Category Archives: Human respiratory

September 23, 2019

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This Monday, check out the largest ever study of neonatal microbiomes, the study where researchers alter mouse gut microbiomes by feeding good bacteria their preferred fibers, and the study about the significant effect of antibiotics, antivirals and cofactors on the gut microbiome. Happy reading!

Pregnancy and early life

*Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth – Yan Shao – Nature

Gut microbiome

*Interspecies Competition Impacts Targeted Manipulation of Human Gut Bacteria by Fiber-Derived Glycans – Michael Patnode – Cell

*Distinct impact of antibiotics on the gut microbiome and resistome: a longitudinal multicenter cohort study – Matthias Willmann – BMC Biology

Identification of gut microbiome markers for schizophrenia delineates a potential role of Streptococcus – Feng Zhu – bioRxiv

Fecal Microbiotas of Indonesian and New Zealand Children Differ in Complexity and Bifidobacterial Taxa during the First Year of Life – Blair Lawley – Applied and Environmental Microbiology

Light-entrained and brain-tuned circadian circuits regulate ILC3s and gut homeostasis – Cristina Godinho-Silva – Nature

Baseline human gut microbiota profile in healthy people and standard reporting template – Charles H. King – PlosOne

Oral microbiome

Taste perception and oral microbiota are associated with obesity in children and adolescents – Chiara Mameli – PlosOne

Urinary microbiome

The urobiome of continent adult women: a cross-sectional study – Travis Price – Obstetrics & Gynaecology

The Urinary Microbiota in Relation to the Reproductive Tract Microbiota – Fei Li – bioRxiv

Respiratory microbiome

The effects of e-cigarette vapor exposure on the transcriptome and virulence of Streptococcus pneumoniae – Kamal Bagale – bioRxiv

Water microbiome

Diversity patterns of marine heterotrophic culturable bacteria along vertical and latitudinal gradients – Isabel Sanz-Sáez – bioRxiv

Laundry wastewater and domestic sewage pilot-scale anaerobic treatment: Microbial community resilience regarding sulfide production – A.G.L. Moura – Journal of Environmental Management

Distinct responses from bacterial, archaeal and fungal streambed communities to severe hydrological disturbances – G. Gionchetta – Scientific reports

Metagenome of a polluted river reveals a reservoir of metabolic and antibiotic resistance genes – Parul Mittal – Environmental Microbiome

Plant/root/soil microbiome

Host-Associated Quantitative Abundance Profiling Reveals the Microbial Load Variation of Root Microbiome – Xiaoxuan Guo – Plant Communications

Metatranscriptomics reveals climate change effects on the rhizosphere microbiomes in European grassland – Qicheng Bei – Soil Biology and Biochemistry

Phages and viruses

Beyond cells – The virome in the human holobiont – Rodrigo García-López – Microbial cells

ViraMiner: Deep learning on raw DNA sequences for identifying viral genomes in human samples – Ardi Tampu – PlosOne

Bioinformatics

Review: The signal and the noise – characteristics of antisense RNA in complex microbial communities – Thomas Yssing Michaelsen – bioRxiv

SuRF: a New Method for Sparse Variable Selection, with Application in Microbiome Data Analysis – Lihui Liu – arXiv

September 20, 2019

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Have a nice day! In this digest, an interesting study about the relationship between peripheral serotonin synthesis and host glucose homeostasis, as well as another study showing the long-term maintained high levels of Proteobacteria in Crohn’s disease. And, of course, more papers!

 

Human and General Microbiome

Are we Ready for a “Microbiome-Guided Behaviour” Approach? – Andrea Lavazza – Cambridge Quarterly of Healthcare Ethics

The gut microbiome regulates host glucose homeostasis via peripheral serotonin – Alyce M. Martin – PNAS

Increased abundance of proteobacteria in aggressive Crohn’s disease seven years after diagnosis – M. K. Vester-Andersen – Scientific Reports

The Gut Microbiome and Pediatric Cancer: Current Research and Gaps in Knowledge – Roma Bhuta – JNCI Monographs

Time to test antibacterial therapy in Alzheimer’s disease – Francesco Panza – Brain

Discrepant gut microbiota markers for the classification of obesity-related metabolic abnormalities – Qiang Zeng – Scientific Reports

Altered Fecal Small RNA Profiles in Colorectal Cancer Reflect Gut Microbiome Composition in Stool Samples – Sonia Tarallo – mSystems

Analysis of gut microbiome, nutrition and immune status in autism spectrum disorder: a case-control study in Ecuador – María Fernanda Zurita – Gut Microbes 

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 – BJOG

Development of an Index Score for Intestinal Inflammation-Associated Dysbiosis Using Real-World Stool Test Results – Lihong Chen – Digestive Diseases and Sciences

Benchmarking urine storage and collection conditions for evaluating the female urinary microbiome – Carrie E. Jung – Scientific Reports

Dysbiotic microbiota in autistic children and their mothers: persistence of fungal and bacterial wall-deficient L-form variants in blood – N. Markova – Scientific Reports

Features of Fecal and Colon Microbiomes Associate With Responses to Biologic Therapies for Inflammatory Bowel Diseases: a Systematic Review – Maria Manuela Estevinho – Clinical Gastroenterology and Hepatology

Loss of microbial diversity and pathogen domination of the gut microbiota in critically ill patients – Anuradha Ravi – Microbial Genomics

Complex interactions between the microbiome and cancer immune therapy – Drew J. Schwartz – Critical Reviews in Clinical Laboratory Sciences

Disentangling the effect of host genetics and gut microbiota on resistance to an intestinal parasite – Bruno Faivre – International Journal for Parasitology

Small talk: microbial metabolites involved in the signaling from microbiota to brain – Giorgia Caspani – Current Opinion in Pharmacology

Sputum microbiota and inflammation at stable state and during exacerbations in a cohort of chronic obstructive pulmonary disease (COPD) patients – Solveig Tangedal – PLoS One

 

Animal Microbiome / Animal Experiments

Microbiome composition shapes rapid genomic adaptation of Drosophila melanogaster – Seth M. Rudman – PNAS

Abnormal composition of gut microbiota is associated with resilience versus susceptibility to inescapable electric stress – Kai Zhang – Translational Psychiatry

Adenovirus infection is associated with altered gut microbial communities in a non-human primate – Wasimuddin – Scientific Reports

 

Beneficial Microbes and Compounds

Honey Polyphenols Ameliorate DSS-induced Ulcerative Colitis Via Modulating Gut Microbiota in Rats – Haoan Zhao – Molecular Nutrition and Food Research

ω-3 PUFAs Alleviate High-fat Diet Induced Circadian Intestinal Microbes Dysbiosis – Lifeng Gui – Molecular Nutrition and Food Research

Additional Candida albicans administration enhances the severity of dextran sulfate solution induced colitis mouse model through leaky gut-enhanced systemic inflammation and gut-dysbiosis but attenuated by Lactobacillus rhamnosus L34 – Wimonrat Panpetch – Gut Microbes

Equol: A Bacterial Metabolite from The Daidzein Isoflavone and Its Presumed Beneficial Health Effects –  Baltasar Mayo – Nutrients

Dietary cranberry suppressed colonic inflammation and alleviated gut microbiota dysbiosis in dextran sodium sulfate-treated mice – Xiaokun Cai – Food and Function

 

Food Microbiome

Deciphering the microbiome shift during fermentation of medicinal plants – Martina Köberl – Scientific Reports

 

Plant Microbiome

The aeroponic rhizosphere microbiome: community dynamics in early succession suggest strong selectional forces – Jennifer W. Edmonds – Antonie van Leeuwenhoek

 

Extremophiles

A shared core microbiome in soda lakes separated by large distances – Jackie K. Zorz – Nature Communications

 

Methods

Phylogenetic microbiota profiling in fecal samples depends on combination of sequencing depth and choice of NGS analysis method – Sukithar K. Rajan – PLoS One

Gut microbiome comparability of fresh-frozen versus stabilized-frozen samples from hospitalized patients using 16S rRNA gene and shotgun metagenomic sequencing – Emma E. Ilett – Scientific Reports

 

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

September 6, 2019

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

General microbiology

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

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

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

Antimicrobial resistance

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

Pregnancy and early life

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

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

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

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

Human oral and esophageal microbiome

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

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

Human respiratory microbiome

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

Human gut microbiome

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

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

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

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

Human gut-microbiome-brain axis

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

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

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

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

Human multi-site microbiome

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

Metabolomics

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

Animal experiments

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

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

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

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

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

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

Animal microbiome

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

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

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

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

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

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

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

Plant, root and soil microbiome

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

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

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

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

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

Water and extremophile microbiome

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

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

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

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

Built environment microbiome

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

Phages and viruses

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

Bioinformatics

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

Microbes in the news

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

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

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

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

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

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

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

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

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

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

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

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

Microbes on the market

Metagenomic Analysis of the Human Microbiome – Technology Networks

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

August 24, 2019

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This weekend, read about the microbial index of skin health for children with eczema, gut microbiome of koalas, and interactions between the gut bacterial microbiome and virome of rhesus monkey. Happy reading!

General microbiome

Why we need a small data paradigm – Eric B. Hekler – BMC Medicine

Correspondence: The importance of genome sequence quality to microbial comparative genomics – Theo H. M. Smits – BMC Genomics

The applications of Big Data in molecular diagnostics – Yin Kwan Evelyn Wong – Expert Review of Molecular Diagnostics

Tiny Hidden Genes within Our Microbiome – Karin Mittelman & David Burstein – Cell

Skin microbiome

*A Microbiome-Based Index for Assessing Skin Health and Treatment Effects for Atopic Dermatitis in Children – Zheng Sun – mSystems

Gut microbiome

Reproducible changes in the gut microbiome suggest a shift in microbial and host metabolism during spaceflight – Peng Jiang – Microbiome

Review: Gut Microbiota, Dietary Phytochemicals, and Benefits to Human Health – Ran Yin – Current Pharmacology Reports

Mild cognitive impairment has similar alterations as Alzheimer’s disease in gut microbiota – Binyin Li – Alzheimer’s & Dementia

Design of synthetic microbial consortia for gut microbiota modulation – Jorge F. Vázquez-Castellanos – Current Opinion in Pharmacology

Intestinal microbiota and colorectal cancer: changes in the intestinal microenvironment and their relation to the disease – Sandra Aparecida dos Reis – Journal of Medical Microbiology

Review: Celiac disease: a comprehensive current review – Giacomo Caio – BMC Medicine

Pregnancy and early life

Maternal IgA protects against the development of necrotizing enterocolitis in preterm infants – Kathyayini P. Gopalakrishna – Nature Medicine

Oral microbiome

Oral Microbiome and Cancer Therapy-Induced Oral Mucositis – Jean-Luc C Mougeot – JNCI Monographs

Respiratory microbiome

Deciphering the Ecology of Cystic Fibrosis Bacterial Communities: Towards Systems-Level Integration – Annamaria Bevivino – Trends in Molecular Medicine

Water and extremophile microbiome

Effects of water recirculation rate on the microbial community and water quality in relation to the growth and survival of white shrimp (Litopenaeus vannamei) – Zhao Chen – BMC Microbiology

Pseudomethylobacillus aquaticus gen. nov., sp. nov., a new member of the family Methylophilaceae isolated from an artificial reservoir – Ceshing Sheu – International Journal of Systematic and Evolutionary Microbiology

Bacterial Communities from Extreme Environments: Vulcano Island – Camilla Fagorzi – Diversity

Diversity and biogeography of SAR11 bacteria from the Arctic Ocean – Susanne Kraemer – bioRxiv

Review: Metal and organic pollutants bioremediation by extremophile microorganisms – Patricia Giovanella – Journal of Hazardous Material

Animal microbiome

*Faecal inoculations alter the gastrointestinal microbiome and allow dietary expansion in a wild specialist herbivore, the koala – Michaela D. J. Blyton – Animal microbiome

Impact of pine leaf biochar amendment on bacterial dynamics and correlation of environmental factors during pig manure composting – Jiao Li – Bioresource Technology

Animal experiment

Potential roles of gut microbiome and metabolites in modulating ALS in mice – Eran Blacher – Nature

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

Inhibitory and nutrient use phenotypes among co‐existing Fusarium and Streptomyces populations suggest local coevolutionary interactions in soil – Adil Essarioui – Environmental Microbiology

Phages and viruses

*The altered gut virome community in rhesus monkeys is correlated with the gut bacterial microbiome and associated metabolites – Heng Li – Virology Journal

August 15, 2019

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Have a nice Thursday! Today we have a set of papers showing randomized trials related to antibiotic use and alimentary interventions, metabolic networks associated with C. difficile infection, and analysis of E. coli isolates from human stool. Today, we also include a couple of protocol papers about the use of stable isotope probing in plant microbiome research.

 

Human and General Microbiome

Gut microbiome alteration in MORDOR I: a community-randomized trial of mass azithromycin distribution – T. Doan – Nature Medicine 

Fecal microbiome and metabolome of infants fed bovine MFGM supplemented formula or standard formula with breast-fed infants as reference: a randomized controlled trial – Xuan He – Scientific Reports

Antibiotic Resistance, Virulence Factors, Phenotyping, and Genotyping of E. coli Isolated from the Feces of Healthy Subjects – Stefano Raimondi – Microorganisms

Metabolomic networks connect host-microbiome processes to human Clostridioides difficile infections – John I. Robinson – The Journal of Clinical Investigation

Antibiotic exposure and ‘response failure’ for subsequent respiratory tract infections: an observational cohort study of UK preschool children in primary care – Oliver van Hecke – British Journal of General Practice 

Abnormal vaginal microbiome associated with vaginal mesh complications – Nikolaus Veit‐Rubin – Neurology and Urodynamics

Acceptability, Tolerability and Safety of Faecal Microbiota Transplantation in patients with active Ulcerative Colitis (AT&S Study) – Ajit Sood – Journal of Gastroenterology and Hepatology

The bacteriome of otitis media with effusion: Does it originate from the adenoid? – Oguz Ari – International Journal of Pediatric Otorhinolaryngology 

An Exploratory Analysis of Fecal Immunochemical Test Performance for Colorectal Cancer Screening in Nigeria – Gregory C. Knapp – World Journal of Surgery

Isolates from colonic spirochaetosis in humans show high genomic divergence and potential pathogenic features but are not detected using standard primers for the human microbiota – Kaisa Thorell – Journal of Bacteriology

Microbiota-derived Trimethylamine N-oxide Predicts Cardiovascular Risk After STEMI – Yasushi Matsuzawa – Scientific Reports

Review: Targeting Microbiota: What Do We Know about It at Present? – Aleksejs Derovs – Medicina

Tech News: Reproducibility: the search for microbiome standards – Joseph Martin – BioTechniques

 

Animal Microbiome

Intestinal microbial products from alcohol-fed mice contribute to intestinal permeability and peripheral immune activation – Derrick R. Samuelson – Alcoholism

Comparative metagenomic sequencing analysis of cecum microbiotal diversity and function in broilers and layers – Zhao Qi – 3 Biotech

Oligosaccharides Modulate Rotavirus-Associated Dysbiosis and TLR Gene Expression in Neonatal Rats – Ignasi Azagra-Boronat – Cells

Role of coprophagy in the cecal microbiome development of an herbivorous bird Japanese rock ptarmigan – Atsushi Kobayashi – Journal of Veterinary Medical Science

 

Beneficial compounds and microbes

Review: The role of gut microbiota for the activity of medicinal plants traditionally used in the European Union for gastrointestinal disorders – Timo A. Thumann – Journal of Ethnopharmacology

Commentary: Microbiome, probiotics and dermatology – J.A. Cardenas‐de la Garza – British Journal of Dermatology

Cooked Red Lentils Dose-Dependently Modulate the Colonic Microenvironment in Healthy C57Bl/6 Male Mice – Daniela Graf – Nutrients

Health Benefits of Lactobacillus gasseri CP2305 Tablets in Young Adults Exposed to Chronic Stress: A Randomized, Double-Blind, Placebo-Controlled Study – Kensei Nishida – Nutrients 

Effect of coffee on the compositional shift of oral indigenous microbiota cultured in vitro – 

 

Food Microbiome

Microbial Transformations of Organically Fermented Foods – Ruma Raghuvanshi – Metabolites

 

Plant Microbiome

Protocol: Stable Isotope Probing of Microbiota Structure and Function in the Plant Rhizosphere – Wafa Achouak – Stable Isotope Probing (Methods in Molecular Biology)

Protocol: Targeted Metatranscriptomics of Soil Microbial Communities with Stable Isotope Probing – Ang Hu – Stable Isotope Probing (Methods in Molecular Biology)

Environmental pollution effects on plant microbiota: the case study of poplar bacterial-fungal response to silver nanoparticles – Francesco Vitali – Applied Microbiology and Biotechnology

August 3, 2019

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Have a happy weekend! Today, in this Digest: an interesting study of the human placenta microbiome, papers showing associations between microbiome and pancreatic or lung cancer, and an update of the pathogenesis of bacterial vaginosis. In addition, a paper showing that the microbiome in primates has a different evolutionary pattern in comparison with the host.  Enjoy!

 

Human and General Microbiome

Human placenta has no microbiome but can contain potential pathogens – Marcus C. de Goffau – Nature

Microbial dysbiosis and polyamine metabolism as predictive markers for early detection of pancreatic cancer – Roberto Mendez – Carcinogenesis

Plasticity in the Human Gut Microbiome Defies Evolutionary Constraints – Andres Gomez – mSphere

Whole genome sequencing revealed microbiome in lung adenocarcinomas presented as ground-glass nodules – Yijiu Ren – Translational Lung Cancer Research

An Updated Conceptual Model on the Pathogenesis of Bacterial Vaginosis – Christina A Muzny – The Journal of Infectious Diseases

Review: Gut microbes and metabolites as modulators of blood-brain barrier integrity and brain health – Aimeé Parker – Gut Microbes

Editorial: The only thing that stops a bad microbiome, is a good microbiome – Jessica R. Galloway-Peña – Haematologica

Review: Consumer Safety Considerations of Skin and Oral Microbiome Perturbation – Andrew J. McBain – Clinical Microbiology Reviews

News: Microbiome therapeutics go small molecule – Megan Cully – Nature Reviews Drug Discovery

Pharmacomicrobiomics informs clinical pharmacogenomics – Theodora Katsila – Future Medicine

Each Additional Day of Antibiotics is Associated with Lower Gut Anaerobes in Neonatal Intensive Care Unit Patients – Ashley M Rooney, BSc – Clinical Infectious Diseases

Prevention and treatment of recurrent Clostridioides difficile infection – Jae Shin – Current Opinion in Infectious Diseases

An integrated respiratory microbial gene catalogue to better understand the microbial aetiology of Mycoplasma pneumoniae pneumonia – Wenkui Dai – Gigascience

Review: Connection between gut microbiome and the development of obesity – Cuiting Zhi – European Journal of Clinical Microbiology & Infectious Diseases

Animal Microbiome

Hyperuricemia is associated with impaired intestinal permeability in mice – Daxing Xu – Gastrointestinal and Liver Physiology

 

Beneficial compounds and Foods

Prevention of Vascular Inflammation by Pterostilbene via Trimethylamine-N-Oxide Reduction and Mechanism of Microbiota Regulation – Yen‐Chun Koh – Molecular Nutrition and Food Research

Interactions of tea polyphenols with intestinal microbiota and their implication for cellular signal conditioning mechanism – Yongyong Li – Journal of Food Biochemistry

Hass Avocado Inclusion in a Weight-Loss Diet Supported Weight Loss and Altered Gut Microbiota: A 12-Week Randomized, Parallel-Controlled Trial – Susanne M Henning – Current Developments in Nutrition

 

Plant Microbiome

Host plant-dependent effects of microbes and phytochemistry on the insect immune response – Su’ad A. Yoon – Oecologia

Engineering transkingdom signalling in plants to control gene expression in rhizosphere bacteria – Barney A. Geddes – Nature Communications 

July 29, 2019

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Good Morning! Highlights of today’s digest include a revisited study that showed a significant alterations in the gut microbiome by the consumption of low/no-calorie sweeteners (LNCS), such as Splenda, and raising safety concerns, another work tells us development of Burkholderia-free host plant model to show how Burkholderia helps plant development, and finally a study finds a mechanistic link between the gut microbiome and early childhood asthma as shown with highthened expression of bacterial genes that make 12,13-diHOME which alters immune response.

Human gut microbiome

***Revisited: Assessing the in vivo data on low/no-calorie sweeteners and the gut microbiota – Susan S. Schiffman et al. – Food and Chemical Toxicology

A structured weight loss program increases gut microbiota phylogenetic diversity and reduces levels of Collinsella in obese type 2 diabetics: A pilot study – Fabian Frost et al. – PLOS ONE

Human respiratory microbiome

Chronic obstructive pulmonary disease upper airway microbiome is associated with select clinical characteristics – Alexa A. Pragman et al. – PLOS ONE

Animal experiments

***Elevated faecal 12,13-diHOME concentration in neonates at high risk for asthma is produced by gut bacteria and impedes immune tolerance – Sophia R. Levan et al. – Nature Microbiology

Effect of live yeast Saccharomyces cerevisiae supplementation on the performance and cecum microbial profile of suckling piglets – Tadele G. Kiros et al. – PLOS ONE

Low-dose inoculation of Escherichia coli achieves robust vaginal colonization and results in ascending infection accompanied by severe uterine inflammation in mice – Valerie P. O’Brien – PLOS ONE

Probiotic strains improve high-fat diet-induced hypercholesterolemia through modulating gut microbiota in ways different from atorvastatin – Dun Su et al. – bioRxiv

Host Genotype-shaped Gut Microbiome Modulate Atherosclerosis Development in Mice – Kazuyuki Kasahara et al. – Arteriosclerosis, Thrombosis, and Vascular Biology

Animal microbiome

Fecal microbiota of different reproductive stages of the central population of the lesser-long nosed bat, Leptonycteris yerbabuenae – Osiris Gaona et al. – PLOS ONE

Taxon appearance from extraction and amplification steps demonstrates the value of multiple controls in tick microbiome analysis – Emilie Lejal et al. – bioRxiv

Characterization of the gastrointestinal bacterial microbiome of farmed juvenile and adult white Cachama (Piaractus brachypomus) – Victor Alfonso et al. – Aquaculture

Biosynthesis and Characterization, Antioxidant and Antimicrobial Activities
of Selenium Nanoparticles from Ethanol Extract of Bee Propolis – Shubharani R. et al. – Journal of Nanomedicine & Nanotechnology

Plant, root and soil microbiome

The role of inoculum dispersal and plant species identity in the assembly of leaf endophytic fungal communities – Kevin D. Ricks et al. – PLOS ONE

***Is the bacterial leaf nodule symbiosis obligate for Psychotria umbellata? The development of a Burkholderia-free host plant – Arne Sinnesael et al. – PLOS ONE

AOA and AOB communities respond differently to changes of soil pH under long-term fertilization – Rubio Sun et al. – Soil Ecology Letters

***Negative plant-microbiome feedback limits productivity in aquaponics – Jessica A. Day et al. – bioRxiv

Do plant–microbe interactions and aluminum tolerance influence
alpine sedge species’ responses to nitrogen deposition? – Teal S. Potter et al. – Ecosphere

Plant diversity and fertilizer management shape the belowground microbiome of native grass bioenergy feedstocks – Daniel Revillini et al. – Frontiers in Plant Science

Microbial taxonomical composition in spruce phyllosphere, but not community functional structure, varies by geographical location – Yunshi Li et al. – PeerJ

Responses of plant growth, physiological, gas exchange parameters of super and non-super rice to rhizosphere temperature at the tillering stage – Shuying Li at al. – Nature Scientific Reports

Influence of introduced arbuscular mycorrhizal fungi and phosphorus sources on plant traits, soil properties, and rhizosphere microbial communities in organic legume-flax rotation – Yunliang Li et al. – Plant and Soil

Effects of arbuscular mycorrhizal fungi on inoculated seedling growth and rhizosphere soil aggregates – Zhongfeng Zhang et al. – Soil and Tillage Research

Properties of bacterial community in the rhizosphere soils of Achyranthes bidentata tolerant to consecutive monoculture – Juanying Wang et al. – Plant Growth Regulation

The role of volatile organic compounds and rhizosphere competence in the mode of action of the non-pathogenic Fusarium oxysporum FO12 towards Verticillium wilt – Mulero-Aparicio et al. – Frontiers in Microbiology

Dynamic changes in soil chemical properties and microbial community structure in response to different nitrogen fertilizers in an acidified celery soil – Yuping Wu et al. – Soil Ecology Letters

Improved rhizoremediation for decabromodiphenyl ether (BDE-209) in E-waste contaminated soils – Jiayin Feng et al. – Soil Ecology Letters

Review: Soil biofilms: microbial interactions, challenges, and advanced techniques for ex-situ characterization – Peng Cai et al. – Soil Ecology Letters

Organic amendment effects on nematode distribution within aggregate fractions in agricultural soils – Xiaoke Zhang et al. – Soil Ecology Letters

Water and extermophile microbiome

Book chapter: New Perspectives on the Distribution and Roles of Thermophilic Fungi – Miriam I. Hutchinson et al. – Fungi in Extreme Environments: Ecological Role and Biotechnological Significance

Diversity and biogeography of eukaryotic microorganism in the deepsea sediment of the Eastern Indian Ocean – Xiaoxia Ma et al. – International Journal of Science

Phages and viruses

Phage composition of a fermented milk and colostrum product assessed by microbiome array; putative role of open reading frames – Stefania Pacini et al. – bioRxiv

Techniques

Modelling approaches for studying the microbiome – Manish Kumar et al. – Nature Microbiology

Guest Editorial: Beyond sequencing: fast and easy microbiome profiling by flow cytometry – Charlotte Esser at al. – Archives of Toxicology

View Point: Opportunities at the Intersection of Synthetic Biology, Machine Learning, and Automation – Pablo Carbonell et al. – ACS Synthetic Biology

Microbes in the News

***Elevated Concentration of Lipid in Neonatal Microbiome Predicts Later Risk for Asthma, Allergy – Allison Inserro – AJMC Newsroom

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

July 9, 2019

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Today’s digest features an overview of the “microbiota–nutrient metabolism–epigenetics” axis, a study on the human bile microbiota, an interesting selection of probiotics studies, and more. Check out the new Everything Hertz podcast episode “Improving the scientific poster”. Happy reading/listening!

Gut microbiome

*Epigenetic Regulation at the Interplay Between Gut Microbiota and Host Metabolism – Joan Miro-Blanch and Oscar Yanes – Frontiers in Genetics

Microbiome and type 1 diabetes – Heli Siljander – EBioMedicine

Framework for rational donor selection in fecal microbiota transplant clinical trials – Claire Duvallet – medRxiv

A calcium-rich multi-mineral intervention to modulate colonic microbial communities and metabolic profiles in humans: Results from a 90-day trial – Muhammad N. Aslam – medRxiv

*The human gallbladder microbiome is related to the physiological state and the biliary metabolic profile – Natalia Molinero – Microbiome

Oral microbiome

Microbial differences between dental plaque and historic dental calculus are related to oral biofilm maturation stage – Irina M. Velsko – Microbiome

Respiratory microbiome

Microbial Composition of the Human Nasopharynx Varies According to Influenza Virus Type and Vaccination Status – Tao Ding – mBio

Skin microbiome

Trait-based analysis of the human skin microbiome – Sharon Bewick – Microbiome

Probiotics

Intermittent Lactobacilli-containing Vaginal Probiotic or Metronidazole Use to Prevent Bacterial Vaginosis Recurrence: Safety and Preliminary Efficacy by Microscopy and Sequencing – Janneke H.H.M. van de Wijgert – medRxiv

Impact of spray‐drying on the pili of Lactobacillus rhamnosus GG – Shari Kiekens – Microbial Biotechnology

The Probiotic Mixture VSL#3 Reverses Olanzapine-Induced Metabolic Dysfunction in Mice – Navneet Dhaliwal – Psychiatric Disorders

Prophylactic Effects of Bifidobacterium adolescentis on Anxiety and Depression-Like Phenotypes After Chronic Stress: A Role of the Gut Microbiota-Inflammation Axis – Ying Guo – Frontiers in Behavioral Neuroscience

Water microbiome

Active eukaryotes in drinking water distribution systems of ground and surface waterworks – Jenni Inkinen – Microbiome

Detection of introduced and resident marine species using environmental DNA metabarcoding of sediment and water – Luke E. Holman – bioRxiv

Plant/root/soil microbiome

Microscale interactions between immigrant bacteria and plant leaf microbiota as revealed by live imaging – Shifra Steinberg – bioRxiv

Soil bacterial populations are shaped by recombination and gene-specific selection across a meadow – Alexander Crits-Christoph – bioRxiv

Bioinformatics

DeepMicrobes: taxonomic classification for metagenomics with deep learning – Qiaoxing Liang – bioRxiv

Misclassification of a whole genome sequence reference defined by the Human Microbiome – DJ Darwin R. Bandoy – medRxiv

CarboLogR: a Shiny/R application for statistical analysis of bacterial utilisation of carbon sources – Kevin Vervier – bioRxiv

Using collaboration networks to identify authorship bias in meta-analyses – Thiago C. Moulin and Olavo B. Amaral – medRxiv

Podcast

*Episode 87: Improving the scientific poster (with Mike Morrison) – Dan Quintana and James Heathers – Everything Hertz

A terrific interview with @mikemorrison about the Better Poster format and UX design principles in science.