December 6, 2019

Today’s post is about metabolic networks of the human gut microbiota with host, how aging affects microbial world in humans, microbiome in honey bee and lifestyle dependent gut microbiota gradients in diverse Indian population. Have a nice weekend!

General microbiome

Review: Metabolic networks of the human gut microbiota – Susannah Selber-Hnatiw – Microbiology

Review: Cannabinoids and the Microbiota‐Gut‐Brain‐Axis: Emerging Effects of Cannabidiol and Potential Applications to Alcohol Use Disorders – Hollis C. Karoly – Alcoholism Clinical and Experimental Research

Review: The Unexplored World of Human Virome, Mycobiome, and Archaeome in Aging – Oscar Salvador Barrera-Vázquez – Journal of Gerontology

Review: Nanotechnology intervention of the microbiome for cancer therapy – Wantong Song – Nature Nanotechnology

Commentary: Gut microbiome influences exercise response – Claire Greenhill – Nature Reviews Endocrinology

Human microbiome

Bacterial DNA induces the formation of heat-resistant disease-associated proteins in human plasma – Victor Tetz – Scientific Reports

Lifestyle induced microbial gradients: An Indian perspective – Rashmi Singh – Frontiers in Microbiology

Microbiota, type 2 diabetes and non-alcoholic fatty liver disease: protocol of an observational study – Benedetta M. Motta – Journal of Translational Medicine

Antibiotic exposure and the risk of colorectal adenoma and carcinoma: systematic review and meta‐analysis of observational studies – Leigh N. Sanyaolu – Colorectal Disease

Higher frequency of vertebrate‐infecting viruses in the gut of infants born to mothers with type 1 diabetes – Ki Wook Kim – Pediatric Diabetes

Animal experiments

Integrative analysis of the gut microbiota and metabolome in rats treated with rice straw biochar by 16S rRNA gene sequencing and LC/MS-based metabolomics – Jie Han – Scientific Reports

Division of labor in honey bee gut microbiota for plant polysaccharide digestion – Hao Zheng – PNAS

The effect of carbohydrate sources: Sucrose, invert sugar and components of mānuka honey, on core bacteria in the digestive tract of adult honey bees (Apis mellifera) – Michelle A. Taylor – PlosOne

Seven-day Green Tea Supplementation Revamps Gut Microbiome and Caecum/Skin Metabolome in Mice from Stress – Eun Sung Jung – Scientific Reports

Cattle intestinal microbiota shifts following Escherichia coli O157:H7 vaccination and colonization travel – Raies A. Mir – PlosOne

Characterization of the cecal microbiome composition of Wenchang chickens before and after fattening – Zhen Tan – PlosOne

SOD1 deficiency alters gastrointestinal microbiota and metabolites in mice – Haruka Sagi – Experimental Gerontology

Plant, soil, root microbiome

Host-mediated microbiome engineering (HMME) of drought tolerance in the wheat rhizosphere – Michael D. Jochum – PlosOne

Arctic tundra soil bacterial communities active at subzero temperatures detected by stable isotope probing – Preshita S. Gadkari – FEMS Microbiology Ecology

Techniques

Comparison of extraction methods for recovering ancient microbial DNA from paleofeces – Richard W. Hagan – American Journal of Physical Anthropology

Microbes in the news

How Microbiomes Affect Fear – Quanta Magazine

Rainforest Dwellers and Urbanites Have Consistently Different Microbiomes – Scientific American

Human Microbiome Modulators Market is Furbishing worldwide with Bayer, BioGaia, Chr. Hansen Holding, DowDuPont – News Description

December 4, 2019

Highlights: Microbiome of human milk, AMON to integrate microbiome and metabolome data, soil microbiomes, skin microbiome based news and many more!

General microbiome

The fight for glycans in reproductive tract microbial ecology – MIH Pishchany – AJOG

Microbiota, a Third Player in the Host–Plasmodium Affair – D Mukherjee – Trends in Parasitology

Pregnancy and early life

Baby’s First Microbes: The Microbiome of Human Milk – MC Collado – How Fermented Foods Feed a Healthy Gut Microbiota

Human respiratory microbiome

Anterior Nares Diversity and Pathobionts Represent Sinus Microbiome in Chronic Rhinosinusitis – ID Boeck – mSphere

Animal microbiome 

Next generation sequencing reveals significant variations in bacterial compositions across the gastrointestinal tracts of the Indian major carps, rohu (Labeo rohita), catla (Catla catla) and mrigal (Cirrhinus cirrhosis) – MJ Foysal – Letters in Applied Microbiology

Plant, root, and soil microbiome

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

The influence of substrate concentration on the culturability of heterotrophic soil microbes isolated by high-throughput dilution-to-extinction cultivation –  R Bartelme – bioRxiv

Rhizosphere: a home for human pathogens – R Sharma – Plant Biotic Interactions

Amplicon sequencing and imputed metagenomic analysis of waste soil and sediment microbiome reveals unique bacterial communities and their functional attributes – SD Mandal – Environmental Monitoring and Assessment

Soil bacterial and fungal communities exhibit distinct long-term responses to disturbance in temperate forests – ED Osburn – Frontiers in Microbiology

Decomposition of mixtures of cover crop residues increases microbial functional diversity – SM Drost – Geoderma

Techniques

AMON: annotation of metabolite origins via networks to integrate microbiome and metabolome data – M Shaffer – BMC Bioinformatics

Identification and quantitation of clinically relevant microbes in patient samples: Comparison of three k-mer based classifiers for speed, accuracy, and sensitivity – GS Watts – PLoS Computational Biology

Extracting the GEMs: Genotype, Environment and Microbiome interactions shaping host phenotypes – BO Oyserman – bioRxiv

Microbes in the news

Korean beauty makers join the rush towards new skin gold mine of microbiome – Pulse

Mode of Delivery May Alter Microbiome, But Study Finds No Link to Later GI Issues – Gastro Endo News

Smart Skin care – Cosmetics Design Europe

The Dynamic Microbiome – Gen Eng News

microRNA Found in Gut Microbiome May Unlock Future Therapeutic Approach for MS – Multiple Sclerosis News Today

A Matchmaker for Microbiomes – Identifying Relationships of Microbes and Metabolites – Scitech Daily

November 11, 2019

Monday’s morning digest is all about interesting updates in microbiome field – real time sampling of international travelers to study antibiotic resistant bacteria, new techniques on using rectal swabs instead of fecal samples to study infant microbiota, 16srRNA gene sequencing for strain level identification and if neutraceutical consumption helps in multiple sclerosis! Finally some interesting review articles on microbial ecology in wine making and a Movember month featured article on association of gut microbiome with men’s sexual health. Enjoy reading!

General microbiome

From the vineyard to the winery: how microbial ecology drives regional distinctiveness of wine – Di Liu – Frontiers in Microbiology

The Gut Microbiome and Men’s Sexual Health – Mohamad M. Osman – Current Sexual Heath Reports

Antibacterial Soaps and Other Cleaners May Actually Be Aiding in the Development of Super Bacteria – Shimon Shatzmiller – Pharmacology, Toxicology and Pharmaceutics

Dietary lipids, gut microbiota and lipid metabolism – Marc Schoeler – Reviews in Endocrine and Metabolic Disorders

Human microbiome

Functional characterisation of gut microbiota and metabolism in Type 2 diabetes indicates that Clostridiales and Enterococcus could play a key role in the disease – Marina Mora-Ortiz – BioRxiv

Real-time sampling of travelers shows intestinal colonization by multidrug-resistant bacteria to be a dynamic process with multiple transient acquisitions – A. Kantele – BioRxiv

A multi-omic cohort as a reference point for promoting a healthy human gut microbiome – Zhuye Jie – BioRxiv

Antimicrobial resistance gene prevalence in a population of patients with advanced dementia is related to specific pathobionts – Aislinn D. Rowan-Nash – BioRxiv

Genomic characterization of the non-O1/non-O139 Vibrio cholerae strain that caused a gastroenteritis outbreak in Santiago, Chile, 2018 – Mónica Arteaga – BioRxiv

Molecular Reconstruction of the Diet in Human Stool Samples – Frank Maixner – mSystems

Infant microbiome

Impacts of Delivery Mode on Very Low Birth Weight Infants’ Oral Microbiome – Hongping Li – Pediatrics and Neonatology

Biomarker Research in ADHD: the Impact of Nutrition (BRAIN) – study protocol of an open-label trial to investigate the mechanisms underlying the effects of a few-foods diet on ADHD symptoms in children – Tim Stobernack – BMJ Open

Immunometabolic approaches to prevent, detect, and treat neonatal sepsis – Maria Giulia Conti – Pediatric Research

Rectal swabs are a reliable proxy for faecal samples in infant gut microbiota research based on 16S-rRNA sequencing – Marta Reyman – Scientific Reports

Gut microbiome of treatment-naïve MS patients of different ethnicities early in disease course – R. E. Ventura – Scientific Reports

Animal experiments

Vasoactive intestinal peptide deficiency is associated with altered gut microbiota communities in male and female C57BL/6 mice – Manpreet Bains – Frontiers in Microbiology

Metabolic analysis of regionally distinct gut microbial communities using an in vitro platform – Jenni Firrman – Agricultural and Environmental Chemistry

Effect of Diet on the Enteric Microbiome of the Wood-Eating Catfish Panaque nigrolineatus – Harold J. Schreier – Frontiers in Microbiology

A high-fat/high-protein, Atkins-type diet exacerbates Clostridioides (Clostridium) difficile infection in mice, whereas a high-carbohydrate diet protects – Chrisabelle C. Mefferd – BioRxiv

Plant, soil, root microbiome

Effects of repeated applications of urea with DMPP on ammonia oxidizers, denitrifiers, and non-targeted microbial communities of an agricultural soil in Queensland, Australia – Aineah Obed Luchibia – Applied Soil Ecology

Covariation of diet and gut microbiome in African megafauna – Tyler R. Kartzinel – PNAS

Fungal communities resist recovery in sand mine restoration – Miranda Hart – Frontiers in Forest and Global Change

Microbial community structure and ecology in sediments of a pristine mangrove forest – C.O.Santana – BioRxiv

Bridging the gap between single-strain and community-level plant-microbe chemical interactions – Bridget O’Banion – Molecular Plant-Microbe Interactions

A brief from the leaf: latest research to inform our understanding of the phyllosphere microbiome – Johan HJ Leveau – Current Opinion in Microbiology

Water microbiome

Metabolic and biogeochemical consequences of viral infection in aquatic ecosystems Amy E. Zimmerman – Nature Reviews Microbiology

Down to the bone: the role of overlooked endolithic microbiomes in reef coral health – Mathieu Pernice – ISME Journal

Differential responses of stream water and bed sediment microbial communities to watershed degradation – Hehuan Liao – Environment International

B12 production by marine microbial communities and Dinoroseobacter shibae continuous cultures under different growth and respiration rates – Josue Villegas-Mendoza – Aquatic Microbial Ecology

Quantifying the contribution of microbial immigration in engineered water systems – Ran Mei – Microbiome

Microbial community rearrangements in power-to-biomethane reactors employing mesophilic biogas digestate – Norbert Ács – Frontiers in Energy Research

Techniques

Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis – Jethro S. Johnson – Nature Communications

AMR – An R Package for Working with Antimicrobial Resistance Data – Matthijs S. Berends – BioRxiv

Probiotics Prebiotics

The effect of emerging nutraceutical interventions for clinical and biological outcomes in multiple sclerosis: A systematic review – Wolfgang Marx – Multiple Sclerosis and Related Disorders

Resveratrol treatment improves the altered metabolism and related dysbiosis of gut programed by prenatal high-fat diet and postnatal high-fat diet exposure – Yi-Chuan Huang – The Journal of Nutritional Biochemistry

The effects of inulin on gut microbial composition: a systematic review of evidence from human studies – Quentin Le Bastard – European Journal of Clinical Microbiology & Infectious Diseases

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

September 20, 2019

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 13, 2019

In today’s edition, you’ll find a whole new textbook about microbes affecting ecosystem sustainability, reviews about phages and plant viruses, New York Times coverage of clinical trials of FMT for obesity, how to banish “manels” from scientific meetings, and microbiota-related metabolites as biomarkers of aging. Enjoy!

General microbiome
Review: Microbial invasions in terrestrial ecosystems – Madhav P. Thakur – Nature Reviews Microbiology

Preprint: Therapeutically exploring persister metabolism in bacteria – Sayed G. Mohiuddin – bioRxiv

Preprint: Delayed antibiotic exposure induces population collapse in enterococcal communities with drug-resistant subpopulations – Kelsey M Hallinen – bioRxiv

Human gut microbiome
Review: Pairing phages with their hosts in the human gut – Ursula Hofer – Nature Reviews Microbiology

Book chapter: Gut Microbiota and Microbiota-Related Metabolites as Possible Biomarkers of Cognitive Aging – Andrea Ticinesi – Reviews on Biomarker Studies in Aging and Anti-Aging Research

Animal microbiome
Habitat disturbance and the organization of bacterial communities in Neotropical hematophagous arthropods – Kelly L. Bennett – PLOS One

Plant, root, soil microbiome
Book chapter: Rhizospheric Microbiome Engineering as a Sustainable Tool in Agriculture: Approaches and Challenges – Shubham Dubey – Microbial Diversity in Ecosystem Sustainability and Biotechnological Applications

Book chapter: Dynamics of Plant Microbiome and Its Effect on the Plant Traits – Shivali Sharma – Microbial Diversity in Ecosystem Sustainability and Biotechnological Applications

Book chapter: Microbial Diversity of the Sundarbans, the World’s Largest Tidal Mangrove Forest, and Its Bioprospects – Kaushik Biswas – Microbial Diversity in Ecosystem Sustainability and Biotechnological Applications

Water and extremophile microbiome
Capability for arsenic mobilization in groundwater is distributed across broad phylogenetic lineages – Robert E. Danczak – PLOS One

Food microbiology
Book chapter: Microbial Diversity on Grapes and Other Fruits: Role and Significance in Fermentation – M. V. Deshpande – Microbial Diversity in Ecosystem Sustainability and Biotechnological Applications

The Dynamics Analysis of Fungal Community Diversity During the Fermentation Process of Chinese Traditional Soybean Paste – Jingping Ge – Waste and Biomass Valorization

Phages and viruses
Review: Evolution and ecology of plant viruses – Pierre Lefeuvre – Nature Reviews Microbiology

Bioinformatics
An Integrated Approach for Efficient Multi-Omics Joint Analysis – Massimiliano S. Tagliamonte – Proceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics

Techniques
Polysaccharide-based liquid storage and transport media for non-refrigerated preservation of bacterial pathogens – Janine R. Hutchison – PLOS One

Microbes in the news
Seeking an Obesity Cure, Researchers Turn to the Gut Microbiome -Anahad O’Connor – NY Times

Exclusive: Behind the front lines of the Ebola wars – Amy Maxmen – Nature

Science, publishing, and career
How to banish manels and manferences from scientific meetings – Holly Else – Nature