in bacteria and fungi – Robert Starke et al. – Journal of Proteomics

Animal experiments

Allergic inflammation alters the lung microbiome and hinders synergistic co-infection with H1N1 influenza virus and Streptococcus pneumoniae in C57BL/6 mice – Kim S. LeMessurier et al. – Scientific Reports

Jatrorrhizine Balances the Gut Microbiota and Reverses Learning and Memory Deficits in APP/PS1 transgenic mice – Sheng Wang et al. – Scientific Reports

The impact of gut microbiota manipulation with antibiotics on colon tumorigenesis in a murine model – Jae Gon Lee et al. – PLoS One

Maternal milk and fecal microbes guide the spatiotemporal development of mucosa-associated microbiota and barrier function in the porcine neonatal gut – Hongbin Liu et al. – BMC Biology

Built environment microbiome

** The dishwasher rubber seal acts as a reservoir of bacteria in the home environment – Jerneja Zupančič et al. – BMC Microbiology

Plant, root and soil microbiome

Development of microbial communities in organochlorine pesticide contaminated soil: A post-reclamation perspective – Helga E.Balázs et al. – Applied Soil Ecology

Towards simple tools to assess functional effects of contaminants on natural microbial and invertebrate sediment communities – Stéphane Pesce et al. – Environmental Science and Pollution Research

Core rhizosphere microbiomes of dryland wheat are influenced by location and land-use history – Daniel C Schlatter et al. – Applied and Environmental Microbiology

Water and extremophile microbiome

Single molecule sequencing reveals response of manganese-oxidizing microbiome to different biofilter media in drinking water systems – Xin Zhao et al. – Water Research

Prokaryotic Population Dynamics and Viral Predation in a Marine Succession Experiment Using Metagenomics – Jose M. Haro-Moreno et al. – Frontiers in Microbiology

Phages and viruses

News & Views: Phages build anti-defence barriers – Eugene V. Koonin & Mart Krupovic – Nature Microbiology

Microbes in the news

The Best Thing That Happened This Week: Dogs Rule Because They Drool – Sandy Hingston – Philadelphia Magazine

** A guide to the best probiotics – Louisa Richards/Katherine Marengo – Medical News Today

Having a Dog as a Child Is Tied to a Lower Risk of Schizophrenia as an Adult – Nicholas Bakalar – New York Times

Expanding virophage diversity – DOE/Joint Genome Institute

Microbes on the market

Carbiotix to partner with Italian university on neuroinflammation project – Nathan Gray – Nutraingredients

Human Microbiome Market is Expected to Touch US$ 1888.9 Mn by 2026 – Sheila Shipman – News Cast Report

The next frontier – Aaron Massecar – Today’s Veterinary Business

November 8, 2019

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Today’s week-end digest is about new bioinformatic tools (MGnify, PIME, MDiNE) for microbiota analysis, how chemical and built environment of home affects human microbiota and  guidelines for the gut microbiome studies in hypertension.

General microbiome

Adaptation of the Gut Microbiota to Modern Dietary Sugars and Sweeteners – Sara C. Di Rienzi – Advances in Nutrition

Bacteriophages in gastroenterology—from biology to clinical applications – João Sabino – Alimentary Pharmacology and Therapeutics

Boosting natural history research via metagenomic clean-up of crowdsourced feces – Amrita Srivathsan – Plos Biology

Human microbiome

Lower gut microbiome diversity and higher abundance of proinflammatory genus Collinsella are associated with biopsy-proven nonalcoholic steatohepatitis – Stuart Astbury – Gut Microbes

Guidelines for Transparency on Gut Microbiome Studies in Essential and Experimental Hypertension – Francine Z. Marques – Hypertension

The association between dietary fibre deficiency and high-income lifestyle-associated diseases: Burkitt’s hypothesis revisited – Stephen J. O’Keefe – The Lancet Gastroenterology and Hepatology

Animal experiments

Bacterial Swarming as a Protective Response to Intestinal Stress – Weijie Chen – BioRxiv

Flaxseed oil supplementation improves intestinal function and immunity, associated with altered intestinal microbiome and fatty acid profile in pigs with intrauterine growth retardation – Lianqiang Che – Food and Function

Gamma-aminobutyric acid-producing lactobacilli positively affect metabolism and depressive-like behaviour in a mouse model of metabolic syndrome – E. Patterson – Scientific Reports

Plant, root and soil microbiome

Short term effects of different green manure amendments on the composition of main microbial groups and microbial activity of a submerged rice cropping system – Muhammad Israr Khan – Applied Soil Ecology

Cost-effective in-situ remediation technologies for complete mineralization of dyes contaminated soils – Vipul R. Patel – Chemosphere

Distinct Microbial Community of Phyllosphere Associated with Five Tropical Plants on Yongxing Island, South China Sea – Lijun Bao – Microorganisms

Tracing the evolutionary routes of plant–microbiota interactions – Carmen Escudero-Martinez – Current Opinion in Microbiology

Water microbiome

Diet shapes cold‐water corals bacterial communities – Pierre E. Galand – Environmental Microbiology

Built Environment

Home chemical and microbial transitions across urbanization – Laura-Isobel McCall – Nature Microbiology

Techniques

Learning representations of microbe–metabolite interactions – James T. Morton – Nature Methods

MGnify: the microbiome analysis resource in 2020 – Alex L. Mitchell – Nucleic Acids Research

PIME: A package for discovery of novel differences among microbial communities – Luiz Fernando W. Roesch – Molecular Ecology Resources

MDiNE: A model to estimate differential co-occurrence networks in microbiome studies – Kevin McGregor – Bioinformatics

Probiotics

Fermentation of plant-based milk alternatives for improved flavour and nutritional value – Muzi Tangyu – Applied Microbiology and Biotechnology

Modulations of Probiotics on Gut Microbiota in a 5‐Fluorouracil‐Induced Mouse Model of Mucositis – Chun Yan Yeung – Journal of Gastroenterology and Hepatology

The effect of an additive containing three Lactobacillus species on the fermentation pattern and microbiological status of silage – Maja Fijałkowska – Journal of the Science of Food and Agriculture

Microbes in the news

Gut Microbiome Puts the Brakes on Iron Absorption – Michigan Medicine

The Link Between Sleep and Your Gut Microbiome – Health central

Microbiome in China: Cosmetic trend will ‘heat up’ by the end of 2020, says expert – Cosmetics Design-Asia

Enterome Enters Research Collaboration With Major Cancer Center Focused on New Microbiome-derived Immunotherapies – Yahoo Finance

Non Microbiology Picks

Is running associated with a lower risk of all-cause, cardiovascular and cancer mortality, and is the more the better? A systematic review and meta-analysis – Zeljko Pedisic – British Journal of Sports Medicine

October 26, 2019

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Highlights: Bacterial communities in aquaculture, crocodiles, tadpoles, mushrooms, coasts, sports facilities; viruses; standardization issues of human microbiome research; some cool events and news hot off the press!

 

Events and jobs

2019 Genome Center Halloween Symposium – 31/10/2019 – UCD, USA

MB Seminar: Marine Host-Microbiome Interactions: Challenges and Opportunities (Dr. Jonathan Eisen, UC Davis) – 22/11/2019 – UCSD, USA

General microbiome 

Metabolic specializations within a bacterial community to create living rocks – Samantha C Waterworth – bioRxiv

Analysis of bacterial microbiome associated with nylon and copper nets in an aquaculture context – Paula Canada – Aquaculture

The gut-eye-lacrimal gland-microbiome axis in Sjögren Syndrome – Claudia M. Trujillo-Vargas – The Ocular Surface

Multi-site human microbiome

DNA extraction for human microbiome studies: the issue of standardization  – K. Leigh Greathouse Genome Biology

Storage media and not extraction method has the biggest impact on recovery of bacteria from the oral microbiome – Xiaoyan Zhou – Nature

Factors contributing to interindividual variation in retronasal odor perception from aroma glycosides: the role of odorant sensory detection threshold, oral microbiota and hydrolysis in saliva – Mango Parker – ACS

Animal experiments 

Contribution of fungal microbiome to intestinal physiology, early-life immune development and mucosal inflammation in mice – Erik van Tilburg Bernardes – bioRxiv

Animal microbiome 

Gut microbiota structure differs between honey bees in winter and summer – Lucie Kešnerová – bioRxiv

Characterisation of the intestinal microbiota of commercially farmed saltwater crocodiles, Crocodylus porosus – Nicky-Lee Willson – Applied Microbiology and Biotechnology

Changes in intestinal microbial community of Rana chensinensis tadpoles during metamorphosis – Hongyu Yang – Aquaculture

Plant, root, and soil microbiome

Impact of agro-farming activities on microbial diversity of acidic red soils in a Camellia Oleifera Forest – Jun Li – Revista Brasileira de Ciência do Solo

A horizon scan of priorities for coastal marine microbiome research – Stacey M. Trevathan-Tackett – Nature

Water and extremophile microbiome 

Effects of disinfection efficiency on microbial communities and corrosion processes in drinking water distribution systems simulated with actual running conditions – Ying Zhu – Journal of Environmental Sciences

Built environment 

Microbial diversity of bioaerosol inside sports facilities and antibiotic resistance of isolated Staphylococcus spp. – Marta Małecka-Adamowicz – Aerobiologia

Food microbiology

Comparing approaches for capturing bacterial assemblages 2 associated with symptomatic (bacterial blotch) and asymptomatic 3 mushroom (Agaricus bisporus) caps – Samuel J. Martins – APS

Comprehensive Understanding of the Bacterial Populations and Metabolites Profile of Fermented Feed by 16S rRNA Gene Sequencing and Liquid Chromatography–Mass Spectrometry – Wei Jin – MDPI Metabolites

Phages and viruses

Viruses RIG up intestinal immunity – Sanghyun Lee – Nature Immunology

Gut DNA Virome Diversity and Its Association with Host Bacteria Regulate Inflammatory Phenotype and Neuronal Immunotoxicity in Experimental Gulf War Illness – Ratanesh K Seth – MDPI Viruses

Viral quasispecies – Esteban Domingo – PLoS Genetics

Techniques

Effective application of machine learning to microbiome-based classification problems – Begüm D. Topçuoğlu – bioRxiv

LEMMI: A continuous benchmarking platform for metagenomics classifiers – Mathieu Seppey – bioRxiv

Microbes in the news

Even the Fetus Has Gut Bacteria, Study Shows – News Wise

Tropical Air Microbiome Analysis Reveals Daily Cycle, Environmental Drivers – genomeweb

Global Microbiome Sequencing Market – Yahoo

How our day-to-day food intake shapes our gut microbiota – Gut microbiota for health

Tracking down the functions of the microbiome – phys.org

Unhealthy gut microbiome reduces brain synaptic pruning, impairs learning – News Medical

Harnessing the Power of Microbes to Fight Cancer – Medscape.com

October 16, 2019

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Happy Wednesday! Today’s digest includes the human gut virome, microbiome recovery after antibiotics, and the fungi growing on museum skeletons. Enjoy!

Pregnancy and early life

The vaginal microbial communities of healthy expectant Brazilian mothers and its correlation with the newborn’s gut colonization – Dobbler – World Journal of Microbiology and Biotechnology

Human skin microbiome

In vitro Antimicrobial Activity of Acne Drugs Against Skin-Associated Bacteria – Blaskovich – Scientific Reports

Human gut microbiome

Review: The Human Gut Virome Is Highly Diverse, Stable, and Individual Specific – Shkoporov – Cell Host & Microbe

Review: Inflammatory Bowel Disease: A Potential Result from the Collusion between Gut Microbiota and Mucosal Immune System – Yue – Microorganisms

Individualized recovery of gut microbial strains post antibiotics – Koo – npj Biofilms and Microbiomes

Animal experiments

Depletion of dietary aryl hydrocarbon receptor ligands alters microbiota composition and function – Brawner – Scientific Reports

Rat H1 parvovirus infection leads to alterations in gut microbiota – Xiang – Pathogens and Disease

Positive effect of an electrolyzed reduced water on gut permeability, fecal microbiota and liver in an animal model of Parkinson’s disease – Bordoni – PLoS One

The Sulfate-Reducing Microbial Communities and Meta-Analysis of Their Occurrence during Diseases of Small–Large Intestine Axis – Kushkevych – Journal of Clinical Medicine

Plant, root, and soil microbiome

Spatial gradients in the characteristics of soil-carbon fractions are associated with abiotic features but not microbial communities – Sengupta – Biogeosciences

Water and extremophile microbiome

Diversity, Distribution, and Ecology of Fungi in the Seasonal Snow of Antarctica – Menezes – Microorganisms

Interaction and assembly processes of abundant and rare microbial communities during a diatom bloom process – Zhang – Environmental Microbiology

Built environment

Changes in the Bacterioplankton Community Structure from Southern Gulf of Mexico During a Simulated Crude Oil Spill at Mesocosm Scale – Valencia-Agami – Microorganisms

Increased loading leads to convergence of microbial communities and high methane yield in adapted anaerobic co-digesters – Wang – Water Research

Skeleton bones in museum indoor environments offer niches for fungi and are affected by weathering and deposition of secondary minerals – Pinzari – Environmental Microbiology

Bioinformatics

Species abundance information improves sequence taxonomy classification accuracy – Kaehler – Nature Communications

September 17, 2019

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Happy Tuesday! Today’s digest includes wastewater treatment biofilms, the microbiome during Crohn’s disease remission, and the bacteria associated with acid mine drainage. Enjoy!

Human oral microbiome

Succession of oral microbiota community as a tool to estimate postmortem interval – Dong – Scientific Reports

Human gut microbiome

Remission in Crohn’s disease is accompanied by alterations in the gut microbiota and mucins production – Magro – Scientific Reports

Specific gut microbiome members are associated with distinct immune markers in pediatric allogeneic hematopoietic stem cell transplantation – Ingham – Microbiome

Effect of a Chinese medical nutrition therapy diet on gut microbiota and short chain fatty acids in the simulator of the human intestinal microbial ecosystem (SHIME) – Wu – Journal of Functional Foods

A comprehensive assessment of demographic, environmental, and host genetic associations with gut microbiome diversity in healthy individuals – Scepanovic – Microbiome

Animal experiments

Dietary Bovine Milk Exosomes Elicit Changes in Bacterial Communities in C57BL/6 Mice – Zhou – American Journal of Physiology

Microbial Metabolism Modulates Antibiotic Susceptibility within the Murine Gut Microbiome – Cabral – Cell Metabolism

Animal microbiome

Maternal vs artificial rearing shapes the rumen microbiome having minor long‐term physiological implications – Belanche – Environmental Microbiology

Plant, root, and soil microbiome

Impact of continuous Panax notoginseng plantation on soil microbial and biochemical properties – Zhang – Scientific Reports

Three Bermudagrass-suppression techniques have little effect on soil-nutrient availability and microbial communities 200 days after application – Farthing – Applied Soil Ecology

Water and extremophile microbiome

Effect of salinity on mature wastewater treatment biofilm microbial community assembly and metabolite characteristics – Wang – Science of the Total Environment

Diversity and functional profile of bacterial communities at Lancaster acid mine drainage dam, South Africa as revealed by 16S rRNA gene high-throughput sequencing analysis – Lukhele – Extremophiles

Abiotic stress resistance, plant growth promotion and antifungal potential of halotolerant bacteria from a Tunisian solar saltern – Masmoudi – Microbiological Research

Built environment

Effective removal of antibiotic resistance genes and potential links with archaeal communities during vacuum-type composting and positive-pressure composting – Fan – Journal of Environmental Science

Hydraulically Fractured Natural-Gas Well Microbial Communities Contain Genomic Halogenation and Dehalogenation Potential – Evans – Environmental Science & Technology Letters

Successional trophic complexity and biogeographical structure of eukaryotic communities in waterworks rapid sand filters – Harder – FEMS Microbiology Ecology

September 6, 2019

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Today’s rich Digest features a report on how persister pathogens can spread antibiotic resistant plasmids, a study on how diet might alleviate Alzheimer’s, and a screen for the effect of microbiome on diabetes drug efficacy. Other highlights include the evolution and ecology of animal gut microbial communities, microbial communities in soils with radioactive contamination, and free microbiome standards by Zymo Research. Happy reading!

General microbiology

The horizontal gene transfer of Agrobacterium T-DNAs into the series Batatas (Genus Ipomoea) genome is not confined to hexaploid sweetpotato – Dora G. Quispe-Huamanquispe et al. – Scientific Reports

Simulations reveal challenges to artificial community selection and possible strategies for success – Li Xie et al. – PLoS Biology

Primer: Artificially selecting microbial communities: If we can breed dogs, why not microbiomes? – Flor I. Arias-Sánchez et al. – PLoS Biology

Antimicrobial resistance

** Salmonella persisters promote the spread of antibiotic resistance plasmids in the gut – Erik Bakkeren et al. – Nature

Pregnancy and early life

Prenatal antibiotics exposure and the risk of autism spectrum disorders: A population-based cohort study – Amani F. Hamad et al. – PLoS One

Visualization of microbes by 16S in situ hybridization in term and preterm placentas without intraamniotic infection – Maxim D. Seferovic et al. – AJOG

Fetal exposure to the maternal microbiota in humans and mice – Noelle Younge et al. – JCI Insight

Fungi form interkingdom microbial communities in the primordial human gut that develop with gestational age – Kent A. Willis et al. – FASEB J.

Human oral and esophageal microbiome

In vitro: The inhibitory effect of quaternary ammonium salt on bacteria in root canal – Sanjay Kumar Tiwari et al. – Scientific Reports

Alterations to the Esophageal Microbiome Associated with Progression from Barrett’s Esophagus to Esophageal Adenocarcinoma – Erik J. Snider et al. – Cancer Epidemiology, Biomarkers & Prevention

Human respiratory microbiome

Review: The microbiome in bronchiectasis – Hollian Richardson et al. – European Respiratory Review

Human gut microbiome

Gut microbiota alterations associated with reduced bone mineral density in older adults – Mrinmoy Das et al. – Rheumatology

Press: Confounding factors in the effect of gut microbiota on bone density – Rajeev Aurora – Rheumatology

Characterization of Proximal Small Intestinal Microbiota in Patients With Suspected Small Intestinal Bacterial Overgrowth – Andrea S. Shin et al. – Clinical and Translational Gastroenterology

Gut microbiota shifts in patients with gastric cancer in perioperative period – Liang, Weiren et al. – Medicine

Human gut-microbiome-brain axis

** Modified Mediterranean-ketogenic diet modulates gut microbiome and short-chain fatty acids in association with Alzheimer’s disease markers in subjects with mild cognitive impairment – Ravinder Nagpal et al. – EBioMedicine

Press: Diet’s effect on gut bacteria could play role in reducing Alzheimer’s risk – Science Daily

Systemic review and meta-analysis of alcohol induced gut dysbiosis and the resulting behavioral impact – Nayab Qamar et al. – Behavioral Brain Research

Review: The Microbiota-Gut-Brain Axis – John F. Cryan et al. – Physiological Reviews

Human multi-site microbiome

Prosthetic joint infections present diverse and unique microbial communities using combined whole-genome shotgun sequencing and culturing methods – Abigail A. Weaver et al. – Journal of Medical Microbiology

Metabolomics

Metabolic switches from quiescence to growth in synchronized Saccharomyces cerevisiae – Jinrui Zhang et al. – Metabolomics

Animal experiments

Dietary inulin alters the gut microbiome, enhances systemic metabolism and reduces neuroinflammation in an APOE4 mouse model – Jared D. Hoffman et al. – PLoS One

Beneficial roles of probiotics on the modulation of gut microbiota and immune response in pigs – Donghyun Shin et al. – PLoS One

Effects of antibacterial peptides on rumen fermentation function and rumen microorganisms in goats – Zhihua Ren et al. – PLoS One

** Host-Microbe-Drug-Nutrient Screen Identifies Bacterial Effectors of Metformin Therapy – Rosina Pryor et al. – Cell

Press: An Elegan(t) screen shows how the microbiome improves drug efficacy – MRC Research News

Rat: Variation in the gut microbial community is associated with the progression of liver regeneration – Qiongling Bao et al. – Hepatology Research

Animal microbiome

The Pacific harbor seal gut microbiota in Mexico: Its relationship with diet and functional inferences – Arlette Pacheco-Sandoval et al. – PLoS One

Gut microbiota features associated with Clostridioides difficile colonization in puppies – Alexander S. F. Berry et al. – PLoS One

Gut microbiota and their putative metabolic functions in fragmented Bengal tiger population of Nepal – Dibesh Karmacharya et al. – PLoS One

Cadmium and selenate exposure affects the honey bee microbiome and metabolome, and bee-associated bacteria show potential for bioaccumulation – Jason A. Rothman et al. – Applied and Environmental Microbiology

* Review: Evolutionary and Ecological Consequences of Gut Microbial Communities – Nancy A. Moran et al. – Annual Reviews of Ecology, Evolution & Systemactics

Defining the distinct skin and gut microbiomes of the northern pike (Esox lucius) – Elizabeth M. Reinhart et al. – Frontiers in Microbiology

Predicting the unpredictable: How host specific is the mycobiota of bark and ambrosia beetles? – Kirsten E. Miller et al. – Fungal Ecology

Plant, root and soil microbiome

Preprint: The microbiome as a biosensor: functional profiles elucidate hidden stress in hosts – Avihai Zolti et al. – bioRxiv

Soil indigenous microbiome and plant genotypes cooperatively modify soybean rhizosphere microbiome assembly – Fang Liu et al. – BMC Microbiology

* Community structure and functional genes in radionuclide contaminated soils in Chernobyl and Fukushima – Carolina Hoyos-Hernandez et al. – FEMS Microbiology Letters

Microalgae and phototrophic purple bacteria for nutrient recovery from agri-industrial effluents: Influences on plant growth, rhizosphere bacteria and putative carbon and nitrogen cycling genes – Somayeh Zarezadeh et al. – Frontiers in Plant Science

Shifts and recovery of soil microbial communities in a 40-year field trial under mineral fertilization – Jiří Čuhel et al. – Pedobiologia

Water and extremophile microbiome

Identification of soluble microbial products (SMPs) from the fermentation and methanogenic phases of anaerobic digestion – C. Kunacheva et al. – Science of the Total Environment

Review: Microbial mercury methylation in the cryosphere: Progress and prospects – Prakriti Sharma Ghimire et al. – Science of the Total Environment

Rapid Colonization of Uranium Mining-Impacted Waters, the Biodiversity of Successful Lineages of Phytoplankton Extremophiles – Beatriz Baselga-Cervera – Microbial Ecology

Relationship between microbial community and environmental conditions in a constructed wetland system treating greywater – F.S.Bernardes et al. – Ecological Engineering

Built environment microbiome

Microbial Exchange via Fomites and Implications for Human Health – Brent Stephens et al. – Current Pollution Reports

Phages and viruses

Faecal Virome Analysis of Wild Animals from Brazil – Matheus A. Duarte et al. – Viruses

Bioinformatics

Accurate estimation of microbial sequence diversity with Distanced – Timothy J Hackmann – Bioinformatics

Microbes in the news

Researchers reveal how bacteria behind hospital infections block out antibiotics – Dumbarton and Vale of Leven Reporter

Using mouthwash could reduce benefits of exercise – Dumbarton and Vale of Leven Reporter

* A comprehensive catalogue of human digestive tract bacteria – Anne Trafton – MIT News

No poop required: Researchers devise blood test for gut microbiome diversity using data from defunct startup Arivale – James Thorne – Geek Wire

* Zymo Research Distributes Free Microbiome Standards and Controls – PR Newswire

Top List: Trending in microbiome: From comprehensive culture workflows, to novel biotherapeutics, and microbial characterization – Select Science

APC Researcher Awarded Global Grant For Gut Health – APC Microbiome Ireland

* Poop-testing startup uBiome was once valued at $600 million by Silicon Valley’s top VCs. It just filed for bankruptcy – Erin Brodwin & Emma Court – Business Insider

Gut feeling: How a healthy microbiome helps beat stress and lift mood – Scott Anderson – New Scientist

HLA Alleles With Risk for Ankylosing Spondylitis, Rheumatoid Arthritis Affect Gut Microbiome – Hannah Dellabella – Rheumatology Advisor

How the microbiome movement can be beneficial to you overall health – KUSI Newsroom

No microbiome is an island, survey reveals – Elizabeth Pennisi – Science

Microbes on the market

Metagenomic Analysis of the Human Microbiome – Technology Networks

Update note: Added additional pregnancy/neonatal microbiome papers – Sept 15, @kentmd