November 8, 2019

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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

November 6, 2019

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Today’s Digest features a large study on the evolution of diet and microbiota in African animals, a review on how diet can alter gut microbiota to fight infectious diseases, and we might reverse specific antibiotic resistance by removing those antibiotics in the environment. Enjoy!

General microbiology

Letter to the Editor: A conceptual framework for the phylogenetically constrained assembly of microbial communities – Daniel Aguirre de Cárcer – Microbiome

Review: The engineering of spatially linked microbial consortia – potential and perspectives – Sami Ben Said et al. – Current Opinion in Biotechnology

Preprint: Selection of representative genomes for 24,706 bacterial and archaeal species clusters provide a complete genome-based taxonomy – Donovan H. Parks et al. – bioRxiv

Antimicrobial resistance

** Rapid decline of bacterial drug-resistance in an antibiotic-free environment through phenotypic reversion – Anett Dunai et al. – eLife

Human respiratory microbiome

Interplay between host-microbe and microbe-microbe interactions in cystic fibrosis – Catherine R. Armbruster et al. – Journal of Cystic Fibrosis

Human gut microbiome

Review: Gastrointestinal Microbiota and Type 1 Diabetes Mellitus: The State of Art – Marilena Durazzo et al. – Journal of Clinical Medicine

Identification of a Shared Microbiomic and Metabolomic Profile in Systemic Autoimmune Diseases – Chiara Bellocchi et al. – Journal of Clinical Medicine

Gut microbiome composition in the Hispanic Community Health Study/Study of Latinos is shaped by geographic relocation, environmental factors, and obesity – Robert C. Kaplan et al. – Genome Biology

Food microbiome

Comparison of microbial communities and physiochemical characteristics of two traditionally fermented vegetables – Qianqian Guan et al. – Food Research International

Animal experiments

** Review: Diet–microbiome–disease: Investigating diet’s influence on infectious disease resistance through alteration of the gut microbiome – Erica V. Harris et al. – PLoS Pathogen

Supplementation of Sesamin Alleviates Stress-Induced Behavioral and Psychological Disorders via Reshaping the Gut Microbiota Structure – Qianxu Wang et al. – Journal of Agricultural and Food Chemistry

Animal microbiome

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

Press: Study of African animals illuminates links between environment, diet and gut microbiome – Brown University – Phys.org

Plant, root and soil microbiome

Interactive Effects of Nitrogen-Fixing Bacteria Inoculation and Nitrogen Fertilization on Soybean Yield in Unfavorable Edaphoclimatic Environments – Carlos Felipe dos Santos Cordeiro & Fábio Rafael Echer – Scientific Reports

Impacts of Maize Domestication and Breeding on Rhizosphere Microbial Community Recruitment from a Nutrient Depleted Agricultural Soil – Vanessa L. Brisson et al. – Scientific Reports

Microbial communities and soil chemical features associated with commercial production of the medicinal mushroom Ganoderma lingzhi in soil – Le-Qin Ke et al. – Scientific Reports

Feasibility of bioleaching of heavy metals from sediment with indigenous bacteria using agricultural sulfur soil conditioners – Chuncheng Wu et al. – Science of the Total Environment

Land management and microbial seed load effect on rhizosphere and endosphere bacterial community assembly in wheat – Tim H. Mauchline et al. – Frontiers in Microbiology

Water and extremophile microbiome

Comparative metagenomic analysis of microbial taxonomic and functional variations in untreated surface and reclaimed waters used in irrigation applications – Jessica Chopyk et al. – Water Research

Strong seasonality in arctic estuarine microbial food webs – Colleen T. Kellogg et al. – Frontiers in Microbiology

Evaluation of degradation behavior over tetracycline hydrochloride by microbial electrochemical technology: Performance, kinetics, and microbial communities – Xinhong Peng et al. – Ecotoxicology and Environmental Safety

Groundwater microbial communities and their connection to hydrochemical environment in Golmud, Northwest China – Liang Guo et al. – Science of the Total Environment

Performance of enhanced anaerobic digestion with different pyrolysis biochars and microbial communities – Ruixia Shen et al. – Bioresource Technology

Technology

Optimizing sequencing protocols for leaderboard metagenomics by combining long and short reads – Jon G. Sanders et al. – Genome Biology

Bioinformatics

Microbiota analysis optimization for human bronchoalveolar lavage fluid – Pierre H. H. Schneeberger et al. – Microbiome

The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities – James J Davis et al. – Nucleic Acids Research

Microbes in the news

Gut microbiome of premature babies is associated with stunted growth – EurekAlert!

Shark Skin Microbiome Protects Wounds From Infection – SciTechDaily

Fiber-rich diet eases son’s asthma, launches professor’s interdisciplinary microbiome research – Jeff Dodge – Colorado State University

Researchers identify certain gut bacteria that may be involved in causing bowel cancer – University of Bristol

Some gut bacteria may increase bowel cancer risk, research suggests – Nicola Davis – The Guardian

Certain Gut Bacteria May Contribute to Bowel Cancer – Technnology Networks

China Approves Alzheimer’s Treatment that Targets the Microbiome – Kerry Grens – The Scientist

Microbes on the market

Loop Genomics launches long-read Microbiome sequencing service at short-read price – Loop Genomics – PR Newswire

November 5, 2019

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Today, in this brief digest:  microbiome and metabolic signatures in IBS, the influence of US immigration on antimicrobial resistance gene spreading, the importance of microbiota delivery, the potential role of the microbiome in head and neck cancer oncogenesis, and more other papers. Have a nice day!

 

Human or General Microbiome

The internationalization of human microbiome research – Ana Maria Porras – Current Opinion in Microbiology 

Identification of Gut Microbiota and Metabolites Signature in Patients With Irritable Bowel Syndrome – Shengtao Zhu – Frontiers in Cellular and Infection Microbiology 

Incidence of Bloodstream Infections, Length of Hospital Stay, and Survival in Patients With Recurrent Clostridioides difficile Infection Treated With Fecal Microbiota Transplantation or Antibiotics: A Prospective Cohort Study – Gianluca Ianiro – Annals of Internal Medicine

Delivery to the gut microbiota: A rapidly proliferating research field – Adi Seifert – Advances in Colloid and Interface Science

Potential role of microbiome in oncogenesis, outcome prediction and therapeutic targeting for head and neck cancer – Ester Orlandi – Oral Oncology

Alterations in Oral Microbiota in HIV are Related to Decreased Pulmonary Function – Libing Yang – American Journal of Respiratory and Critical Care Medicine

Impact of delivery mode-associated gut microbiota dynamics on health in the first year of life – Marta Reyman – Nature Communication

Periodontopathogenic microbiota, infectious mechanisms and preterm birth: analysis with structural equations (cohort-BRISA) – Elisa Miranda Costa – Archives of Gynecology and Obstetrics

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

US immigration is associated with rapid and persistent acquisition of antibiotic resistance genes in the gut – Quentin Le Bastard – Clinical Infectious Diseases

 

Beneficial compounds and microbes

Changes in stool frequency following chicory inulin consumption, and effects on stool consistency, quality of life and composition of gut microbiota – Anthony W. Watson – Food Hydrocolloids

Prophages in Lactobacillus reuteri are associated with fitness trade-offs but can increase competitiveness in the gut ecosystem – Jee-Hwan Oh – Applied and Environmental Microbiology

 

Animal Microbiome / Animal Experiments

Effect of Metformin on Short-Term High-Fat Diet-Induced Weight Gain and Anxiety-Like Behavior and the Gut Microbiota – Shuqin Ji – Frontiers in Endocrinology 

Both gut microbiota and cytokines act to atherosclerosis in ApoE-/- mice – Qiuxia Liu – Microbial Pathogenesis 

The Effect of Clostridium butyricum on Gut Microbiota, Immune Response and Intestinal Barrier Function During the Development of Necrotic Enteritis in Chickens – Ting Huang – Frontiers in Microbiology

Lactic Acid Treatment of Cereals and Dietary Phytase Modified Fecal Microbiome Composition Without Affecting Expression of Virulence Factor Genes in Growing Pigs – Jutamat Klinsoda – Frontiers in Microbiology

Spatial and temporal axes impact ecology of the gut microbiome in juvenile European lobster (Homarus gammarus) – Corey C. Holt – The ISME Journal 

An antibiotic depleted microbiome drives severe Campylobacter jejuni-mediated Type 1/17 colitis, Type 2 autoimmunity and neurologic sequelae in a mouse model – Phillip T. Brooks – Journal of Neuroimmunology

 

Environmental Microbiome

Exploration of the antibiotic resistome in a wastewater treatment plant by a nine-year longitudinal metagenomic study – Xiaole Yin – Environment International

 

Bioinformatics

Embracing Ambiguity in the Taxonomic Classification of Microbiome Sequencing Data – Nidhi Shah – Frontiers in Genetics

Fueling ab initio folding with marine metagenomics enables structure and function predictions of new protein families – Yan Wang – Genome Biology

 

Techniques

Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing – Shailesh K. Shahi – JoVE

Optimizing microbiome sequencing for small intestinal aspirates: validation of novel techniques through the REIMAGINE study – Gabriela Guimaraes Sousa Leite – BMC Microbiology

November 4, 2019

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Good Morning! Highlights of today’s digest include a skin microbiome study in leprosy disease in Indian patients, another study shows findings from a mouse model and suggests vitamin B6 may have a therapeutic potential for treatment of chronic stress-induced gastritis. Finally, metagenomic sequencing and assembly of bacteria from different soils show how a soil type can influence genetic potential of bacteria for production of specialized metabolites such as antibiotics.

General microbiome

Review: Recent metabolomics and gene editing approaches for synthesis of microbial secondary metabolites for drug discovery and development – Sinha et al. – World Journal of Microbiology and Biotechnology

Human oral microbiome

Targeted polymerase chain reaction-based expression of putative halitogenic bacteria and volatile sulphur compound analysis among halitosis patients at a tertiary hospital in Nigeria – Adedapo et al. – Odontology

Human respiratory microbiome

The composition and functional protein subsystems of the human nasal microbiome in granulomatosis with polyangiitis: a pilot study – Wagner et al. – BMC Microbiome

Human skin microbiome

*16S rDNA based skin microbiome data of healthy individuals and leprosy patients from India – Bayal et al. – Nature Scientific Data

Human vaginal microbiome

Associations between the vaginal microbiome and Candida colonization in women of reproductive age – Tortelli et al. – American Journal of Obstetrics and Gynecology

Vaginal Biomarkers That Predict Cervical Length and Dominant Bacteria in the Vaginal Microbiomes of Pregnant Women – Witkin et al. – mBio

Human gut microbiome

Cohabitation is associated with a greater resemblance in gut microbiota which can impact cardiometabolic and inflammatory risk – Finnicum et al. – BMC Microbiology

Animal experiments

*Hydrogen sulfide‐mediated resistance against water avoidance stress‐induced gastritis by maintenance of gastric microbial homeostasis – Han et al. – MicrobiologyOpen

Animal microbiome

Bacterial communities associated with the midgut microbiota of wild Anopheles gambiae complex in Burkina Faso – Zoure et al. – Molecular Biology Reports

It’s what’s on the inside that counts: stress physiology and the bacterial microbiome of a wild urban mammal – Stothart et al. – Proceedings of the Royal Society B

Analysis of the Microbiota in the Fecal Material of Painted Turtles (Chrysemys picta) – Fugate et al. – Current Microbiology

Plant, root and soil microbiome

*Bacterial secondary metabolite biosynthetic potential in soil varies with phylum, depth, and vegetation type – Sharrar et al. – bioRxiv

Evidence for extensive anaerobic dechlorination and transformation of the pesticide chlordecone (C10Cl10O) by indigenous microbes in microcosms from Guadeloupe soil – Lomheim et al. – bioRxiv

Functional screening of a soil metagenome for DNA endonucleases by acquired resistance to bacteriophage infection – Mtimka et al. – Molecular Biology Reports

Exploring Actinobacteria Associated with Rhizosphere and Endosphere of the Native Alpine Medicinal Plant Leontopodium Nivale Subspecies Alpinum – Oberhofer et al. – Frontiers in Microbiology

Plant communities are more sensitive than soil microbial communities to multiple environmental changes in the Eurasian steppe – Zhou et al. – Global Ecology and Conservation

Floral organs act as environmental filters and interact with pollinators to structure the yellow monkeyflower (Mimulus guttatus) floral microbiome – Gomez and Ashman – Molecular Ecology

Characterization of Bacterial and Fungal Communities in Soils under Different Farming Systems. The Cacao Plantation in Sulawesi Island—Indonesia – Suwastika et al. – Eurasian Soil Science

Soil microbial biomass, activity and community structure as affected by mineral phosphorus fertilization in grasslands – She et al. – Applied Soil Ecology

Water and extremophile microbiome

Artificial substrata increase pond farming density of grass carp (Ctenopharyngodon idella) by increasing the bacteria that participate in nitrogen and phosphorus cycles in pond water – Li et al. – PeerJ

High-throughput sequencing revealed differences of microbial community structure and diversity between healthy and diseased Caulerpa lentillifera– Liang et al. – BMC MIcrobiology

Stochastic processes shape microeukaryotic community assembly in a subtropical river across wet and dry seasons – Chen et al. – BMC Microbiome

Built-environment

Prediction of microbial communities for urban metagenomics using neural network approach – Zhou et al. – Human Genomics

Food microbiology

Fermented cereal-based Munkoyo beverage: Processing practices, microbial diversity and aroma compounds – Phiri et al. – PLOS ONE

Phages and viruses

High Diversity and Novel Enteric Viruses in Fecal Viromes of Healthy Wild and Captive Thai Cynomolgus Macaques (Macaca fascicularis) – Sawaswong et al. – Viruses

Techniques

HS-SPME-GC-MS approach for the analysis of volatile salivary metabolites and application in a case study for the indirect assessment of gut microbiota – Campanella et al. – Analytical and Bioanalytical Chemistry

Unraveling interspecies interactions across heterogeneities in complex biofilm communities – Roder et al. -2920.14834 – Environmental Microbiology

The microbiome during lung development

Perinatal maternal antibiotic exposure augments lung injury in experimental bronchopulmonary dysplasia – Willis et al – Am J Physiol Lung Cell Mol Physiol

Editorial: Maternal Antibiotics Augment Hyperoxia Induced Lung Injury in Neonatal Mice – Lal et al – Am J Physiol Lung Cell Mol Physiol

Effects of Hyperoxia on Alveolar and Pulmonary Vascular Development in Germ Free Mice – Dolma et al – Am J Physiol Lung Cell Mol Physiol

Editorial: Mice without a microbiome are partially protected from lung injury by hyperoxia – Willis et al – Am J Physiol Lung Cell Mol Physiol

November 2, 2019

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Good Weekend morning for all!

Today’s digest is highly rich with plant and soil microbiome papers (notice a great Science paper regarding soil suppressiveness phenomena), as well as bacterial metabolism papers and more. Have a great and peaceful weekend!

Human and animal microbiome

Studying the gut virome in the metagenomic era: challenges and perspectives, Sanzhima Garmaeva, BMC Biology

Cortisol-induced signatures of stress in the fish microbiome, Tamsyn M Uren Webster, bioRxiv

Influence of pig gut microbiota on Mycoplasma hyopneumoniae susceptibility, Meera Surendran Nair, Veterinary Research

Natural variation in the contribution of microbial density to inducible immune dynamics, Derrick Jent, Molecular Ecology

Metabolism

The ecology and evolution of microbial metabolic strategies, Djordje Bajic & Alvaro Sanchez, Curr. Opin. In. Biotechnology

Is the enzymatic hydrolysis of soil organic phosphorus compounds limited by enzyme or substrate availability?, K.A. Jarosch ,SBB

Plant and Soil microbiome

Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome, Victor J. Carrio, Science

Drivers of the composition of active rhizosphere bacterial communities in temperate grasslands, Selma Vieira, ISME

Analysis of soil bacterial communities associated with genetically modified drought-tolerant corn, Jose G. Ibaraa ,Applid Soil Ecology

Phyllosphere of Submerged Plants in Bathing Lakes as a Reservoir of Fungi Potential Human Pathogens, Anna Biedunkiewicz, Microbial Ecology

Bacterial microbiome associated with the rhizosphere and root interior of crops in Saskatchewan, Canada, Jorge Cordero, Can. J. of Microbiology

Comparative metagenomics of two distinct biological soil crusts in the Tengger Desert, China, Jin-Yu Li , SBB

In planta bacterial multi-omics analysis illuminates regulatory principles underlying plant-pathogen interactions, Tatsuyas Nobori, bioRxiv

Air microbiome

Microbial communities in the tropical air ecosystem follow a precise diel cycle, Elena S. Gusareva, PNAS

Bioinformatics

Evaluating Bioinformatic Pipeline Performance for Forensic Microbiome Analysis, Kierra F. Kaszubinski, J. o. Forensic Sci.

October 28, 2019

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Monday morning digest is about microbiome and microbial metabolites in depression, neuronal function and fear extinction, and epilepsy in children; functional foods in lung cancer risk and microbiota based novel marker of colorectal cancer.

General microbiome

Gut microbial metabolites in depression: understanding the biochemical mechanisms – Giorgia Caspani – Microbial Cell

Engineering commensal bacteria to rewire host–microbiome interactions – In Young Hwang – Current Opinion in Biotechnology

Human microbiome

The composition and functional protein subsystems of the human nasal microbiome in granulomatosis with polyangiitis: a pilot study – Josef Wagner – Microbiome

Autoinducer-2 of gut microbiota, a potential novel marker for human colorectal cancer, is associated with the activation of TNFSF9 signaling in macrophages – Qing Li – Oncoimmunology

Distinct Gut Microbiota Composition and Functional Category in Children With Cerebral Palsy and Epilepsy – Congfu Huang – Frontiers in Pediatrics

Drug resistant gut bacteria mimic a host mechanism for anticancer drug clearance – Peter Spanogiannopoulos – BioRxiv

A comprehensive human minimal gut metagenome extends the host’s metabolic potential – Marcos Parras-Molto – BioRxiv

Enriched taxa were found among the gut microbiota of centenarians in East China – Na Wang – PlosOne

Animal experiments

The microbiota regulate neuronal function and fear extinction learning – Coco Chu – Nature

Syntrophic growth of alkaliphilic anaerobes controlled by ferric and ferrous minerals transformation coupled to acetogenesis – Daria G. Zavarzina – ISME Journal

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

Plant, root, soil microbiome

Root-associated microbiomes of wheat under the combined effect of plant development and nitrogen fertilization – Shuaimin Chen – Microbiome

Water microbiome

Deterministic and stochastic processes driving the shift in the prokaryotic community composition in wastewater treatment plants of a coastal Chinese city – Liyuan Hou – Applied Microbiology and Biotechnology

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

Probiotics/Prebiotics

Association of Dietary Fiber and Yogurt Consumption With Lung Cancer Risk – Jae Jeong Yang – JAMA Oncology

Effect of probiotics on the occurrence of nutrition absorption capacities in healthy children: a randomized double-blinded placebo-controlled pilot study – A. Ballini – European Review for Medical and Pharmacological Sciences

Microbes in the news

Can we predict the future? Bill Gates says yes, in this one area – CNBC

Exposure to Sunlight Boosts Good Gut Microbiome Bacteria, and Vitamin D Levels – Genetic Engineering and Biotechnology News

Harnessing the Power of Microbes to Fight Cancer – Medscape

October 26, 2019

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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 23, 2019

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A rich Digest today featuring the “Prime Editing” invented by the David R. Liu lab, which promises to correct 89% of point mutations, an ultra-deep metagenomic study of phages in aquatic systems and strain level interaction between bacteria and plants. Enjoy!

General microbiology

** Search-and-replace genome editing without double-strand breaks or donor DNA – Andrew V. Anzalone et al. – Nature

Resolving a piece of the archaeal lipid puzzle – Ann Pearson – PNAS

Antimicrobial resistance

Commentary: Surveillance and monitoring of antimicrobial resistance: limitations and lessons from the GRAM project – Jesse Schnall et al. – BMC Medicine

Preprint: In vitro Efficacy of Novel Glucan Synthase Inhibitor, Ibrexafungerp (SCY-078), Against Multidrug- and Pan-resistant Candida auris Isolates from the Outbreak in New York – Yan Chun Zhu et al. – bioRxiv
https://www.biorxiv.org/content/10.1101/811182v1.abstract

Review: Proteomics approach to understand bacterial antibiotic resistance strategies – Bo Peng et al. – Expert Review of Proteomics

Human oral microbiome

Subgingival Microbiota and Longitudinal Glucose Change: The Oral Infections, Glucose Intolerance and Insulin Resistance Study (ORIGINS) – R.T. Demmer et al. – Journal of Dental Research

Human gut microbiome

Review: Systems biology perspective for studying the gut microbiota in human physiology and liver diseases – Ozlem Altay et al. – EBioMedicine

Review: Intestinal microbiota and colorectal carcinoma: Implications for pathogenesis, diagnosis, and therapy – Ana Montalban-Arques & Michael Scharl – EBioMedicine

Perspective: Carbohydrate-based Prebiotics in Targeted Modulation of Gut Microbiome – Ka-Lung Lam & Peter Chi Keung Cheung – Journal of Agricultural and Food Chemistry

Metabolomics

Early Detection of Cystic Fibrosis Acute Pulmonary Exacerbations by Exhaled Breath Condensate Metabolomics – Xiaoling Zang et al. – Journal of Proteome Research

Food microbiome

Peer pressure: Evolutionary responses to biotic pressures in wine yeasts – C. G. Conacher et al. – FEMS Yeast Research

Animal experiments

Disruption of gut integrity and permeability contributes to enteritis in a fish-parasite model: a story told from serum metabolomics – Ariadna Sitjà-Bobadilla et al. – Parasites & Vectors

Animal microbiome

Estimating the burden of dengue and the impact of release of wMel Wolbachia-infected mosquitoes in Indonesia: a modelling study – Kathleen M. O’Reilly et al. – BMC Medicine

Plant, root and soil microbiome

Preprint: Insights into the desert living skin microbiome: geography, soil depth, and crust type affect biocrust microbial communities and networks in Mojave Desert, USA – Nuttapon Pombubpa et al. – bioRxiv

** Metabolites in the root exudates of groundnut change during interaction with plant growth promoting rhizobacteria in a strain-specific manner – Sravani Ankati & Appa Rao Podile – Journal of Plant Physiology

Environmental and biotic drivers of soil microbial β-diversity across spatial and phylogenetic scales – Loïc Chalmandrier et al. – Ecography

Soil hydrology drives ecological niche differentiation in a native prairie microbiome – James S Griffin et al. – FEMS Microbiology Ecology

Consistent host and organ occupancy of phyllosphere bacteria in a community of wild herbaceous plant species – Julien Massoni et al. – The ISME Journal

Effect of aridity and dune type on rhizosphere soil bacterial communities of Caragana microphylla in desert regions of northern China – Jiangli Gao et al. – PLoS One

Rhizosphere bacterial community in watermelon-wheat intercropping was more stable than in watermelon monoculture system under Fusarium oxysporum f. sp. niveum invasion – Hongjie Yu et al. – Plant and Soil

Phosphorus-acquisition strategies of canola, wheat and barley in soil amended with sewage sludges – C. Nobile et al. – Scientific Reports

Water and extremophile microbiome

Distinctive microbial communities in subzero hypersaline brines from Arctic coastal sea ice and rarely sampled cryopegs – Zachary S. Cooper et al. – FEMS Microbiology Ecology

Performance and microbial communities of different biofilm membrane bioreactors with pre-anoxic tanks treating mariculture wastewater – Huining Zhang et al. – Bioresource Technology

Do organic substrates drive microbial community interactions in Arctic snow? – Benoît Bergk Pinto et al. – Frontiers in Microbiology

Genomic signatures for sedimentary microbial utilization of phytoplankton detritus in a fast-flowing estuary – Mariya W. Smit et al. – Frontiers in Microbiology

pH control and microbial community analysis with HCl or CO2 addition in H2-based autotrophic denitrification – Wei Xing et al. – Water Research

Extremophilic nitrite-oxidizing Chloroflexi from Yellowstone hot springs – Eva Spieck et al. – The ISME Journal

Phages and viruses

** Phage-centric ecological interactions in aquatic ecosystems revealed through ultra-deep metagenomics – Vinicius S. Kavagutti et al. – Microbiome

Review: Phage Therapy with a Focus on the Human Microbiota – Sharita Divya Ganeshan & Zeinab Hosseinidoust – Antibiotics

Technology

Preprint: Gene copy normalization of the 16S rRNA gene cannot outweigh the methodological biases of sequencing – Robert Starke & Daniel Morais – bioRxiv

Review: Third generation sequencing in the clinical laboratory: Exploring the advantages and challenges of nanopore sequencing – Lauren M. Petersen et al. – Journal Clinical Microbiology

Microbes in the news

Which foods are beneficial for a healthy gut microbiome? – Ana Sandoiu – Medical News Today

Microbiome: Untapped source of novel antimicrobials – Delthia Ricks – Medical Xpress

The Problem With Labeling Gut Troubles ‘Dysbiosis’ – Elizabeth Preston – Undark

Bacteria for beauty: why you need to start thinking about your skin microbiome – Hannah Ebelthite – Telegraph

Research Finds These Mediterranean Diet Foods Protect The Gut Microbiome – Jamie Schneider – Mind Body Green

Are undiscovered antibiotics ‘silently waiting’ in our own bodies? Researchers scour microbiome for helpful genes – Shelly Fan – Genetic Literacy Project

Reprogramming the microbiome: Antara Lifesciences targets the human health space with dual targeted formulation – Tingmin Koe – Food Navigator Asia

Transient and long-term disruption of gut microbes after antibiotics – Jeff Hansen – UAB News

Microbes on the market

Microba, Psomagen Partner to Launch Microbiome Test in US – GenomeWeb

October 21, 2019

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Good Morning! Highlights of today’s digest include malaria parasite control by a symbiont: investigation of a host immune response and mosquito development in responds to the mosquito symbiont Asaia. On a relating note, please also check out Parasite Microbiome Project, which aims to provide interactive centralized platform and resources for researchers to dissect complex interactions between parasites, hosts and their respective microbiota. Finally, a plant-microbe interactions study aimed to define a core microbiota of wheat crop and a possibility to use certain microbial taxa for management of stripe rust, a widely occuring wheat leaf disease.

General microbiome
*Asaia Activates Immune Genes in Mosquito Eliciting an Anti-Plasmodium Response: Implications in Malaria Control – Cappelli et al. – Frontiers in Genetics

*Opinion: Parasite microbiome project: Grand challenges – Dheilly et al. – PLOS PATHOGENS

Human oral microbiome
Deep metagenomics examines the oral microbiome during dental caries, revealing novel taxa and co-occurrences with host molecules – Baker et al. – bioRxiv

Human gut microbiome
Review: Is there any association between gut microbiota and type 1 diabetes? A systematic review – Jamshidi et al. – Gut Pathogens

Differential Effects of Typical Korean Versus American-Style Diets on Gut Microbial Composition and Metabolic Profile in Healthy Overweight Koreans: A Randomized Crossover Trial – Shin et al. – Nutrients

Animal experiments
Colonic Microbiota and Metabolites Response to Different Dietary Protein Sources in a Piglet Model – Li et al. – Frontiers in Nutrition

Antibiotics and Host-Tailored Probiotics Similarly Modulate Effects on the Developing Avian Microbiome, Mycobiome, and Host Gene Expression – Ward et al. – mBio

Evaluation of the bacterial ocular surface microbiome in clinically normal cats before and after treatment with topical erythromycin – Darden et al. – PLOS ONE

Animal microbiome
Effects of Nutritional Deprivation and Re-Alimentation on the Feed Efficiency, Blood Biochemistry, and Rumen Microflora in Yaks (Bos grunniens) – Zou et al. – MDPI Animals

Plant, root and soil microbiome
* Wheat‐associated microbiota and their correlation with stripe rust reaction – Dai et al. – Journal of Applied Microbiology

Prophage induction mediated by quorum sensing signals alters soil bacterial community structure – Liang et al. – bioRxiv

Water and extremophile microbiome
Chemical and biological dispersants differently affect the bacterial communities of uncontaminated and oil-contaminated marine water – de Almeida Couto et al. – Brazilian Journal of Microbiology

Shift of Sediments Bacterial Community in the Black-Odor Urban River during In Situ Remediation by Comprehensive Measures – Zhang et al. – MDPI Water

Built environment
Pathogen surveillance in the informal settlement, Kibera, Kenya, using a metagenomics approach – Hendriksen et al. – PLOS ONE

October 20, 2019

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In today’s microbiome digest, several interesting studies have been covered including a) the relationships between multidrug-resistant bacteria (MDRB) colonization and dysbiosis after liver transplantation, b) microbiome and host transcriptome signature in patients with Atopic dermatitis or psoriasis, c) in the animal microbiome section- effect of host genetics on the gut microbiome composition of Avian, Bovine, and Drosophila models, d) a study which shows Composition of gut microbiota can modulate adaptive immune responses in chickens to vaccination against influenza viruses, e) CSMD, a bioinformatics pipeline specifically developed to generate accurate species-level microbiome profiles for clinical samples with low microbial loads and many more. Enjoy your Sunday with the latest microbiome feed.

General microbiome

Research highlight: Your microbiome is what you eat – Ashley York – Nature Reviews Microbiology

Gastro-intestinal and oral microbiome signatures associated with healthy aging – Harinder Singh – GeroScience

The future of microbiome‐based therapeutics in clinical applications – Anukriti Sharma – Clinical Pharmacology and Therapeutics

Human gut microbiome

Colonizing multidrug-resistant bacteria and the longitudinal evolution of the intestinal microbiome after liver transplantation – Medini K. Annavajhala – Nature Communication

Normal gut microbiome in NMDA receptor encephalitis – Julia Herken – Neurology, Neuroimmunology and Neuroinflammation

Urolithin Metabotypes Can Determine the Modulation of Gut Microbiota in Healthy Individuals by Tracking Walnuts Consumption over Three Days – Izaskun García-Mantrana – Nutrients 

Fecal microbiota transplantation results in bacterial strain displacement in patients with inflammatory bowel diseases – Manli Zou – FEBS openbio

Alterations to the Gastrointestinal Microbiome Associated with Methamphetamine Use among Young Men who have Sex with Men – Ryan R. Cook – Scientific Reports

Human skin microbiome

Microbe-host interplay in atopic dermatitis and psoriasis – Nanna Fyhrquist – Nature Communications

Human reproductive tract microbiome

Review: Maternal microbiome and the hypertensive disorder of pregnancy, preeclampsia – Kalie F Beckers – American Journal of Physiology Heart and Circulatory Physiology

Animal microbiome / Animal experiments

Changes in Microbiota and Development of Nonspecific Inflammation of Genitals in Female C57Bl/6 Mice after Aerosol Infection with Mycobacterium tuberculosis – S. I. Kayukova – Bulletin of Experimental Biology and Medicine

Land-use change has host-specific influences on avian gut microbiomes – Priscilla A. San Juan – The ISME Journal

Host genetic effects upon the early gut microbiota in a bovine model with graduated spectrum of genetic variation – Peixin Fan – The ISME Journal

Host determinants of among-species variation in microbiome composition in drosophilid flies – Karen L. Adair – The ISME Journal

Faecal microbiome sequences in relation to the egg-laying performance of hens using amplicon-based metagenomic association analysis – A. A. Elokil – Animal

Of microbes and mange: consistent changes in the skin microbiome of three canid species infected with Sarcoptes scabiei mites – Alexandra L. DeCandia – Parasites & Vectors

Commensal gut microbiota can modulate adaptive immune responses in chickens vaccinated with whole inactivated avian influenza virus subtype H9N2 – AlexanderYitbarek – Vaccine

Bioinformatics

CSMD: A computational subtraction-based microbiome discovery pipeline for species-level characterization of clinical metagenomic samples – Yu Liu – Bioinformatics

Microbiome news

MICROBE TALK: THE ROLE OF MICROBES IN CANCER

EcoBiome Innovation Center Launches MyEcoBiome™ Personal Soil Health Test