April 7, 2020

Hi everyone! This is my first contribution to the daily digest, and I’ll follow others’ lead by starting with the latest preprints concerning Covid-19. Away from the ongoing pandemic, some of the highlights include a look at how commensal gut microbes interact with pathogens, and an insight into deep sea oceanic crust microbiomes.

It seems to be a relatively quiet day today, so I’ve included an article from the University of Bristol which looks at how nanoscopic pillars on the surface of some insect wings protect them against bacteria. Perhaps only loosely a microbiome paper, but it’s worth a read for its electron microscopy alone!

COVID-19

Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor – Lan et al. – Nature

Preprint: Atazanavir inhibits SARS-CoV-2 replication and pro-inflammatory cytokine production – Fintelman-Rodrigues et al.

Preprint: Amantadine disrupts lysosomal gene expression; potential therapy for COVID19 – Smieszek et al.

Preprint: Potent Antiviral Activities of Type I Interferons to SARS-CoV-2 Infection – Mantlo et al.

Human gut microbiome

Dissecting individual pathogen-commensal interactions within a complex gut microbiota community – Hassall and Unnikrishnan

Animal microbiome

Antibacterial effects of nanopillar surfaces are mediated by cell impedance, penetration and induction of oxidative stress – Jenkins et al. – Nature Communications

Water and extremophile microbiome

Deep microbial proliferation at the basalt interface in 33.5–104 million-year-old oceanic crust – Suzuki et al.Communications Biology

Food microbiology

How does the microbiome impact pig health? – Sarah Mikesell – The Pig Site

Microbes in the news

Lifestyle trumps geography in determining makeup of gut microbiomeEurekAlert!

Microbes on the market

Gilead taps Second Genome for microbiome biomarker help in a potential $1.5B deal – Connor Hale – FierceBiotech.com

March 24, 2020

Today’s Digest features a study to use engineered Acinetobacter to boost host immunity against bacterial pneumonia, and a review on the relationship between plant-microbe symbiosis and agriculture.The coronavirus is probably on the mind of all of us. Listen to Dr. Blaser talk about it. Stay well and keep reading.

Job

Research Tech II – CHOP Microbiome Center

COVID-19

Editorial: Coronavirus: three things all governments and their science advisers must do now – Nature

World View: Don’t rush to deploy COVID-19 vaccines and drugs without sufficient safety guarantees – Shibo Jiang – Nature

Q&A: The novel coronavirus outbreak causing COVID-19 – Dale Fisher & David Heymann – BMC Medicine

** Dr. Martin Blaser answers coronavirus questions from Twitter (full video available) – mlive.com

General microbiology

Regulation of fungal decomposition at single-cell level – Michiel Op De Beeck et al. – The ISME Journal

Antimicrobial resistance

** Broad-spectrum suppression of bacterial pneumonia by aminoglycoside-propagated Acinetobacter baumannii – M. Indriati Hood-Pishchany et al. – PLoS Pathogens

Vulnerability and resistance in the spatial heterogeneity of soil microbial communities under resource additions – Kelly Gravuer et al. – PNAS

Discovery of a novel integron-borne aminoglycoside resistance gene present in clinical pathogens by screening environmental bacterial communities – Maria-Elisabeth Böhm et al. – Microbiome

Characterization of antibiotic resistance and host-microbiome interactions in the human upper respiratory tract during influenza infection – Lingdi Zhang et al. – Microbiome

Human gut microbiome

The role of gut microbiota in bone homeostasis – Jyotirmaya Behera et al. – Bone

Animal experiments

Docosahexaenoate-enriched fish oil and medium chain triglycerides shape the feline plasma lipidome and synergistically decrease circulating gut microbiome-derived putrefactive postbiotics – Matthew I. Jackson & Dennis E. Jewell – PLoS One

Animal microbiome

The rodent vaginal microbiome across the estrous cycle and the effect of genital nerve electrical stimulation – Micah Levy et al. – PLoS One

The different dietary sugars modulate the composition of the gut microbiota in honeybee during overwintering – Hongfang Wang et al. – BMC Microbiology

Most dominant roles of insect gut bacteria: digestion, detoxification, or essential nutrient provision? – Tian-Zhong Jing et al. – Microbiome

Predictive ability of host genetics and rumen microbiome for subclinical ketosis – Grum Gebreyesus et al. – Journal of Dairy Science

Plant, root and soil microbiome

** Review: Agriculture and the Disruption of Plant–Microbial Symbiosis – Stephanie S. Porter & Joel L. Sachs – Trends in Ecology & Evolution

Taxon-specific microbial growth and mortality patterns reveal distinct temporal population responses to rewetting in a California grassland soil – Steven J. Blazewicz et al. – The ISME Journal

Reusing oil and gas produced water for agricultural irrigation: Effects on soil health and the soil microbiome – Hannah Miller et al. – Science of the Total Environment

Network analysis reveals the strengthening of microbial interaction in biological soil crust development in the Mu Us Sandy Land, northwestern China – Hong Zhou et al. – Soil Biology and Biochemistry

Water and extremophile microbiome

Performance and functional microbial communities of denitrification process of a novel MFC-granular sludge coupling system – Qiujin Deng et al. – Bioresource Technology

Microbial community structure and functional properties in permanently and seasonally flooded areas in Poyang Lake – Yang Liu et al. – Scientific Reports

Associations between redox-sensitive trace metals and microbial communities in a Proterozoic ocean analogue – Kathryn I. Rico et al. – Geobiology

Reactor configuration influences microbial community structure during high-rate, low-temperature anaerobic treatment of dairy wastewater – Paul G McAteer et al. – Bioresource Technology

Bioinformatics

Multiple-Disease Detection and Classification across Cohorts via Microbiome Search – Xiaoquan Su et al. – mSystems

Microbes in the news

How the mi­cro­biome is in­volved in the de­vel­op­ment of can­cer – Christian Urban – MedicalXpress

How a Fiber-Rich Plant-Based Diet Keeps Your Gut Microbiome Happy and Healthy – Chelsea Debret – One Green Planet

Gerhart: Keeping well during a pandemic – Timothy Gerhart – Your Valley

Study shows positive effect of cover crops on soil microbiome – AgriNews

Microbiome search engine can increase efficiency in disease detection and diagnosis – Chinese Academy of Sciences – EurekAlert

7 Ways A Gastroenterologist Supports His Microbiome & Overall Health – Marvin Singh – mbg Health

Infliximab Helps Gut Microbiome in Children with Crohn’s, Study Finds – Ana Pena – IBD News Today

Microbes on the market

DuPont, APC Microbiome Ireland link up for babies – Melody M. Bomgardner – C&EN

March 5, 2020

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

 

January 17, 2020

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

January 16, 2020

Good morning/night everyone!

What I love about writing for MD is the huge diversity of topics we’re meeting along the process of making the daily digest. Even though I’m mostly working on plant and root microbiome, it’s amazing to see how diverse is the world of microbiome and how much more there is to accomplish. Check out today’s digest- and don’t forget the News section as well! it is highly interesting!

General Microbiology

Detection of phylogenetic core groups in diverse microbial ecosystems, Marcos Parras Molto, bioRxiv

Isolation of an archaeon at the prokaryote–eukaryote interface, Hiroyuki Imachi, Nature

Ferrosomes are iron storage organelles formed by broadly conserved gene clusters in bacteria and archaea, Carly R. Grant , bioRxiv

Human microbiome

Distribution of microbial communities and core microbiome in successive wound grades of diabetic foot ulcer individuals, Apoorva Jnana, AEM

Animal microbiome

Parasites modulate the gut-microbiome in insects: A proof-of-concept study, Brian Fredensborg, PlosONE

The effect of diet on the gastrointestinal microbiome of juvenile rehabilitating green turtles (Chelonia mydas), Jennifer Bloodgood ,PlosONE

Rotten-skin disease significantly changed giant spiny frog(Paa spinosa) gut microbiota, Tuoyu He, bioRxiv

Bacterial Biogeography of the Colon in Dogs With Chronic Inflammatory Enteropathy, Paula Giaretta, Veterniary Pathology

Plant and environmental microbiome

Biostimulants applied to maize seeds modulate the enzymatic activity and metaproteome of the rhizosphere, Monica Mattarozzi, Applied Soil Ecology

Biological inhibition of soil nitrification by forest tree species affects Nitrobacter populations, Amandine Laffite, Environmental Microbiology

Extremophile microalgae: An overview, Veronica Malavasi , Journal of Phycology

Methods in microbiome

**Taxonomic classification method for metagenomics based on
core protein families with Core-Kaiju
, Anna Tovo, bioRxiv

**Metagenomic sequencing with spiked primer enrichment for viral diagnostics and genomic surveillance, Xianding Deng , Nature Microbiology

Quantitative PCR provides a simple and accessible method for quantitative microbiota profiling, Ching Jian, PlosONE

The effect of storage conditions on microbial communities in stool, Kristien Nel Van Zyl, PlosONE

Beyond mass spectrometry, the next step in proteomics, Winston and Gregory Timp, Science Advances

Microbiome in the news

Illumina Announces New Sequencing System, Partnership with Roche and Software Suite to Accelerate Adoption of Genomics

Integrating microbiomes into clinical trials – the importance of time

Bayer and Azitra partnership looks to develop skin microbiome products for eczema

**Please read! our mental health is the MOST important thing in our life! Researchers facing ‘shocking’ levels of stress, survey reveals

January 11, 2020

Science doesn’t rest! Today’s Digest brings you several seminal papers and many news pieces. Highlights include a mouse study probing the mechanism behind maternally provisioned immunity for infants, a major effect to characterize mouse gut microbiota, a study on the diversity of the uncultured viruses of bacteria and archaea, and last but not least, a DIY method to deplete ribosomal RNA from your total RNA!

General microbiology

Preprint: Detection of phylogenetic core groups in diverse microbial ecosystems – Marcos Parras-Moltó & Daniel Aguirre de Cárcer – bioRxiv

Antimicrobial resistance

Preprint: Investigating the impact of combination phage and antibiotic therapy: a modeling study – Selenne Banuelos et al. – bioRxiv

Human liver microbiome

Intrahepatic bacterial metataxonomic signature in non-alcoholic fatty liver disease – Silvia Sookoian et al. – Gut

Cancer microbiome

Review: Roles of microbiota in response to cancer immunotherapy – Kentaro Inamura – Seminars in Cancer Biology

Animal experiments

Butyrate attenuated fat gain through gut microbiota modulation in db/db mice following dapagliflozin treatment – Tae Jung Oh et al. – Scientific Reports

Microvesicles from Lactobacillus reuteri (DSM-17938) completely reproduce modulation of gut motility by bacteria in mice – Christine L. West et al. – PLoS One

** Mouse: Microbiota-targeted maternal antibodies protect neonates from enteric infection – Wen Zheng et al. – Nature

Press: Maternal Microbiome Protects Newborns from Deadly Diarrheal Infections – Genengnews

Animal microbiome

** The Mouse Gut Microbial Biobank expands the coverage of cultured bacteria – Chang Liu et al. – Nature Communications

Energy conservation involving 2 respiratory circuits – Marie Charlotte Schoelmerich et al. – PNAS

Press: New metabolic pathway discovered in rumen microbiome – EurekAlert

Plant, root and soil microbiome

Soil bacterial diversity mediated by microscale aqueous-phase processes across biomes – Samuel Bickel & Dani Or – Nature Communications

Fungal community assembly in drought-stressed sorghum shows stochasticity, selection, and universal ecological dynamics – Cheng Gao et al. – Nature Communications

Phages and viruses

** Charting the diversity of uncultured viruses of Archaea and Bacteria – F. H. Coutinho, R. A. Edwards & F. Rodríguez-Valera – BMC Biology

Technology

** Preprint: A simple, cost-effective, and robust method for rRNA depletion in RNA-sequencing studies – Peter H. Culviner et al. – bioRxiv

Microbes in the news

Gut Microbiomes Are Linked To Diet And Evolution—Except In Flying Animals – Linh Anh Cat – Forbes

7 Effects of Greasy Food on Your Body – Elise Mandl – Healthline

Gut microbes may improve stroke recovery – University of Kentucky – EurekAlert

Surprising Ways A Virus Can Be A Man’s Best Friend – Mishal Shaheen et al. – The Health Mania

Twin Studies Examine Cohabiting Affect on Gut Microbiome – Technology Networks

Microbes on the market

Shoreline Biome expands presence in Asia to include Japan – Yahoo! Finance

Synthetic Biologics Receives FDA Guidance at Type C Meeting for SYN-004 (ribaxamase) Phase 1b/2a Clinical Trial in Allogeneic HCT Recipients – Synthetic Biologics – PR Newswire

Johnson & Johnson To Collaborate With Microbiome Biotech On Childhood Allergies – Taylor Carmichael – The Motley Fool

Kaleido Bio teams up with J&J to identify microbiome metabolic candidates – Douglas W. House – Seeking Alpha

Finch Therapeutics Completes Enrollment in Potentially Pivotal Trial of CP101, an Investigational Oral Full-Spectrum Microbiota® Therapy for the Prevention of Recurrent C. difficile Infection – The Tullahoma News

December 27, 2019

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