May 19, 2020

Good afternoon from sunny South Wales!

Today’s digest has a lot of great papers, with something for just about everyone. We’ll start off with a bang, and highlight a great paper in which Rajasekaran and collegaues challenge the current dogma that human intervertebral discs are sterile using a 16S rRNA sequencing approach.

We then have an interesting, or perhaps concerning paper looking at the prevalence of underreported parasites in laboratory zebrafish populations. A must read for anybody using zebrafish models. We also have plenty of papers concerning plant and water microbiomes, including a rather huge report on ocean systems.

Finally, with the current health climate, what better paper peruse than the contribution of Qureshi et al. who have demonstrated that gender neutral bathrooms are more rapidly colonised than single gender bathrooms. If recent anecdotal news articles are to be believed (although they seldom are) it’s usually the men letting the side down. You’ve got to wash those hands!

I hope everyone is staying safe, and enjoys today’s post!

COVID-19

Preprint: Identification of five antiviral compounds from the Pandemic Response Box targeting SARS-CoV-2 – Holwerda et al.

General microbiome

Longitudinal Study of Oral Microbiome Variation in Twins – Freire et al.Sci Rep

Human nearly-sterile sites

Human intervertebral discs harbour a unique microbiome and dysbiosis determines health and disease – Rajasekaran et al.European Spine Journal

Human gut microbiome

Early signs of gut microbiome aging: biomarkers of inflammation, metabolism, and macromolecular damage in young adulthood – Gaydosh et al. The Journals of Gerontology

Animal experiments

Behavioural effects of the common brain-infecting parasite Pseudoloma neurophilia in laboratory zebrafish (Danio rerio) – Midttun et al.Sci Rep

Lactobacillus plantarum FRT10 alleviated high-fat diet–induced obesity in mice through regulating the PPARα signal pathway and gut microbiota – Cai et al.Applied Microbial and Cell Physiology

Animal microbiome

Factors affecting the microbiome of Ixodes scapularis and Amblyomma americanum – Brinkerhoff et al.PLoS ONE

Preprint: Distinct Microbial Assemblages Associated with Genetic Selection for High- and Low- Muscle Yield in Rainbow Trout – Walker et al.

Whole-genome sequences of an abortive Bacillus safensis strain isolated from a mare’s uterus – Little, Hillhouse and Lawhorn – Genome Sequences

Plant, root, and soil microbiome

Preprint: A fungal member of the microbial phyllosphere antagonizes infection of Arabidopsis thaliana by the oomycete pathogen Albugo laibachii via a putative secreted hydrolase – Eitzen et al.

Preprint: Diazotrophic bacteria from maize exhibit multifaceted plant growth promotion traits in multiple hosts – Higdon et al.

Fungal communities and their association with nitrogen-fixing bacteria affect early decomposition of Norway spruce deadwood – Gómez-Brandón et al. – Sci Rep

Fruitbody chemistry underlies the structure of endofungal bacterial communities across fungal guilds and phylogenetic groups – Pent, Bahram and Põldmaa – ISME J

Endophytic fungal community in grape is correlated to foliar age and domestication – Fan et al.Annals of Microbiology

Water and extremophile microbiome

Microbial genomics of the global ocean system – Joye and Kostka – Coloqium Report

How do microbiota associated with an invasive seaweed vary across scales? – Bonthond et al.Molecular Ecology

Preprint: Differences in the microbiota of native and non-indigenous gelatinous zooplankton organisms in a low saline environment – Jaspers et al.

Built environment

Gender‐neutral bathroom surfaces recolonized by microbes more quickly than single gender bathrooms – Qureshi, Kedo and Berthrong – Letters in Applied Microbiology

Food microbiology

Dynamic distribution of gut microbiota in meat rabbits at different growth stages and relationship with average daily gain (ADG) – Fang et al.BMC Microbiology

Techniques

Preprint: Evaluation of Methods to Optimise Shotgun Metagenomic Sequencing-Based Analysis of the Microbiome of Milk – Feehily et al.

April 5, 2020.

All the break-neck speed with which the progress that is happening today in tracking, detecting and treating the disease, like everything else, is owed in part to the giants whose shoulders we’re standing on. One such thing is the usage of serum (from recovered patients or derived elsewhere) for treatment. So, as a little tribute, I would like to share with you today, on the birthday of Dr. Hattie Elizabeth Alexander (born April 5, 1901), the information that she pioneered the work in using anti-influenzal rabbit serums to treat the then always-fatal influenzal meningitis (effectively bringing down the fatality rate to 20%!), and was also sone of the very first to study bacterial mutations that come along with antibiotic resistance !

So we’ve come a long way and are forging our way forward. Here are a few interesting articles that are slowly pushing this boundary, a piece at a time.

COVID-19

From PREDICT to prevention, one pandemic later – Colin J Carlson – The Lancet.

Human Microbiome

Review: Risk factors associated with gastric malignancy during chronic Helicobacter pylori infection – Ami Y Seegar – Medical Research Archives.

Review: From Association to Causality: the Role of the Gut Microbiota and Its Functional Products on Host Metabolism – Ara Koh – Molecular Cell.

Pregnancy and Early Life

Breast Milk and Microbiota in the Premature Gut: A Method of Preventing Necrotizing Enterocolitis – Orga PL et al – Karger.

Human Brain and Microbiome

Book: Integrative and Functional Medical Nutrition Therapy. Chapter: The Microbiome and Brain Health – Sharon L. Norling -Springer

Animal Experiments


Integrated omics profiling of dextran sodium sulfate-induced colitic mice supplemented with Wolfberry (Lycium barbarum). Wanping Aw et al – NPJ Science of Food.

Botany

Rhizobacteriome: Promising Candidate for Conferring Drought Tolerance in Crops – Vinod Yadav et al – Journal of Pure Applied Microbiology

Legionella species: A potential problem associated with rain water harvesting systems? – Judith A Taylor et al – SAGE Journals

Bioinformatics

Applications of Machine Learning Predictive Models in the Chronic Disease Diagnosis – Gopi Battineni et al – Journal of Personalized Medicine

PS: I know, I am with you on this — the lockdown isn’t ideal. But we are also the generation, who for the first time can end articles signing off as “Stay Safe and Wash Your Hands” and manage to prevent a large proportion of its species from suffering / dying. Isn’t that crazy! Have a great day!

More information on Dr. Hattie Elizabeth Alexander — here and here.

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

 

February 18, 2020

Highlights for today’s Digest: a study takes us deep into bacterial community of the dermal compartment of the skin, skin microbiota predicts chronological age most accurately, and a review on network analyses using multi-omics data. Enjoy!

General microbiology

A biphasic growth model for cell pole elongation in mycobacteria – Mélanie T. M. Hannebelle et al. – Nature Communications

Press: Bacteria under the microscope: A new growth model for tuberculosis – Lionel Pousaz, Ecole Polytechnique Federale de Lausanne – Phys.org

Metabolic dependencies govern microbial syntrophies during methanogenesis in an anaerobic digestion ecosystem – Xinyu Zhu et al. – Microbiome

Antimicrobial resistance

Stepwise evolution and convergent recombination underlie the global dissemination of carbapenemase-producing Escherichia coli – afael Patiño-Navarrete et al. – Genome Medicine

Pregnancy and early life

The effect of legume supplementation on the gut microbiota in rural Malawian infants aged 6 to 12 months – M Isabel Ordiz et al. – The American Journal of Clinical Nutrition

Human skin microbiome

** Universal Dermal Microbiome in Human Skin – Lene Bay et al. – mBio

Human cancer microbiome

Opinion: The Cancer Microbiome: Distinguishing Direct and Indirect Effects Requires a Systemic View – Joao B. Xavier et al. – Trends in Cancer

Human gut microbiome

Interactions between the gut microbiome and host gene regulation in cystic fibrosis – Gargi Dayama et al. – Genome Medicine

Human multi-site microbiome

Review: Blood Microbiota and Circulating Microbial Metabolites in Diabetes and Cardiovascular Disease – Ganesan Velmurugan et al. – Trends in Endocrinology & Metabolism

** Human Skin, Oral, and Gut Microbiomes Predict Chronological Age – Shi Huang et al. – mSystems

Press: Human Skin, Oral Microbiomes Can Estimate People’s Ages to Within Few Years – GenomeWeb

Animal experiments

Self-reinoculation with fecal flora changes microbiota density and composition leading to an altered bile-acid profile in the mouse small intestine – Said R. Bogatyrev et al. – Microbiome

Mouse: It’s the fiber, not the fat: significant effects of dietary challenge on the gut microbiome – Kathleen E. Morrison et al. – Microbiome

Animal microbiome

Trait-Based Comparison of Coral and Sponge Microbiomes – Cara L. Fiore et al. – Scientific Reports

Plant, root and soil microbiome

Functional relationships between aboveground and belowground spinach (Spinacia oleracea L., cv. Racoon) microbiomes impacted by salinity and drought – A. Mark Ibekwe et al. – Science of the Total Environment

Water and extremophile microbiome

Constraints on microbial communities, decomposition and methane production in deep peat deposits – Laurel A. Kluber et al. – PLoS One

Machine learning-aided analyses of thousands of draft genomes reveal specific features of activated sludge processes – Lin Ye et al. – Microbiome

Phages and viruses

Pearls: Virus interactions with bacteria: Partners in the infectious dance – Ursula Neu & Bernardo A. Mainou – PLoS Pathogens

Coronavirus: hospitals must learn from past pandemics – Nahid Bhadelia – Nature

Review: Phage diversity, genomics and phylogeny – Moïra B. Dion et al. – Nature Reviews Microbiology

Technology

Uncovering a hidden diversity: optimized protocols for the extraction of dsDNA bacteriophages from soil – Pauline C. Göller et al. – Microbiome

Review: Combining omics technologies with CRISPR-based genome editing to study food microbes – Meichen Pan & Rodolphe Barrangou – Current Opinion in Biotechnology

Complete, closed bacterial genomes from microbiomes using nanopore sequencing – Eli L. Moss et al. – Nature Biotechnology

Press: Closing bacterial genomes from the human gut microbiome using long-read sequencing – Dylan Maghini – Nature Bioengineering Community

Bioinformatics

A pipeline for targeted metagenomics of environmental bacteria – Anissa Grieb et al. Microbiome

** Review: Network analyses in microbiome based on high-throughput multi-omics data – Zhaoqian Liu et al. – Briefings in Bioinformatics

Microbes in the news

Getting the Band (of Microbes) Back Together – Jessica Messier – Worcester Polytechnic Institute

Gut microbe imbalance may stunt CF babies’ growth – Leila Gray – University of Washington

The Big Idea: The Microbiome – Purdue University

Moscow’s Subway Microbiome Looks Similar to that of New York’s – GenEngNews

A guide to caring for the Indian gut – Cherylann Mollan – Hindustan Times
 

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

November 23, 2019

In today’s digest read about the Darobactin (a new antibiotic that selectively kills Gram-negative pathogens by binding to the BamA protein, located in the external membrane of Gram-negative bacteria), temporal stability of the rumen microbiota, and Gardnerella species (Gardnerella leopoldii, G. swidsinskii, G. piotii, and G. vaginalis) in the vaginal microbiome. And, check out 2019 Holiday Gift Guide For Microbe Lovers. Happy weekend!

General microbiome

*A new antibiotic selectively kills Gram-negative pathogens – Yu Imai – Nature

Read the story behind the paper by Roberto Molar Candanosa, Northeastern University.

Gut microbiome

Review: The human gut bacteria Christensenellaceae are widespread, heritable, and associated with health – Jillian L. Waters & Ruth E. Ley – BMC Biology

The gut microbiota influences how circulating immune cells in humans change from one day to the next – Jonas Schluter – bioRxiv

Vaginal microbiome

*Resolution and Cooccurrence Patterns of Gardnerella leopoldii, G. swidsinskii, G. piotii, and G. vaginalis within the Vaginal Microbiome – Janet E. Hill – Infection and Immunity

Clinical validation of the Aptima Bacterial Vaginosis and Aptima Candida/Trichomonas Vaginitis Assays: results from a prospective multi-center clinical study – Jane R. Schwebke – Journal of Clinical Microbiology

Review: Understanding and interpreting community sequencing measurements of the vaginal microbiome – HL Berman – BJOG : an International Journal of Obstetrics and Gynaecology

Endocervical microbiome

Diversity of endocervical microbiota associated with genital Chlamydia trachomatis infection and infertility among women visiting obstetrics and gynecology clinics in Malaysia – Heng Choon Cheong – PlosOne

Uterine microbiome

Does dysbiotic endometrium affect blastocyst implantation in IVF patients? – Tomoko Hashimoto & Koichi Kyono – Journal of Assisted Reproduction and Genetics

Oral microbiome

Oral microbial community composition is associated with pancreatic cancer: A case‐control study in Iran – Emily Vogtmann – Cancer Medicine

Animal microbiome

*Temporal stability of the rumen microbiota in beef cattle, and response to diet and supplements – Timothy J. Snelling – Animal Microbiome

Development of the duodenal, ileal, jejunal and caecal microbiota in chickens – Laura Glendinning – Animal Microbiome

Mammary microbiome of lactating organic dairy cows varies by time, tissue site, and infection status – Tucker Andrews – PlosOne

Inulin improves the egg production performance and affects the cecum microbiota of laying hens – Hongmei Shang – International Journal of Biological Macromolecules

Animal experiments

Effects of Debaryomyces hansenii treatment on intestinal mucosa microecology in mice with antibiotic-associated diarrhea – Ao Zeng – PlosOne

Microbe-metabolite associations linked to the rebounding murine gut microbiome post-colonization with vancomycin resistant Enterococcus faecium – Andre Mu – bioRxiv

Hepatitis B Virus Infection Alters Gut Microbiota Composition in Mice – Qingfeng Zhu – Front. Cell. Infect. Microbiol.

Human Gut Microbiome Transplantation in Ileitis Prone Mice: A Tool for the Functional Characterization of the Microbiota in Inflammatory Bowel Disease Patients – Abigail R Basson – Inflammatory Bowel Diseases

Effects of an Escherichia coli exopolysaccharide on human and mouse gut microbiota in vitro – Baiyuan Li – International Journal of Biological Macromolecules

Ion Transport Basis of Diarrhea in a Mouse Model of Adoptive T Cell Transfer Colitis – Dulari Jayawarden – Digestive Diseases and Sciences

Water microbiome

Rewetting of three drained peatlands drives congruent compositional changes in pro- and eukaryotic microbiomes through environmental filtering – Micha Weil – bioRxiv

Phages and viruses

Herpes Simplex Virus Infection, Acyclovir and IVIG Treatment All Independently Cause Gut Dysbiosis – Chandran Ramakrishna – bioRxiv

Svetlana’s pick

Gift guide for this holiday season!
by Justine Dees

August 10, 2019

This weekend, read about the role that gut microbes play in inflammation, microbes in the placenta-maternal interface, BactMAP R package, and more. Happy reading!

General microbiome

High proportions of bacteria and archaea across most biomes remain uncultured – Andrew D. Steen – The ISME Journal

Isolation of an archaeon at the prokaryote-eukaryote interface – Hiroyuki Imachi – bioRxiv

Urinary microbiome

A Prospective Study of the Urinary and Gastrointestinal Microbiome in Prepubertal Males – Borna Kassir – Urology

Gut microbiome

*Review: The intestinal microbiota fuelling metabolic inflammation – Herbert Tilg – Nature Reviews Immunology

Long-term dietary intervention reveals resilience of the gut microbiota despite changes in diet and weight – Gabriela K Fragiadakis – bioRxiv

Recovery of the gut microbiota after antibiotics depends on host diet and environmental reservoirs – Katharine M. Ng – bioRxiv

Differential detection of Entamoeba species in stool samples collected from children in District Swat, Khyber Pakhtunkhwa Pakistan – Muhammad Iftikhar Khan – bioRxiv

Association network analysis identifies enzymatic components of gut microbiota that significantly differ between colorectal cancer patients and healthy controls – Dongmei Ai – PeerJ

Specific changes in faecal microbiota are associated with familial Mediterranean fever – Samuel Deshayes – Annals of the Rheumatic Diseases

Pregnancy and early life

*Functional characterization of Ralstonia insidiosa, a bona fide resident at the maternal-fetal interface – Lindsay A. Parnell – bioRxiv

The association between caesarean section delivery and later life obesity in 21-24 year olds in an Urban South African birth cohort – Eniola Sogunle – bioRxiv

Water and extremophile microbiome

Microbial community and geochemical analyses of trans-trench sediments for understanding the roles of hadal environments – Satoshi Hiraoka – bioRxiv

Metabolically-active obligate aerobes in anoxic (sulfidic) marine sediments – Sabyasachi Bhattacharya – bioRxiv

Plant microbiome

Shared mycorrhizae but distinct communities of other root-associated microbes on co-occurring native and invasive maples – Tonia DeBellis – PeerJ

Non-target Effects of Trichoderma on Plants and Soil Microbial Communities – Monika Jangi – Plant Microbe Interface

Bioinformatics

*BactMAP: an R package for integrating, analyzing and visualizing bacterial microscopy data – Renske van Raaphorst – bioRxiv

Podcast

The placental microbiome, and advances in artificial intelligence – Nick Howe and Noah Baker – Nature Podcast