Category Archives: Events and jobs

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

January 17, 2020

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I 100% concur with Barak about our great Microbiome Digest, and we invite YOU to join us to create useful content for our community. Today’s Digest hopefully brings you much food for thought. I would draw your attention towards two papers about insecticide and antibiotic resistance. The first is about the mechanism for malaria transmitting mosquitoes to tolerate the common pesticide, pyrethroid. The second is on a potential genetic engineering approach to replacing antibiotic resistant plasmids with artificial ones. Of course, there are many more articles and news pieces to read from. Enjoy!

Jobs and Events

MICROBIOME CONNECT SKIN USA 2020 – Global Cosmetics News

Postdoc Computational and Statistical Analysis of Microbiome Data (0.8 – 1.0 FTE) – Universiteit Utrecht

Digest this! New exhibition explores the hidden world of microbes inside — and on — you! – Ottawa Citizen

Call for papers: Cancer Evolution and Metastasis – Genome Biology

General microbiology

Setting the agenda for social science research on the human microbiome – Beth Greenhough et al. – University of Nottingham

Exploring microbial worlds – Lei Tang – Nature Methods

Community-driven Metadata Standards for Agricultural Microbiome Research – JP. Dundore-Arias et al – Phytobiomes Journal

Antimicrobial/Insecticide resistance

Mobile resistome of human gut and pathogen drives anthropogenic bloom of antibiotic resistance – Kihyun Lee et al. – Microbiome

Structures of lipoprotein signal peptidase II from Staphylococcus aureus complexed with antibiotics globomycin and myxovirescin – Samir Olatunji et al. – Nature Communications

** A sensory appendage protein protects malaria vectors from pyrethroids – Victoria A. Ingham et al. – Nature

Press: Malaria-carrying mosquitoes get a leg up on insecticides – Flaminia Catteruccia – Nature

** Potentiation of curing by a broad-host-range self-transmissible vector for displacing resistance plasmids to tackle AMR – Alessandro Lazdins et al. – PLoS One

Promising antifungal activity of new oxadiazole against Candida krusei – Daniella Renata Faria et al. – PLoS One

Impact of multi-drug resistant bacteria on economic and clinical outcomes of healthcare-associated infections in adults: Systematic review and meta-analysis – Miquel Serra-Burriel et al. – PLoS One

Pregnancy and early life

The association between dietary patterns before and in early pregnancy and the risk of gestational diabetes mellitus (GDM): Data from the Malaysian SECOST cohort – Heng Yaw Yong et al. – PLoS One

Nucleic Acid-Based Screening of Maternal Serum to Detect Viruses in Women with Labor or PROM – Ankit A. Shah et al. – Reproductive Sciences

Provision of Lipid-Based Nutrient Supplements to Mothers During Pregnancy and 6 Months Postpartum and to Their Infants from 6 to 18 Months Promotes Infant Gut Microbiota Diversity at 18 Months of Age but Not Microbiota Maturation in a Rural Malawian Setting: Secondary Outcomes of a Randomized Trial – Arox W Kamng’ona et al. – The Journal of Nutrition

Human skin microbiome

Distribution of microbial communities and core microbiome in successive wound grades of diabetic foot ulcer individuals – Apoorva Jnana et al. – Applied and Environmental Microbiology

Review: The skin microbiome as a clinical biomarker in atopic eczema: Promises, navigation, and pitfalls – Matthias Reiger et al. – The Journal of Allergy and Clinical Immunology

Characterization and Analysis of the Skin Microbiota in Acne: Impact of Systemic Antibiotics – Seo-Yeon Park et al. – Journal of Clinical Medicine

Human gut microbiome

Review: Microbial Production of Bioactive Chemicals for Human Health – Xia Wu et al. – Current Opinion in Food Science

Gut microbiota compositional profile and serum metabolic phenotype in patients with primary open-angle glaucoma – Haijun Gong et al. – Experimental Eye Research

Inulin-type fructan intervention restricts the increase in gut microbiome–generated indole in patients with peritoneal dialysis: a randomized crossover study – Li Li et al. – The American Journal of Clinical Nutrition

Human reproductive microbiome

Review: The Reproductive Microbiome: An Emerging Driver of Sexual Selection, Sexual Conflict, Mating Systems, and Reproductive Isolation – Melissah Rowe et al. – Trends in Ecology & Evolution

Press: What we’re learning about the reproductive microbiome – Cell Press – Phys.org

Cancer microbiome

Assessment of peritoneal microbial features and tumor marker levels as potential diagnostic tools for ovarian cancer – Ruizhong Miao – PLoS One

Animal experiments

Acute oral methylmercury exposure perturbs the gut microbiome and alters gut-brain axis related metabolites in rats – Xiaoying Lin et al. – Ecotoxicology & Environmental Safety

Perfluorooctane sulfonate alters gut microbiota-host metabolic homeostasis in mice – Limin Zhang et al. – Toxicology

Fecal transplant prevents gut dysbiosis and anxiety-like behaviour after spinal cord injury in rats – Emma K. A. Schmidt et al. – PLoS One

Impact of antibiotic-resistant bacteria in the mouse intestine on immune activation and Clostridioides difficile infection – James Keith et al. – Infection and Immunity

Animal microbiome

Evolutionary signal in the gut microbiomes of 74 bird species from Equatorial Guinea – Darien C. Capunitan et al. – Molecular Ecology

Whole blood transcriptomic analysis of beef cattle at arrival identifies potential predictive molecules and mechanisms that indicate animals that naturally resist bovine respiratory disease – Matthew A. Scott et al. – PLoS One

Body-site specific microbiota reflect sex and age-class among wild spotted hyenas – Connie A Rojas et al. – FEMS Microbiology Ecology

Plant, root and soil microbiome

Biochar mediates microbial communities and their metabolic characteristics under continuous monoculture – Hongmiao Wu et al. – Chemosphere

Functional Metagenomic Exploration Identifies Novel Prokaryotic Copper Resistance Genes from Soil Microbiome – Chao Xing et al. – Metallomics

** A Pathogen-Responsive Gene Cluster for Highly Modified Fatty Acids in Tomato – Ju Eun Jeon et al. – Cell

Effects of soil physicochemical properties on microbial communities in different ecological niches in coastal area – Tianyun Shao et al. – Applied Soil Ecology

Soil microbial community structure and function mainly respond to indirect effects in a multifactorial climate manipulation experiment – Evi Deltedesco et al. – Soil Biology and Biochemistry

Long term effects of management practice intensification on soil microbial community structure and co-occurrence network in a non-timber plantation – Liang Xue et al. – Forest Ecology and Management

Soil microbial and macrofauna dynamics under different green manure termination methods – Carolyn B. Marshall & Derek H. Lynch – Applied Soil Ecology

Microbial abundance, composition, and function in nectar are shaped by flower visitor identity – Megan M Morris et al. – FEMS Microbiology Ecology

Ecological clusters based on responses of soil microbial phylotypes to precipitation explain ecosystem functions – Ying Wu et al. – Soil Biology and Biochemistry

Phylogenetic Analysis of Symbiotic Bacteria Associated with Two Vigna Species under Different Agro-Ecological Conditions in Venezuela – María Daniela Artigas Ramírez et al. – Microbes and Environments

Diversity and structure of bacterial community in rhizosphere of lima bean – Regina Maria Silva Sousa et al. – Applied Soil Ecology

Distinct factors drive the assembly of quinoa-associated microbiomes along elevation – Zhiquan Cai et al. – Plant and Soil

Influence of plant fraction, soil and plant species on the microbiota: a multi-kingdom comparison – Tkacz, A et al. – mBio

Spatial Variation in Soil Fungal Communities across Paddy Fields in Subtropical China – Pengfa Li et al. – mSystems

Water and extremophile microbiome

Impacts of antimony and arsenic co-contamination on the river sedimentary microbial community in an antimony-contaminated river – Rui Xu et al. – Science of the Total Environment

Interactions of PAH-degradation and nitrate-/sulfate-reducing assemblages in anaerobic sediment microbial community – Xunan Yang et al. – Journal Hazardous Materials

Influence of wastewater microbial community on the performance of miniaturized microbial fuel cell biosensor – Nan Xiao et al. – Bioresource Technology

Intra-host symbiont diversity in eastern Pacific cold seep tubeworms identified by the 16S-V6 region, but undetected by the 16S-V4 region – Corinna Breusing et al. – PLoS One

Phages and viruses

Biogeographic study of human gut-associated crAssphage suggests impacts from industrialization and recent expansion – Tanvi P. Honap et al. – PLoS One

Bioinformatics

Gclust: A Parallel Clustering Tool for Microbial Genomic Data – Ruilin Li et al. – Genomics, Proteomics & Bioinformatics

Microbes in the news

Insomnia: When I took part in a sleep study – Yella Hewings-Martin – Medical News Today

How to Keep Your Baby’s Skin Healthy When It’s Cold Outside – Joane Amay – Ebony

Prebiotics, cosmeceuticals may improve skin condition – Ingrid Torjesen – Dermatology Times

Next frontier is to identify and use good bacteria to treat specific diseases – Namita Kohli – The Week

Five next-gen depression treatments that could revolutionize the field – Alexandra Pattillo – Inverse

Coeliac disease linked to bacteria exposure – Liam Mannix – The Sydney Morning Herald

GETTING TO KNOW YOUR MICROBIOME BETTER – Kim-Anh Lê Cao – Pursuit

Common foods can help ‘landscape’ the jungle of our gut microbiome – San Diego State University – Medical Xpress

Pioneering scientists create designer prebiotics to disrupt the microbiome health space – Nikki Hancocks – NutraIngredients

Applying knowledge of the human microbiome to pig health – The Pig Site

Your microbiome reveals more about your health than your genes do – Michael Le Page – New Scientist

UH joins new national consortium to advance microbiome research – University of Hawaiʻi at Mānoa

Check out these awesomely creepy puppets of microbial creatures – Thom Dunn – BoingBoing

Microbes on the market

Bloom Science Granted Exclusive Option to License Microbiome-Based Technology for the Development of Novel Treatments for Multiple Neurological and Oncology Conditions – Bloom Science – PR Newswire

Mawi and CosmosID Collaborate to Enable More Precise Microbiome Analysis – Business Wire – Yahoo! Finance

December 20, 2019

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This may be our last edition of the Microbiome Digest before the holidays kick in. A rich and dynamic Digest brings you all things microbiome (apologies for the tight formatting). An encouraging report on how we can reduce antimicrobial resistance organically, an amazing recovery of a human genome and an oral microbiome from chewed birch pitch thousands of years ago, and a network analysis reveals four levels of hierarchical trophic interactions in the human gut microbiome. Enjoy Reading and Happy Holidays!
Events
BMC Medicine’s upcoming collection, New Frontiers in Diagnosis, Treatment and Management of Neuromuscular Disorders, is soliciting submissions.
Current Issue of The ISME Journal
The 9th Gut Microbiota for Health World Summit – March 7 and 8 2020 in Madrid, Spain
General microbiology
High-order interactions distort the functional landscape of microbial consortia – Sanchez-Gorostiaga & Bajić et al. – PLoS Biology
Antimicrobial resistance
Human skin microbiome
Human oral microbiome
** A 5700 year-old human genome and oral microbiome from chewed birch pitch – Theis Z. T. Jensen et al. – Nature Communications
Press: Ancient “Chewing Gum” Reveals a 5,700-Year-Old Microbiome – Jim Daley – Scientific American
Human respiratory microbiome
Press: Child asthma flare-ups coincide with microbiome changes – JULIA EVANGELOU STRAIT-WUSTL – Futurity
Human gut microbiome
Human vaginal microbiome
Human gut-microbiota-brain axis
Review: Tryptophan Metabolism: A Link Between the Gut Microbiota and Brain – Kan Gao et al. – Advances in Nutrition
Cancer microbiome
Metabolomics
The total microbiome functions in bacteria and fungi – Robert Starke et al. – Journal of Proteomics
Animal experiments
Animal microbiome
Plant, root and soil microbiome
Root microbiomes as indicators of seagrass health – Belinda C Martin et al. – FEMS Microbiology Ecology
Water and extremophile microbiome
Phages and viruses
Technology
Manipulating rod-shaped bacteria with optical tweezers – Zheng Zhang et al. – Scientific Reports
Bioinformatics
** Evidence for a multi-level trophic organization of the human gut microbiome – Tong Wang et al. – PLoS Computational Biology
Microbes in the news
The microbiome is fundamental to both health and disease – Fabian Brockotter – Poultry World
Low FODMAP Diet Helps IDB Patients – Kenny Walter – MDMAG
Oral Health: Caring for the Other Microbiome – Julia Peterman – Whole Foods Magazine
Non-microbiology pick

 

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 5, 2019

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This weekend, read about how cooking food modifies the microbiome, how bacteria ‘strip off’ to evade antibiotics, and more. Check out an interesting pilot study looking at potential inclusion and exclusion criteria of donors for safe vaginal microbiota transplant. Enjoy!

Events

Bioinformatics for the Microbiome Symposium 2019, Stanford University, Monday October 28.
Some tickets are still available!

General microbiome

Mobile phones as fomites for potential pathogens in hospitals: microbiome analysis reveals hidden contaminants – Rebecca Simmonds – Journal of Hospital Infection

Review: Microbiomes as sources of emergent host phenotypes – J. B. Lynch and E. Y. Hsiao – Science

Vaginal microbiome

*Conceptual Design of a Universal Donor Screening Approach for Vaginal Microbiota Transplant – Kevin DeLong – Frontiers in Cellular and Infection Microbiology

Highly diverse anaerobe-predominant vaginal microbiota among HIV-infected pregnant women in Zambia – Joan T. Price – PlosOne

Urinary microbiome

*Possible role of L-form switching in recurrent urinary tract infection – Katarzyna M. Mickiewicz – Nature Communications

Aerococcus urinae and Globicatella sanguinis Persist in Polymicrobial Urethral Catheter Biofilms Examined in Longitudinal Profiles at the Proteomic Level – Yanbao Yu – Biochemistry Insights

Gut microbiome

*Cooking shapes the structure and function of the gut microbiome – Rachel N. Carmody – Nature Microbiology

Integrated paired-end enhancer profiling and whole-genome sequencing reveals recurrent CCNE1 and IGF2 enhancer hijacking in primary gastric adenocarcinoma – Wen Fong Ooi – Gut

Effects of Low-FODMAP Diet on Symptoms, Fecal Microbiome, and Markers of Inflammation in Patients With Quiescent Inflammatory Bowel Disease in a Randomized Trial – Selina R.Cox – Gastroenterology

Water microbiome

Trophic networks improve the performance of microbial anodes treating wastewater – Christin Koch – npj Biofilms and Microbiomes

Application of a novel molecular technique to characterise the effect of settling on microbial community composition of activated sludge – Luong N.Nguyen – Journal of Environmental Management

Bacterial diversity in Icelandic cold spring sources and in relation to the groundwater amphipod Crangonyx islandicus – Ragnhildur Guðmundsdóttir – PlosOne

Animal microbiome

Looking like the locals – gut microbiome changes post-release in an endangered species – Rowena Chong – Animal microbiome

Animal experiment

Letrozole treatment of pubertal female mice results in activational effects on reproduction, metabolism and the gut microbiome – Pablo Arroyo – PlosOne

Microbiota of MR1 deficient mice confer resistance against Clostridium difficile infection – Ashley D. Smith – PlosOne

Exploring the microbiota of upper respiratory tract during the development of pneumonia in a mouse model – Yoshitomo Morinaga – PlosOne

Plant microbiome

Microbiome profiling of the onion thrips, Thrips tabaci Lindeman (Thysanoptera: Thripidae) – Suresh J. Gawande – PlosOne

Food

Comparison of the microbial composition of African fermented foods using amplicon sequencing – Maria Diaz – Scientific Reports

The impact of grape processing and carbonic maceration on the microbiota of early stages of winemaking – Raffaele Guzzon – Journal of Applied Microbiology

Fungi

Phyllosphere Fungal Communities of Plum and Antifungal Activity of Indigenous Phenazine-Producing Pseudomonas synxantha Against Monilinia laxa – Tamara Janakiev – Frontiers in Microbiology

Microbial communities associated with the black morel Morchella sextelata cultivated in greenhouses – Gian Maria Niccolò Benucci – PeerJ

Viruses

The gut virome in inflammatory bowel disease pathogenesis: From metagenomics to novel therapeutic approaches – Federica Ungaro – United European Gastroenterology Journal

Association of the Eukaryotic Vaginal Virome with Prophylactic Antibiotic Exposure and Reproductive Outcomes in a Subfertile Population Undergoing In Vitro Fertilization: A Prospective Exploratory Study – Ashley M. Eskew – Obstetrics and Gynaecology

Bioinformatics

ProphET, prophage estimation tool: A stand-alone prophage sequence prediction tool with self-updating reference database – João L. Reis-Cunha – PlosOne

September 11, 2019

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Today’s Digest features a study on how antibiotic use in preterm infants might cause long-term impacts, a report on the effect of antibiotics on vaccine response, and a special issue on microbiome biology. Happy reading!

Course

Nutrition and Health: Human Microbiome – a MOOC by Clara Belzer – Gut Microbiota For Health

General microbiome

** Special Issue: Microbiome Biology – Genome Biology & BMC Biology

Editorial: Expanding the scope and scale of microbiome research – Rob Knight et al. – Genome Biology

Review: Challenges in the construction of knowledge bases for human microbiome-disease associations – Varsha Dave Badal et al. – Microbiome

Review: The Microbiome and Aging – Bianca Bana & Filipe Cabreiro – Annual Review of Genetics

Pregnancy and early life

** Persistent metagenomic signatures of early-life hospitalization and antibiotic treatment in the infant gut microbiota and resistome – Andrew J. Gasparrini et al. – Nature Microbiology

Press: Prolonged antibiotic treatment may alter preterm infants’ microbiome – National Institutes of Health

Review: Maternal Microbiome and Metabolic Health Program Microbiome Development and Health of the Offspring – Marta Calatayud et al. – Trends in Endocrinology & Metabolism

Human respiratory microbiome

In vitro: In vitro evolution of Pseudomonas aeruginosa AA2 biofilms in the presence of cystic fibrosis lung microbiome members – Eva Vandeplassche et al. – Scientific Reports

Human gut microbiome

** Antibiotics-Driven Gut Microbiome Perturbation Alters Immunity to Vaccines in Humans – Thomas Hagan et al. – Cell

Press: Microbiome loss from antibiotic use affects response to flu vaccine – Angela Betsaida B. Laguipo – News Medical

Predictors of Obesity among Gut Microbiota Biomarkers in African American Men with and without Diabetes – Elena Barengolts et al. – Microorganisms

Protocol: Prospective multicentre cohort trial on acute appendicitis and microbiota, aetiology and effects of antimicrobial treatment: study protocol for the MAPPAC (Microbiology APPendicitis ACuta) trial – Sanja Vanhatalo et al. – BMJ Open

Effects of anti-H. pylori triple therapy and a probiotic complex on intestinal microbiota in duodenal ulcer – Lili Wu et al. – Scientific Reports

Cancer microbiome

Review: The Microbiome and Prostate Cancer Risk – Karen M. Wheeler & Michael A. Liss – Current Urology Reports

Press: The Microbiome and Prostate Cancer Risk – Uro Today

Profiling of lung microbiota discloses differences in adenocarcinoma and squamous cell carcinoma – Sílvia Gomes et al. – Scientific Reports

Animal experiments

Triclosan-selected host-associated microbiota perform xenobiotic biotransformations in larval zebrafish – Chelsea A Weitekamp et al. – Toxicological Sciences

Effects of theabrownin on serum metabolite and gut microbiome in rats with high-sugar diet – Suijuan Yue et al. – Food & Function

Animal microbiome

Effects of long-term starvation on health indices, gut microbiota and innate immune response of fresh water crayfish, marron (Cherax cainii, Austin 2002) – Md Javed Foysal et al. – Aquaculture

Plant, root and soil microbiome

Effects of road salt on microbial communities: Halophiles as biomarkers of road salt pollution – Wolf T. Pecher et al. – PLoS One

Conservation of the endophyte microbiome structure across two Panicum grass species – Esther Singer et al. – Frontiers in Microbiology

Characterization of Microbial Communities, Identification of Cr(VI) Reducing Bacteria in Constructed Wetland and Cr(VI) Removal Ability of Bacillus cereus – Hua Lin et al. – Scientific Reports

Review: The plant microbiome: A missing link for the understanding of community dynamics and multifunctionality in forest ecosystems – Sandhya Mishra e al. – Applied Soil Ecology

Combining irrigation scheme and phosphorous application levels for grain yield and their impacts on rhizosphere microbial communities of two rice varieties in a field trial – Yingjiao Zhang et al. – Journal of Agricultural and Food Chemistry

Soil-plant compartments affect fungal microbiome diversity and composition in grapevine – María del PilarMartínez-Diz et al. – Fungal Ecology

Water and extremophile microbiome

The fungicide azoxystrobin promotes freshwater cyanobacterial dominance through altering competition – Tao Lu et al. – Microbiome

Diel oscillation of microbial gene transcription declines with increasing depth in oligotrophic ocean waters – Alice Vislova et al. – Frontiers in Microbiology

Long term performance and dynamics of microbial biofilm communities performing sulfur-oxidizing autotrophic denitrification in a moving-bed biofilm reactor – Yan-Xiang Cui et al. – Water Research

Opportunistic pathogens and large microbial diversity detected in source-to-distribution drinking water of three remote communities in Northern Australia – Mirjam Kaestli et al. – PLoS Neglected Tropical Diseases

The diversity and biogeography of microeukaryotes in the euphotic zone of the northwestern Pacific Ocean – Peng-Fei Wu et al. – Science of the Total Environment

Comparative evaluation of three archaeal primer pairs for exploring archaeal communities in deep-sea sediments and permafrost soils – Shiping Wei et al. – Extremophiles

Characterizations of microbial diversity and machine oil degrading microbes in machine oil contaminated soil – Mengjiao Wang et al. – Environmental Pollution

Metaproteomics reveal that rapid perturbations in organic matter prioritize functional restructuring over taxonomy in western Arctic Ocean microbiomes – Molly P. Mikan et al. – The ISME Journal

Microbes in space

Space Station conditions are selective but do not alter microbial characteristics relevant to human health – Maximilian Mora et al. – Nature Communications

Phages and viruses

Preprint: European and tropical Aedes albopictus mosquito populations have similar systemic Zika virus infection dynamics – Sebastian Lequime et al. – bioRxiv

Technology

Preprint: A novel and direct mobilome approach improves the detection of larger-sized circular elements across kingdoms – Katrine Skov Alanin et al. – bioRxiv

Power production and microbial community composition in thermophilic acetate-fed up-flow and flow-through microbial fuel cells – Paolo Dessì et al. – Bioresource Technology

Microbial Interaction Network Inference in Microfluidic Droplets – Ryan H. Hsu et al. – Cell Systems

Revealing the metabolic capacity of Streblomastix strix and its bacterial symbionts using single-cell metagenomics – Sebastian C. Treitli et al. – PNAS

Bioinformatics

Fast and accurate average genome size and 16S rRNA gene average copy number computation in metagenomic data – Emiliano Pereira-Flores et al. – BMC Bioinformatics

Microbes in the news

The diet-microbiome connection in inflammatory bowel disease – University of Pennsylvania – EurekAlert!

How Bacteria Rule Over Your Body – The Microbiome – YouTube

Will Drinking Red Wine Give You A Healthier Microbiome? – Angela Dowden – American Council on Science and Health

What Role Does Bariatric Surgery Play in Altering the Gut Microbiome? – Suzanne Bujara – Endocrinology Advisor

Microbes on the market

Poised for growth: how to scale a microbiome engineering company – Embriette Hyde – SynbioBeta

August 22, 2019

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Today’s Digest includes several papers on antimicrobial resistance, which is what we should be thinking about all the time. Other highlights include nanoparticle delivered medicine for colitis, and how ants compartmentalize microbiomes. Enjoy reading!

Event

Call for papers: Microbiome in human physiological function – Microbial Cell Factories

General microbiology

Species matter for predicting the functioning of evolving microbial communities – An eco-evolutionary model – Timothy G. Barraclough – PLoS One

Antimicrobial resistance

The impact and mechanism of quaternary ammonium compounds on the transmission of antibiotic resistance genes – Yue Han et al. – Environmental Science and Pollution Research

Characterizing the soil microbiome and quantifying antibiotic resistance gene dynamics in agricultural soil following swine CAFO manure application – Edward Lopatto et al. – PLoS One

Antibiotic resistant bacteria and commensal fungi are common and conserved in the mosquito microbiome – Josephine Hyde et al. – PLoS One

Advanced neonatal medicine in China: Is newborn ward capacity associated with inpatient antibiotic usage? – Yi Ge et al. – PLoS One

Preprint: Resident microbial communities inhibit growth and antibiotic resistance evolution of Escherichia coli in human gut microbiome samples – Michael Baumgartner et al. – bioRxiv

Human gut microbiome

** Hyaluronic acid–bilirubin nanomedicine for targeted modulation of dysregulated intestinal barrier, microbiome and immune responses in colitis – Yonghyun Lee et al. – Nature Materials

Press: Nanoparticle relieved symptoms of inflammatory bowel disease in mice – Phys.org

Genetic risk for autoimmunity is associated with distinct changes in the human gut microbiome – Jordan T. Russell et al. – Nature Communications

Preprint: In vitro modeling: Evidence for a multi-level trophic organization of the human gut microbiome – Tong Wang et al. – bioRxiv

Animal microbiome

Relationships between feeding and microbial faeces indices in dairy cows at different milk yield levels – Stephanie Meyer et al. – PLoS One

** Azteca ants maintain unique microbiomes across functionally distinct nest chambers – Jane M. Lucas et al. – Proceedings of the Royal Society B

Press: For at Least One Species, Ant Nurseries Are Cleaner Than Human Ones – Matt Shipman – NC State University

Unveiled feather microcosm: feather microbiota of passerine birds is closely associated with host species identity and bacteriocin-producing bacteria – Veronika Gvoždíková Javůrková et al. – The ISME Journal

Variability in snake skin microbial assemblages across spatial scales and disease states – Donald M. Walker et al. – The ISME Journal

Food microbiome

Faecalibacterium diversity in dairy cow milk – Keith W. Savin et al. – PLoS One

Plant, root and soil microbiome

Microbial succession on decomposing root litter in a drought-prone Scots pine forest – Claude Herzog et al. – The ISME Journal

Water and extremophile microbiome

Active subseafloor microbial communities from Mariana back-arc venting fluids share metabolic strategies across different thermal niches and taxa – Elizabeth Trembath-Reichert, David A. Butterfield & Julie A. Huber – The ISME Journal

Phages and viruses

Cryptic inoviruses revealed as pervasive in bacteria and archaea across Earth’s biomes – Simon Roux et al. – Nature Microbiology

Sources of Airborne Norovirus in Hospital Outbreaks – Malin Alsved et al. – Clinical Infectious Diseases

Viral taxonomy derived from evolutionary genome relationships – Tyler J. Dougan & Stephen R. Quake – PLoS One

Microbes in the news

Type 1 diabetes: Genetic risk reflected in gut microbiome – Ana Sandoiu – Medical News Today

10 Things Viome’s Gut Test Can Reveal About Your Gut Microbiome – Yahoo! Finance

Stanford Team Uses Imputation Approach to Uncover Thousands of New Microbiome Proteins – Neil Versel – Genome Web

Broccoli Is Dying. Corn Is Toxic. Long Live Microbiomes! – Louise Elizabeth Maher-Johnson & Ayana Elizabeth Johnson – Scientific American

A mother’s microbes may be a signifier of her child’s future health, researchers say – Michael Eisenstein – Medical Xpress

Pharmacomicrobiomic Study Shows Significant Gut Bacteria Role in Drug Metabolism and Exposure – Kristiana A. Avad & Kirk E. Hevener – Contagion Live

3 Reasons Eliminating Grains May Be Harmful For Gut Health – Jason Wachob – Mind Body Green

Levofloxacin Prophylaxis Least Disruptive to Gut Microbiome in Patients With Hematologic Malignancy – Sweta Gupta – Infectious Disease Advisor

August 8, 2019

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Today’s Digest brings you plenty of articles and news pieces, and highlights include mouse experiments with humanized microbiota, with “wilding” microbiota, and a collection of rumen metagenomes. Enjoy reading!

Event

The Expert Is In: Magnetic bacteria pumping iron! – National Museum of Natural History – August 9, 11am-1pm EDT

Antimicrobial resistance

Random peptide mixtures entrapped within a copper-cuprite matrix: new antimicrobial agent against methicillin-resistant Staphylococcus aureus – Tal Stern Bauer et al. – Scientific Reports

ABC Transporter Genes Show Upregulated Expression in Drug-Resistant Clinical Isolates of Candida auris: A Genome-Wide Characterization of ATP-Binding Cassette (ABC) Transporter Genes – Mohd Wasi, Nitesh Kumar Khandelwal & Alexander J. Moorhouse et al. – Frontiers in Microbiology

Preprint: Global Genetic Cartography of Urban Metagenomes and Anti-Microbial Resistance – David C. Danko et al. – bioRxiv

Antimicrobial use in an Indonesian community cohort 0-18 months of age – Jarir At Thobari et al. – PLoS One

Erythromycin-resistant lactic acid bacteria in the healthy gut of vegans, ovo-lacto vegetarians and omnivores – Vesna Milanović et al. – PLoS One

Pregnancy and early life

Predictive value of cervical cytokine, antimicrobial and microflora levels for pre-term birth in high-risk women – Rashmi Manning et al. – Scientific Reports

Human multi-site microbiome

A new issue of the Gastroenterology Clinics of North America

Human oral microbiome

Review: Oral microbial biofilms: an update – Seyed Ali Mosaddad et al. – European Journal of Clinical Microbiology & Infectious Diseases

Amplicon-based microbiome study highlights the loss of diversity and the establishment of a set of species in patients with dentin caries – Diana Wolff et al. – PLoS One

Microbiome in maintained periodontitis and its shift over a single maintenance interval of three months – Hongye Lu et al. – Journal of Clinical Periodontology

Human gut microbiome

Review: Role of microbes, metabolites and effector compounds in host–microbiota interaction: a pharmacological outlook – Bharat Bhushan et al. – Environmental Chemistry Letters

Age-Associated Changes in Gut Microbiota and Dietary Components Related with the Immune System in Adulthood and Old Age: A Cross-Sectional Study – Nuria Salazar et al. – Nutrients

Review: Establishing What Constitutes a Healthy Human Gut Microbiome: State of the Science, Regulatory Considerations, and Future Directions – Michael I McBurney et al. – The Journal of Nutrition

Review: Gut Dysbiosis and the Intestinal Microbiome: Streptococcus thermophilus a Key Probiotic for Reducing Uremia – Luis Vitetta et al. – Microorganisms

Animal experiments

** Baseline microbiota composition modulates antibiotic-mediated effects on the gut microbiota and host – Aonghus Lavelle et al. – Microbiome

Microbiota of newborn calves and their mothers reveals possible transfer routes for newborn calves’ gastrointestinal microbiota – Daniela Klein-Jöbstl et al. – PLos One

Isoorientin attenuates benzo[a]pyrene-induced colonic injury and gut microbiota disorders in mice – Shenyuan He et al. – Food Research International

** Laboratory mice born to wild mice have natural microbiota and model human immune responses – Stephan P. Rosshart et al. – Science

Antibiotic-Induced Perturbations Are Manifested in the Dominant Intestinal Bacterial Phyla of Atlantic Salmon – Shruti Gupta et al. – Microorganisms

Whole Body Vibration-Induced Omental Macrophage Polarization and Fecal Microbiome Modification in a Murine Model – Jack C. Yu et al. – International Journal of Molecular Sciences

Press: Whole body vibration shakes up microbiome, reduces inflammation in diabetes – EurekAlert

Press: Whole body vibration helps reduce inflammation, thanks to the gut microbiome – Angela Betsaida B. Laguipo – News-Medical

Animal microbiome

Sex-specific linkages between taxonomic and functional profiles of tick gut microbiomes – Dasiel Obregón et al. – Frontiers in Cellular and Infection Microbiology

** Compendium of 4,941 rumen metagenome-assembled genomes for rumen microbiome biology and enzyme discovery – Robert D. Stewart et al. – Nature Biotechnology

Humoral immune responses against gut bacteria in dogs with inflammatory bowel disease – Sirikul Soontararak et al. – PLoS One

Plant, root and soil microbiome

Solarization-based pesticide degradation results in decreased activity and biomass of the soil microbial community – M.Díaz-López et al. – Geoderma

Soil microbial carbon metabolism reveals a disease suppression pattern in continuous ginger mono-cropping fields – Xiaojiao Liu et al. – Applied Soil Ecology

Influence of 2,4-D residues on the soil microbial community and growth of tree species – Luciana Monteiro Aguiar et al. – International Journal of Phytoremediation

A Microbiome Study Reveals Seasonal Variation in Endophytic Bacteria Among different Mulberry Cultivars – Ting Ou et al. – Computational and Structural Biotechnology Journal

Biological Soil Crusts from Different Soil Substrates Harbor Distinct Bacterial Groups with the Potential to Produce Exopolysaccharides and Lipopolysaccharides – Barbara Cania et al. – Microbial Ecology

Water and extremophile microbiome

A snapshot of microbial community structures in 20 different field-scale anaerobic bioreactors treating food waste – Seung Gu Shin et al. – Journal of Environmental Management

Microbial uptake kinetics of dissolved organic carbon (DOC) compound groups from river water and sediments – Francesca L. Brailsford et al. – Scientific Reports

Biological removal of selenate in saline wastewater by activated sludge under alternating anoxic/oxic conditions – Yuanyuan Zhang et al. – Frontiers of Environmental Science & Engineering

Built environment microbiome

Environmental factors influencing fungal growth on gypsum boards and their structural biodeterioration: A university campus case study – Negin Kazemian et al. – PLoS One

Phages and viruses

Identification of diverse bat alphacoronaviruses and betacoronaviruses in China provides new insights into the evolution and origin of coronavirus-related diseases – Yelin Han et al. – Frontiers in Microbiology

The respiratory microbiota: Associations with influenza symptomatology and viral shedding – Kyu Han Lee et al. – Annals of Epidemiology

Technology

Review: Simultaneous improving nitrogen removal and decreasing greenhouse gas emission with biofilm carriers addition in ecological floating bed – Shanshan Sun et al. – Bioresource Technology

Comparative evaluation of a novel recombinase polymerase amplification-lateral flow dipstick (RPA-LFD) assay, LAMP, conventional PCR, and leaf-disc baiting methods for detection of Phytophthora sojae – Tingting Dai et al. – Frontiers in Microbiology

Review: Emerging molecular techniques for studying microbial community composition and function in microbiologically influenced corrosion – Susmitha Purnima Kotu et al. – International Biodeterioration & Biodegradation

Microbes in the news

Phase Genomics’ Platform Links Viruses and Antibiotic Resistance Genes to the Microbiome in Study of a Highly Complex Microbial Community – Phase Genomics – Globe Newswire

Mouse Genetics Shape the Gut Microbiome More than Their Environment – Nicoletta Lanese – The Scientist

JMM EDITOR’S CHOICE: HOW DOES SMOKING AFFECT THE ORAL MICROBIOME? – Microbiology Society

NEWSProbiotics brand Life Space celebrates the wonder of the human microbiome – Zoe Wilkinson – Mumbrella

Caveats and clinical implications in the connection between the duodenal microbiome, diet and functional gastrointestinal symptoms – Gut Microbiota for Health

The many modes of microbial magic – Giuliana Viglione – Chemical & Engineering News

The secret lives of microbes – ANNEMIEKE VAN ROEKEL – Euro Scientist

IIT develops state-of-art device to detect bacteria – The Pioneer

The Germiest Places in Your Child’s School – Alex Watt – Red Book

Teresa van Dongen’s Mud Well light uses microorganisms to create electricity – Rima Sabina Aouf – De Zeen

Microbes on the market

Shoreline Biome Announces International Distribution Partnerships – Yahoo Finance

What are the prospects for microbiome skin care in Asia? – Simon Pitman – Cosmetics Design – Europe

Biotech startup joins quest to harness microbiome to untether reliance on antibiotics in women’s health – Natalie Grover – Endpoints News

PanTheryx funding will help intensify growth in animal microbiome-focused products – Joseph Harvey – Informa

July 24, 2019

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Welcome back! Today’s all-around Digest features an animal study identifying a single bacterium as therapy against rheumatoid arthritis, a field trial with bacteria colonizing and sterile Asian tiger mosquitoes to combat vector borne diseases, and a non-microbiology pick about the balance between longevity and immunity. Enjoy!

Event

Microbiome Movement – Oncology Response Summit – Boston

General microbiology

Motile curved bacteria are Pareto-optimal – Rudi Schuech et al. – PNAS

Press: ‘Curvy bacteria’ weigh the benefits of different shapes – Science Daily

Antimicrobial resistance

The burden of antimicrobial resistance at tertiary care hospital, southern Ethiopia: a three years’ retrospective study – Tsegaye Alemayehu et al. – BMC Infectious Diseases

Human oral microbiome

Review: Regulation of oral immune tolerance by the microbiome in food allergy – Emmanuel Stephen-Victor & Talal A Chatila – Current Opinion in Immunology

Human respiratory microbiome

Editorial: Changes in lung microbiome do not explain the development of ventilator-associated pneumonia – Lieuwe D. J. Bos & Andre C. Kalil – Intensive Care Medicine

Human gut microbiome

In vitro: Microbial communities in a dynamic in vitro model for the human ileum resemble the human ileal microbiota – Maria Stolaki et al. – FEMS Microbiology Ecology

Fecal Microbiota Transplantation in Pouchitis: Clinical, Endoscopic, Histologic, and Microbiota Results from a Pilot Study – Daniel Selvig et al. – Digestive Diseases and Sciences

Dysbiosis of the gut microbiome is associated with CKD5 and correlated with clinical indices of the disease: a case–controlled study – Yang Li et al. – Journal of Translational Medicine

Animal experiments

Supplementation of diet with non-digestible oligosaccharides alters the intestinal microbiota, but not arthritis development, in IL-1 receptor antagonist deficient mice – Rebecca Rogier et al. – PLoS One

Microbial metabolite deoxycholic acid shapes microbiota against Campylobacter jejuni chicken colonization – Bilal Alrubaye et al. – PLoS One

Lamb: A novel animal model for regional microbial dysbiosis of the pioneer microbial community – Nilusha Malmuthuge and Philip J. Griebel – Frontiers in Microbiology

** A single bacterium restores the microbiome dysbiosis to protect bones from destruction in a rat model of rheumatoid arthritis – Hudan Pan, Ruijin Guo, Yanmei Ju, Qi Wang et al. – Microbiome

Polybrominated Diphenyl Ethers and Gut Microbiome Modulate Metabolic Syndrome–Related Aqueous Metabolites in Mice – David K. Scoville et al. – Drug Metabolism and Disposition

Animal microbiome

** Incompatible and sterile insect techniques combined eliminate mosquitoes – Xiaoying Zheng et al. – Nature

Commentary: Tiger mosquitoes tackled in a trial – Peter Armbruster – Nature

Host genetics and geography influence microbiome composition in the sponge Ircinia campana – Sarah M. Griffiths et al. – Journal of Animal Ecology

Plant, root and soil microbiome

Non-target Effects of Naphthalene on the Soil Microbial Biomass and Bacterial Communities in the Subalpine Forests of Western China – Liying Lan et al. – Scientific Reports

Drought modulates interactions between arbuscular mycorrhizal fungal diversity and barley genotype diversity – Agnieszka Sendek et al. – Scientific Reports

Variation in rhizosphere microbiota correlates with edaphic factor in an abandoned antimony tailing dump – Enzong Xiao et al. – Environmental Pollution

Structural changes of soil organic matter and the linkage to rhizosphere bacterial communities with biochar amendment in manure fertilized soils – Ruilin Huang & Zhenyi Zhang et al. – Science of the Total Environment

Review: The Postharvest Microbiome: The Other Half of Sustainability – Michael Wisniewski & Samir Droby – Biological Control

Water and extremophile microbiome

Oil degradation potential of microbial communities in water and sediment of Baltic Sea coastal area – Hanna Miettinen et al. – PLoS One

Linking dissolved organic matter composition and bacterioplankton communities in an Amazon floodplain system – Michaela L. de Melo et al. – Limnology and Oceanography

Pollution shapes the bacterial community of a river: a case study – N. Yadav & S. Sharma – International Journal of Environmental Science and Technology

A pollution gradient contributes to the taxonomic, functional, and resistome diversity of microbial communities in marine sediments – Jiarui Chen & Shelby E. McIlroy et al. – Microbiome

Phages and viruses

Review: Human Virome and Disease: High-Throughput Sequencing for Virus Discovery, Identification of Phage-Bacteria Dysbiosis and Development of Therapeutic Approaches with Emphasis on the Human Gut – Tasha M. Santiago-Rodriguez & Emily B. Hollister – Viruses

Technology

Targeting 16S rDNA for Stable Recombinant Gene Expression in Pseudomonas – Maike Otto et al. – ACS Synthetic Biology

Microbes in the news

Gut microbes may help malnourished children – Elizabeth Pennisi – Science

The microbiota–gut–brain axis – Natasha Bray – Nature

Nam June Paik Art Center looks at ecosystems, up close – Shim Woo-hyun – The Korea Herald

DuPont Opens State-of-the-Art Probiotics Fermentation Unit – WholeFoods Magazine

The Art Of Solving Antibiotic Overuse in America – ArtIHolics

MICROBIOME RESEARCH IS MORE THAN CHASING GUT FEELINGS – Chad Campbell – Purdue University

NIH grant to fund research on microbiome’s role in cancer – Healio

PET TALK: Balanced GI tract plays large role in dog’s overall well-being – Texas A&M University College of Veterinary Medicine & Biomedical Sciences

Mathematics helps us understand the complexity of our microbiome – Tim Sandle – Digital Journal

Good bacteria, bad products – Gali Weinreb – Globes

Gut Microbiome May Alter ALS Progression in Mice – Julianna LeMieux – GenEngNews

Xin’s non-microbiology pick

** The longevity-promoting factor, TCER-1, widely represses stress resistance and innate immunity – Francis R. G. Amrit et al. – Nature Communications