December 27, 2019

Today’s Digest brings you a report linking gut microbiota and metabolites, a study on dishwasher rubber as a bacterial reservoir, a news piece for your guide to probiotics, and many more. If we don’t see you again in 2019, Happy New Year! May 2020 bring much success and happiness!

General microbiology

Preprint: The Microbe Directory v2.0: An Expanded Database of Ecological and Phenotypical Features of Microbes – Maria A. Sierra et al. – bioRxiv

A novel graph theoretical approach for modeling microbiomes and inferring microbial ecological relationships – Suyeon Kim et al. – BMC Genomics

Antimicrobial resistance

Preprint: Longitudinal linked read sequencing reveals ecological and evolutionary responses of a human gut microbiome during antibiotic treatment – Morteza Roodgar et al. – bioRxiv

Human oral microbiome

Re-initiation of Oral Food Intake Following Enteral Nutrition Alters Oral and Gut Microbiota Communities – Sayaka Katagiri et al. – Frontiers in Cellular and Infection Microbiology

Human respiratory microbiome

Microbiome in Chronic Obstructive Pulmonary Disease: Role of Natural Products Against Microbial Pathogens – Alessia Santoro et al. – Current Medicinal Chemistry

Human gut microbiome

Comparison of Japanese and Indian intestinal microbiota shows diet-dependent interaction between bacteria and fungi – Siddhika Pareek et al. – npj Biofilms and Microbiomes

Review: The influence of dietary patterns on gut microbiome and its consequences for nonalcoholic fatty liver disease – Qing-Song Zhang et al. – Trends in Food Science and Technology

** Relationship between gut microbiota and circulating metabolites in population-based cohorts – Dina Vojinovic et al. – Nature Communications

Human gut microbiota is associated with HIV-reactive immunoglobulin at baseline and following HIV vaccination – Jacob A. Cram et al. – PLoS One

Preprint: The interplay between host genetics and the gut microbiome reveals common and distinct microbiome features for human complex diseases – Fengzhe Xu & Yuanqing Fu et al. – bioRxiv

Effect of Helicobacter pylori on gastrointestinal microbiota: a population-based study in Linqu, a high-risk area of gastric cancer – Yang Guo et al. – Gut

Human gut-microbiome-brain axis

The relationship between the gut microbiome and mild cognitive impairment in patients without dementia: a cross-sectional study conducted in Japan – Naoki Saji et al. – Scientific Reports

Synergistic effects of APOE and sex on the gut microbiome of young EFAD transgenic mice – Juan Maldonado Weng et al. – Molecular Neurodegeneration

Metabolomics

Tech Note: Boost that metabolomic confidence – Vivien Marx – Nature Methods

The total microbiome functions in bacteria and fungi – Robert Starke et al. – Journal of Proteomics

Animal experiments

Allergic inflammation alters the lung microbiome and hinders synergistic co-infection with H1N1 influenza virus and Streptococcus pneumoniae in C57BL/6 mice – Kim S. LeMessurier et al. – Scientific Reports

Jatrorrhizine Balances the Gut Microbiota and Reverses Learning and Memory Deficits in APP/PS1 transgenic mice – Sheng Wang et al. – Scientific Reports

The impact of gut microbiota manipulation with antibiotics on colon tumorigenesis in a murine model – Jae Gon Lee et al. – PLoS One

Maternal milk and fecal microbes guide the spatiotemporal development of mucosa-associated microbiota and barrier function in the porcine neonatal gut – Hongbin Liu et al. – BMC Biology

Built environment microbiome

** The dishwasher rubber seal acts as a reservoir of bacteria in the home environment – Jerneja Zupančič et al. – BMC Microbiology

Plant, root and soil microbiome

Development of microbial communities in organochlorine pesticide contaminated soil: A post-reclamation perspective – Helga E.Balázs et al. – Applied Soil Ecology

Towards simple tools to assess functional effects of contaminants on natural microbial and invertebrate sediment communities – Stéphane Pesce et al. – Environmental Science and Pollution Research

Core rhizosphere microbiomes of dryland wheat are influenced by location and land-use history – Daniel C Schlatter et al. – Applied and Environmental Microbiology

Water and extremophile microbiome

Single molecule sequencing reveals response of manganese-oxidizing microbiome to different biofilter media in drinking water systems – Xin Zhao et al. – Water Research

Prokaryotic Population Dynamics and Viral Predation in a Marine Succession Experiment Using Metagenomics – Jose M. Haro-Moreno et al. – Frontiers in Microbiology

Phages and viruses

News & Views: Phages build anti-defence barriers – Eugene V. Koonin & Mart Krupovic – Nature Microbiology

Microbes in the news

The Best Thing That Happened This Week: Dogs Rule Because They Drool – Sandy Hingston – Philadelphia Magazine

** A guide to the best probiotics – Louisa Richards/Katherine Marengo – Medical News Today

Having a Dog as a Child Is Tied to a Lower Risk of Schizophrenia as an Adult – Nicholas Bakalar – New York Times

Expanding virophage diversity – DOE/Joint Genome Institute

Microbes on the market

Carbiotix to partner with Italian university on neuroinflammation project – Nathan Gray – Nutraingredients

Human Microbiome Market is Expected to Touch US$ 1888.9 Mn by 2026 – Sheila Shipman – News Cast Report

The next frontier – Aaron Massecar – Today’s Veterinary Business

November 8, 2019

Today’s week-end digest is about new bioinformatic tools (MGnify, PIME, MDiNE) for microbiota analysis, how chemical and built environment of home affects human microbiota and  guidelines for the gut microbiome studies in hypertension.

General microbiome

Adaptation of the Gut Microbiota to Modern Dietary Sugars and Sweeteners – Sara C. Di Rienzi – Advances in Nutrition

Bacteriophages in gastroenterology—from biology to clinical applications – João Sabino – Alimentary Pharmacology and Therapeutics

Boosting natural history research via metagenomic clean-up of crowdsourced feces – Amrita Srivathsan – Plos Biology

Human microbiome

Lower gut microbiome diversity and higher abundance of proinflammatory genus Collinsella are associated with biopsy-proven nonalcoholic steatohepatitis – Stuart Astbury – Gut Microbes

Guidelines for Transparency on Gut Microbiome Studies in Essential and Experimental Hypertension – Francine Z. Marques – Hypertension

The association between dietary fibre deficiency and high-income lifestyle-associated diseases: Burkitt’s hypothesis revisited – Stephen J. O’Keefe – The Lancet Gastroenterology and Hepatology

Animal experiments

Bacterial Swarming as a Protective Response to Intestinal Stress – Weijie Chen – BioRxiv

Flaxseed oil supplementation improves intestinal function and immunity, associated with altered intestinal microbiome and fatty acid profile in pigs with intrauterine growth retardation – Lianqiang Che – Food and Function

Gamma-aminobutyric acid-producing lactobacilli positively affect metabolism and depressive-like behaviour in a mouse model of metabolic syndrome – E. Patterson – Scientific Reports

Plant, root and soil microbiome

Short term effects of different green manure amendments on the composition of main microbial groups and microbial activity of a submerged rice cropping system – Muhammad Israr Khan – Applied Soil Ecology

Cost-effective in-situ remediation technologies for complete mineralization of dyes contaminated soils – Vipul R. Patel – Chemosphere

Distinct Microbial Community of Phyllosphere Associated with Five Tropical Plants on Yongxing Island, South China Sea – Lijun Bao – Microorganisms

Tracing the evolutionary routes of plant–microbiota interactions – Carmen Escudero-Martinez – Current Opinion in Microbiology

Water microbiome

Diet shapes cold‐water corals bacterial communities – Pierre E. Galand – Environmental Microbiology

Built Environment

Home chemical and microbial transitions across urbanization – Laura-Isobel McCall – Nature Microbiology

Techniques

Learning representations of microbe–metabolite interactions – James T. Morton – Nature Methods

MGnify: the microbiome analysis resource in 2020 – Alex L. Mitchell – Nucleic Acids Research

PIME: A package for discovery of novel differences among microbial communities – Luiz Fernando W. Roesch – Molecular Ecology Resources

MDiNE: A model to estimate differential co-occurrence networks in microbiome studies – Kevin McGregor – Bioinformatics

Probiotics

Fermentation of plant-based milk alternatives for improved flavour and nutritional value – Muzi Tangyu – Applied Microbiology and Biotechnology

Modulations of Probiotics on Gut Microbiota in a 5‐Fluorouracil‐Induced Mouse Model of Mucositis – Chun Yan Yeung – Journal of Gastroenterology and Hepatology

The effect of an additive containing three Lactobacillus species on the fermentation pattern and microbiological status of silage – Maja Fijałkowska – Journal of the Science of Food and Agriculture

Microbes in the news

Gut Microbiome Puts the Brakes on Iron Absorption – Michigan Medicine

The Link Between Sleep and Your Gut Microbiome – Health central

Microbiome in China: Cosmetic trend will ‘heat up’ by the end of 2020, says expert – Cosmetics Design-Asia

Enterome Enters Research Collaboration With Major Cancer Center Focused on New Microbiome-derived Immunotherapies – Yahoo Finance

Non Microbiology Picks

Is running associated with a lower risk of all-cause, cardiovascular and cancer mortality, and is the more the better? A systematic review and meta-analysis – Zeljko Pedisic – British Journal of Sports Medicine

October 26, 2019

Highlights: Bacterial communities in aquaculture, crocodiles, tadpoles, mushrooms, coasts, sports facilities; viruses; standardization issues of human microbiome research; some cool events and news hot off the press!

 

Events and jobs

2019 Genome Center Halloween Symposium – 31/10/2019 – UCD, USA

MB Seminar: Marine Host-Microbiome Interactions: Challenges and Opportunities (Dr. Jonathan Eisen, UC Davis) – 22/11/2019 – UCSD, USA

General microbiome 

Metabolic specializations within a bacterial community to create living rocks – Samantha C Waterworth – bioRxiv

Analysis of bacterial microbiome associated with nylon and copper nets in an aquaculture context – Paula Canada – Aquaculture

The gut-eye-lacrimal gland-microbiome axis in Sjögren Syndrome – Claudia M. Trujillo-Vargas – The Ocular Surface

Multi-site human microbiome

DNA extraction for human microbiome studies: the issue of standardization  – K. Leigh Greathouse Genome Biology

Storage media and not extraction method has the biggest impact on recovery of bacteria from the oral microbiome – Xiaoyan Zhou – Nature

Factors contributing to interindividual variation in retronasal odor perception from aroma glycosides: the role of odorant sensory detection threshold, oral microbiota and hydrolysis in saliva – Mango Parker – ACS

Animal experiments 

Contribution of fungal microbiome to intestinal physiology, early-life immune development and mucosal inflammation in mice – Erik van Tilburg Bernardes – bioRxiv

Animal microbiome 

Gut microbiota structure differs between honey bees in winter and summer – Lucie Kešnerová – bioRxiv

Characterisation of the intestinal microbiota of commercially farmed saltwater crocodiles, Crocodylus porosus – Nicky-Lee Willson – Applied Microbiology and Biotechnology

Changes in intestinal microbial community of Rana chensinensis tadpoles during metamorphosis – Hongyu Yang – Aquaculture

Plant, root, and soil microbiome

Impact of agro-farming activities on microbial diversity of acidic red soils in a Camellia Oleifera Forest – Jun Li – Revista Brasileira de Ciência do Solo

A horizon scan of priorities for coastal marine microbiome research – Stacey M. Trevathan-Tackett – Nature

Water and extremophile microbiome 

Effects of disinfection efficiency on microbial communities and corrosion processes in drinking water distribution systems simulated with actual running conditions – Ying Zhu – Journal of Environmental Sciences

Built environment 

Microbial diversity of bioaerosol inside sports facilities and antibiotic resistance of isolated Staphylococcus spp. – Marta Małecka-Adamowicz – Aerobiologia

Food microbiology

Comparing approaches for capturing bacterial assemblages 2 associated with symptomatic (bacterial blotch) and asymptomatic 3 mushroom (Agaricus bisporus) caps – Samuel J. Martins – APS

Comprehensive Understanding of the Bacterial Populations and Metabolites Profile of Fermented Feed by 16S rRNA Gene Sequencing and Liquid Chromatography–Mass Spectrometry – Wei Jin – MDPI Metabolites

Phages and viruses

Viruses RIG up intestinal immunity – Sanghyun Lee – Nature Immunology

Gut DNA Virome Diversity and Its Association with Host Bacteria Regulate Inflammatory Phenotype and Neuronal Immunotoxicity in Experimental Gulf War Illness – Ratanesh K Seth – MDPI Viruses

Viral quasispecies – Esteban Domingo – PLoS Genetics

Techniques

Effective application of machine learning to microbiome-based classification problems – Begüm D. Topçuoğlu – bioRxiv

LEMMI: A continuous benchmarking platform for metagenomics classifiers – Mathieu Seppey – bioRxiv

Microbes in the news

Even the Fetus Has Gut Bacteria, Study Shows – News Wise

Tropical Air Microbiome Analysis Reveals Daily Cycle, Environmental Drivers – genomeweb

Global Microbiome Sequencing Market – Yahoo

How our day-to-day food intake shapes our gut microbiota – Gut microbiota for health

Tracking down the functions of the microbiome – phys.org

Unhealthy gut microbiome reduces brain synaptic pruning, impairs learning – News Medical

Harnessing the Power of Microbes to Fight Cancer – Medscape.com

October 16, 2019

Happy Wednesday! Today’s digest includes the human gut virome, microbiome recovery after antibiotics, and the fungi growing on museum skeletons. Enjoy!

Pregnancy and early life

The vaginal microbial communities of healthy expectant Brazilian mothers and its correlation with the newborn’s gut colonization – Dobbler – World Journal of Microbiology and Biotechnology

Human skin microbiome

In vitro Antimicrobial Activity of Acne Drugs Against Skin-Associated Bacteria – Blaskovich – Scientific Reports

Human gut microbiome

Review: The Human Gut Virome Is Highly Diverse, Stable, and Individual Specific – Shkoporov – Cell Host & Microbe

Review: Inflammatory Bowel Disease: A Potential Result from the Collusion between Gut Microbiota and Mucosal Immune System – Yue – Microorganisms

Individualized recovery of gut microbial strains post antibiotics – Koo – npj Biofilms and Microbiomes

Animal experiments

Depletion of dietary aryl hydrocarbon receptor ligands alters microbiota composition and function – Brawner – Scientific Reports

Rat H1 parvovirus infection leads to alterations in gut microbiota – Xiang – Pathogens and Disease

Positive effect of an electrolyzed reduced water on gut permeability, fecal microbiota and liver in an animal model of Parkinson’s disease – Bordoni – PLoS One

The Sulfate-Reducing Microbial Communities and Meta-Analysis of Their Occurrence during Diseases of Small–Large Intestine Axis – Kushkevych – Journal of Clinical Medicine

Plant, root, and soil microbiome

Spatial gradients in the characteristics of soil-carbon fractions are associated with abiotic features but not microbial communities – Sengupta – Biogeosciences

Water and extremophile microbiome

Diversity, Distribution, and Ecology of Fungi in the Seasonal Snow of Antarctica – Menezes – Microorganisms

Interaction and assembly processes of abundant and rare microbial communities during a diatom bloom process – Zhang – Environmental Microbiology

Built environment

Changes in the Bacterioplankton Community Structure from Southern Gulf of Mexico During a Simulated Crude Oil Spill at Mesocosm Scale – Valencia-Agami – Microorganisms

Increased loading leads to convergence of microbial communities and high methane yield in adapted anaerobic co-digesters – Wang – Water Research

Skeleton bones in museum indoor environments offer niches for fungi and are affected by weathering and deposition of secondary minerals – Pinzari – Environmental Microbiology

Bioinformatics

Species abundance information improves sequence taxonomy classification accuracy – Kaehler – Nature Communications

September 17, 2019

Happy Tuesday! Today’s digest includes wastewater treatment biofilms, the microbiome during Crohn’s disease remission, and the bacteria associated with acid mine drainage. Enjoy!

Human oral microbiome

Succession of oral microbiota community as a tool to estimate postmortem interval – Dong – Scientific Reports

Human gut microbiome

Remission in Crohn’s disease is accompanied by alterations in the gut microbiota and mucins production – Magro – Scientific Reports

Specific gut microbiome members are associated with distinct immune markers in pediatric allogeneic hematopoietic stem cell transplantation – Ingham – Microbiome

Effect of a Chinese medical nutrition therapy diet on gut microbiota and short chain fatty acids in the simulator of the human intestinal microbial ecosystem (SHIME) – Wu – Journal of Functional Foods

A comprehensive assessment of demographic, environmental, and host genetic associations with gut microbiome diversity in healthy individuals – Scepanovic – Microbiome

Animal experiments

Dietary Bovine Milk Exosomes Elicit Changes in Bacterial Communities in C57BL/6 Mice – Zhou – American Journal of Physiology

Microbial Metabolism Modulates Antibiotic Susceptibility within the Murine Gut Microbiome – Cabral – Cell Metabolism

Animal microbiome

Maternal vs artificial rearing shapes the rumen microbiome having minor long‐term physiological implications – Belanche – Environmental Microbiology

Plant, root, and soil microbiome

Impact of continuous Panax notoginseng plantation on soil microbial and biochemical properties – Zhang – Scientific Reports

Three Bermudagrass-suppression techniques have little effect on soil-nutrient availability and microbial communities 200 days after application – Farthing – Applied Soil Ecology

Water and extremophile microbiome

Effect of salinity on mature wastewater treatment biofilm microbial community assembly and metabolite characteristics – Wang – Science of the Total Environment

Diversity and functional profile of bacterial communities at Lancaster acid mine drainage dam, South Africa as revealed by 16S rRNA gene high-throughput sequencing analysis – Lukhele – Extremophiles

Abiotic stress resistance, plant growth promotion and antifungal potential of halotolerant bacteria from a Tunisian solar saltern – Masmoudi – Microbiological Research

Built environment

Effective removal of antibiotic resistance genes and potential links with archaeal communities during vacuum-type composting and positive-pressure composting – Fan – Journal of Environmental Science

Hydraulically Fractured Natural-Gas Well Microbial Communities Contain Genomic Halogenation and Dehalogenation Potential – Evans – Environmental Science & Technology Letters

Successional trophic complexity and biogeographical structure of eukaryotic communities in waterworks rapid sand filters – Harder – FEMS Microbiology Ecology

September 6, 2019

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 20, 2019

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