Category Archives: Water microbiome

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

September 3, 2019

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Happy Tuesday and best of luck to those headed back to school! In today’s Digest, you’ll find the virome of the mosquito gut, leveraging blood metabolomics to predict gut alpha diversity, and a comparison of bacterial taxa consumed in organic vs. conventional apples.

General microbiome
Changes in microbial community structure during dark fermentative hydrogen production – Guang Yang – International Journal of Hydrogen Energy

Pregnancy and early life
Effect of the vaginal microbiome on the pregnancy rate in women receiving assisted reproductive treatment – Andrea Bernabeu – Journal of Assisted Reproduction and Genetics

Maturation of the infant rhesus macaque gut microbiome and its role in the development of diarrheal disease – Nicholas Rhoades – Genome Biology

Human gut microbiome
Blood metabolome predicts gut microbiome α-diversity in humans – Nature Biotechnology – Tomasz Wilmanski

B cell superantigens in the human intestinal microbiota – Jeffrey J. Bunker – Science Translational Medicine

Long-read metagenomic exploration of extrachromosomal mobile genetic elements in the human gut – Yoshihiko Suzuki – Microbiome

Microbiome of death
Preprint: Manner of death and demographic effects on microbial community composition in organs of the human cadaver – Holly L Lutz – bioRxiv

Animal experiments
Diet-induced remission in chronic enteropathy is associated with altered microbial community structure and synthesis of secondary bile acids – Shuai Wang – Microbiome

Animal microbiome
Testing the relationship between microbiome composition and flux of carbon and nutrients in Caribbean coral reef sponges – Shelby E. Gantt – Microbiome

Plant, root, and soil microbiome
A new family of uncultivated bacteria involved in methanogenesis from the ubiquitous osmolyte glycine betaine in coastal saltmarsh sediments – Helen J. Jones – Microbiome

Top-down Enrichment Guides in Formation of Synthetic Microbial Consortia for Biomass Degradation – Sean P. Gilmore – ACS Synthetic Biology

Microbial community response to environmental changes in a technosol historically contaminated by the burning of chemical ammunitions – Hugues Thouin – Science of the Total Environment

Preprint: Intra-genus metabolic diversity facilitates co-occurrence of multiple Ferrovum species at an acid mine drainage site – Christen L Grettenberger – bioRxiv

Water and extremophile microbiome
Exploring the effects of operational mode and microbial interactions on bacterial community assembly in a one-stage partial-nitritation anammox reactor using integrated multi-omics – Yulin Wang – Microbiome

Fungi in salterns – Dawoon Chung – Journal of Microbiology

Distinct temporal dynamics of planktonic archaeal and bacterial assemblages in the bays of the Yellow Sea – Jong-Geol Kim – Plos One

Food microbiology
An Apple a Day: Which Bacteria Do We Eat With Organic and Conventional Apples? – Birgit Wassermann – Frontiers in Microbiology

Preprint: Molecular characterization of bacterial communities in sheep cheese through 16S rRNA gene sequencing – Creciana Maria Endres – bioRxiv

Phages and viruses
Stable distinct core eukaryotic viromes in different mosquito species from Guadeloupe, using single mosquito viral metagenomics – Chenyan Shi – Microbiome

The virome of cerebrospinal fluid: viruses where we once thought there were none – Chandrabali Ghose – Frontiers in Microbiology

Detecting viral sequences in NGS data – Paul G. Cantalupo – Current Opinion in Virology

Bioinformatics
Identification of discriminatory antibiotic resistance genes among environmental resistomes using extremely randomized tree algorithm – Suraj Gupta – Microbiome

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 22, 2019

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

Event

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

General microbiology

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

Antimicrobial resistance

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

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

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

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

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

Human gut microbiome

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

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

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

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

Animal microbiome

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

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

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

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

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

Food microbiome

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

Plant, root and soil microbiome

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

Water and extremophile microbiome

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

Phages and viruses

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

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

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

Microbes in the news

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

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

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

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

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

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

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

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

August 20, 2019

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Today’s digest includes the gut microbiome of sea turtles, microbes on a guyot in the Pacific Ocean, and a review of microbiome animal models. Enjoy!

General microbiome

Review: Simple animal models for microbiome research – Douglas – Nature Reviews Microbiology

Review: An Ecological Loop: Host Microbiomes across Multitrophic Interactions – Liu – Trends in Ecology & Evolution

Review: The antibody/microbiota interface in health and disease – Sterlin – Mucosal Immunology

Pregnancy and early life

Early-life gut microbiome modulation reduces the abundance of antibiotic-resistant bacteria – Casaburi – Antimicrobial Resistance & Infection Control

Human skin microbiome

The prevalence of the culturable human skin aerobic bacteria in Riyadh, Saudi Arabia – Shami – BMC Microbiology

Animal experiments

Oral Administration of Clinically Relevant Antimalarial Drugs Does Not Modify the Murine Gut Microbiota – Denny & Schmidt – Scientific Reports

Animal microbiome

New insights into the gut microbiome in loggerhead sea turtles Caretta caretta stranded on the Mediterranean coast – Arizza – PLoS One

Outcomes of a low birth weight phenotype on piglet gut microbial composition and intestinal transcriptomic profile – Fouhse – Canadian Journal of Animal Science

Plant, root, and soil microbiome

Deciphering rhizosphere microbiome assembly of wild and modern common bean (Phaseolus vulgaris) in native and agricultural soils from Colombia – Pérez-Jaramillo – Microbiome

Preprint: Exploring the microbial diversity in oil-contaminated mangrove sediments using 16S rRNA metagenomics – Ghanbari – BioRxiv

Plant-microorganisms interaction promotes removal of air pollutants in Milan (Italy) urban area – Franzetti – Journal of Hazardous Materials

Effects of natural vegetative restoration on soil fungal and bacterial communities in bare patches of the southern Taihang Mountains – Zhao – Ecology and Evolution

Water and extremophile microbiome

The differentiation of iron-reducing bacterial community and iron-reduction activity between riverine and marine sediments in the Yellow River estuary – Zhang – Marine Life Science & Technology

Bacterial Community on a Guyot in the Northwest Pacific Ocean Influenced by Physical Dynamics and Environmental Variables – Liu – JGR: Biogeosciences

Microdiversity ensures the maintenance of functional microbial communities under changing environmental conditions – García-García – ISME

Built environment

Seasonal diversity of the bacterial communities associated with petroglyphs sites from the Negev Desert, Israel – Nir – Annals of Microbiology

Antibiotic fermentation residue for biohydrogen production using different pretreated cultures: Performance evaluation and microbial community analysis – Yang – Bioresource Technology

Bioinformatics

Metagenomic approaches: effective tools for monitoring the structure and functionality of microbiomes in anaerobic digestion systems – Carabeo-Pérez – Applied Microbiology and Biotechnology

August 19, 2019

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Monday’s digest is about microbiota as biomarker in diverse human diseases such as alopecia areata and bladder cancer, how arabinoxylan and grape pomace affects microbiota in rodents and microbial characterization of multi-strain probiotic VSL3 .

General microbiome

What Pediatricians Should Know Before Studying Gut Microbiota – Lorenzo Drago – Journal of Clinical Medicine

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

Human microbiome

The sex-specific interaction of the microbiome in neurodegenerative diseases – Laura M. Cox – Brain Research

Analysis of the gut microbiota in alopecia areata: identification of bacterial biomarkers – Oscar M. Moreno-Arrenos – Journal of the European Academy of Dermatology and Venereology

The dynamics of the oral microbiome and oral health among patients receiving clear aligner orthodontic treatment – Rui Zhao – Oral Diseases

Urinary microbiota – a potential biomarker and therapeutic target for bladder cancer – Hai Bi – Journal of Medical Microbiology

Animal experiments

Effect of arabinoxylan on colonic bacterial metabolites and mucosal barrier in high‐fat diet‐induced rats – Shanshan Li – Food Science and Nutrition

The Signature Microbiota Driving Rumen Function Shifts in Goat Kids Introduced Solid Diet Regimes – Xiaokang Lv – BioRxiv

Effects of grape pomace and seed polyphenol extracts on the recovery of gut microbiota after antibiotic treatment in high‐fat diet‐fed mice – Feng Lu – Food Science and Nutrition

Microbiota-driven gut vascular barrier disruption is a prerequisite for non-alcoholic steatohepatitis development – Juliette Mouries – Journal of Hepatology

Identification of rumen microbial biomarkers linked to methane emission in Holstein dairy cows – Yuliaxis Ramayo‐Caldas – Journal of Animal Breeding and Genetics

The gastrointestinal fate of limonin and its effect on gut microbiota in mice – Min Gu – Food and Function

Plant, root, soil microbiome

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

Salinity-induced changes in the rhizosphere microbiome improve salt tolerance of Hibiscus hamabo – Yongge Yuan – Plant and Soil

Water and extremophile microbiome

Metagenomic characterization of creek sediment microbial communities from a major agricultural region in Salinas, California – Brittany J. Suttner – BioRxiv

Probiotics

Development of omics-based protocols for the microbiological characterization of multi-strain formulations marketed as probiotics: the case of VSL#3 – Diego Mora – Microbial Biotechnology

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

Probiotic L. gasseri strain (LG21) for the upper gastrointestinal tract acting through improvement of indigenous microbiota – Yasuhiro Koga – BMJ Open Gastroenterology

Non Microbiology Picks

First cells may have emerged because building blocks of proteins stabilized membranes – Science Daily

August 10, 2019

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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

August 8, 2019

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

Event

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

Antimicrobial resistance

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

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

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

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

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

Pregnancy and early life

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

Human multi-site microbiome

A new issue of the Gastroenterology Clinics of North America

Human oral microbiome

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

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

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

Human gut microbiome

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

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

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

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

Animal experiments

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

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

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

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

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

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

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

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

Animal microbiome

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

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

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

Plant, root and soil microbiome

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

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

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

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

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

Water and extremophile microbiome

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

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

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

Built environment microbiome

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

Phages and viruses

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

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

Technology

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

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

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

Microbes in the news

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

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

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

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

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

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

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

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

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

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

Microbes on the market

Shoreline Biome Announces International Distribution Partnerships – Yahoo Finance

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

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

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

August 1, 2019

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Happy Thursday! Today’s digest includes fungi abundance in paddy fields, the microbial quality of treated wastewater, and the oral microbiome of cats. Enjoy!

Animal microbiome

The feline cutaneous and oral microbiota are influenced by breed and environment – Older – PLoS One

Microbial community modulates growth of symbiotic fungus required for stingless bee metamorphosis – Paludo – PLoS One

Preprint: Effects of the copper IUD on composition of the vaginal microbiota in the olive baboon – Eastman – bioRxiv

Plant, root, and soil microbiome

Nitrogen fertilization altered arbuscular mycorrhizal fungi abundance and soil erosion of paddy fields in the Taihu Lake region of China – Zhang – Environmental Science and Pollution Research

Reconciling disparate responses to grazing in the arbuscular mycorrhizal symbiosis – van Der Heyde – Rhizosphere

Redox-driven shifts in soil microbial community structure in the drawdown zone after construction of the Three Gorges Dam – Wang – Soil Ecology Letters

Water and extremophile microbiome

Biomarker Profiling of Microbial Mats in the Geothermal Band of Cerro Caliente, Deception Island (Antarctica): Life at the Edge of Heat and cold – Lezcano – Astrobiology

Microbial diversity analysis and screening for novel xylanase enzymes from the sediment of the Lobios Hot Spring in Spain – Knapik – Scientific Reports

Built environment

How does urban wastewater treatment affect the microbial quality of treated wastewater? – Lopez – Process Safety and Environmental Protection

Identifying microbial community evolution in membrane bioreactors coupled with anaerobic side-stream reactor, packing carriers and ultrasonication for sludge reduction by linear discriminant analysis – Zheng – Bioresource Technology

Food microbiology

Preprint: Deep microbial community profiling along the fermentation process of pulque, a major biocultural resource of Mexico – Rocha-Arriaga – bioRxiv

Bioinformatics

Preprint: µbialSim: constraint-based dynamic simulation of complex microbiomes – Popp and Centler – bioRxiv