Category Archives: Techniques

October 15, 2018

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In today’s Digest, you’ll find a method for museum collections to identify helminth communities in small mammals, new results in the urinary and vaginal microbiome, the effects of HIV PrEP and broccoli on the gut microbiome, and fungal communities associated with plant roots. Happy reading!

General microbiome
Review: Probiotics importance and their immunomodulatory properties. – Bahman Yousefi – Journal of Cellular Physiology

Review: An insight into gut microbiota and its functionalities. – Atanu Adak – Cellular and Molecular Life Sciences

Gut-brain axis
Review: A primer on investigating the role of the microbiome in brain and cognitive development. – Caroline Kelsey – Developmental Psychobiology

Human vaginal microbiome
Preprint: Comparative genomics of human Lactobacillus crispatus isolates reveals genes for glycosylation and glycogen degradation: Implications for in vivo dominance of the vaginal microbiota – Charlotte van der Veer – bioRxiv

Human urinary microbiome
Community profiling of the urinary microbiota: considerations for low-biomass samples. – Lisa Karstens – Nature Reviews Urology

Human gut microbiome
Daily HIV pre-exposure prophylaxis (PrEP) with tenofovir disoproxil fumarate-emtricitabine reduced Streptococcus and increased Erysipelotrichaceae in rectal microbiota. – Michael P. Dubé – Scientific Reports

Broccoli consumption affects the human gastrointestinal microbiota – Jennifer L. Kaczmarek – The Journal of Nutritional Biochemistry

Intestinal dysbiosis in Inflammatory Bowel Disease associated with primary immunodeficiency. – Harry Sokol – Journal of Allergy and Clinical Immunology

Chronic kidney disease after 5/6 nephrectomy disturbs the intestinal microbiota and alters intestinal motility. – Kazuhiro Nishiyama – Journal of Cellular Physiology

Animal microbiome
Museum metabarcoding: a novel method revealing gut helminth communities of small mammals across space and time. – Stephen E. Greiman – International Journal for Parasitology

Showcasing the role of seawater in bacteria recruitment and microbiome stability in sponges. – Marta Turon – Scientific Reports

Animal experiments
Microcapsule of sweet orange essential oil changes gut microbiota in diet-induced obese rats. – Dahu Li – Biochemical and Biophysical Research Communications

Changes in ruminal and reticular pH and bacterial communities in Holstein cattle fed a high-grain diet. – Yo-Han Kim – BMC Veterinary Research

Plant, root, and soil microbiome
Dibutyl phthalate contamination remolded the fungal community in agro-environmental system – Xiao Kong – Chemosphere

Plant‐mediated effects of soil phosphorus on the root‐associated fungal microbiota in Arabidopsis thaliana – Izabela Fabiańska – New Phytologist

Water and extremophile microbiome
Prokaryotic Diversity and Distribution in Different Habitats of an Alpine Rock Glacier-Pond System. – I. Mania – Microbial Ecology

Preprint: Response of extremophile microbiome to a rare rainfall reveals a two-step adaptation mechanism – Gherman Uritskiy – bioRxiv

Bioinformatics
Preprint: Nomenclature Errors in Public 16S rRNA Gene Reference Databases – Kyle James Lesack – bioRxiv

October 14, 2018

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General microbiome

16S rRNA Gene Analysis with QIIME2 – Michael Hall, Microbiome Analysis

Predicting the Functional Potential of the Microbiome from Marker Genes Using PICRUSt – Gavin M. Douglas, Microbiome Analysis

Single-Cell Genomics of Microbial Dark Matter – Christian Rinke, Microbiome Analysis

An ecosystem framework for understanding and treating disease – Michael E. Hochberg, Foundation for Evolution, Medicine, and Public Health

Diet, Gut Microbes and Host Mate Choice – Philip T. Leftwich, BioEssays

Pregnancy and early life

Methods and Strategies to Examine the Human Breastmilk Microbiome – Lauren LeMay-Nedjelski, Microbiome Analysis

Multi-site human microbiome

Potential mechanisms linking gut microbiota and portal hypertension – Gyorgy Baffy, Liver International

Enlisting commensal microbes to resist antibiotic-resistant pathogens –  James W. Keith, Journal of Experimental Medicine

Human oral microbiome

Oral mucosa-on-a-chip to assess layer-specific responses to bacteria and dental materials – Christopher Rahimi, Biomicrofluidics

The effect of breastmilk and saliva combinations on the in vitro growth of oral pathogenic and commensal microorganisms – E. L. Sweeney, Scientific Reports

Human skin microbiome

A Natural History of Actinic Keratosis and Cutaneous Squamous Cell Carcinoma Microbiomes – David L. A. Wood, mBio

Human gut microbiome

The microbiome of Crohn’s disease aphthous ulcers – Claire L. O’Brien, Gut Pathogens

Gut microbiome can be restored without adverse events after Helicobacter pylori eradication therapy in teenagers – Takuji Gotoda, Helicobacter

Animal microbiome

Rethinking the Coral Microbiome: Simplicity Exists within a Diverse Microbial Biosphere – Alejandra Hernandez-Agreda, mBio

Host differentiation and compartmentalization of microbial communities in the azooxanthelate cupcorals Tubastrea coccinea and Rhizopsammia goesi in the Caribbean – Aschwin H. Engelen, Frontiers in Microbiology

Comparison of intestinal microbes in female and male Chinese concave‐eared frogs (Odorrana tormota) and effect of nematode infection on gut bacterial communities – Yilin Shu, Microbiology Open

Change in the intestinal bacterial community structure associated with environmental microorganisms during the growth of Eriocheir sinensis – Chenhe Wang, Microbiology Open

Protective role of the vulture facial skin and gut microbiomes aid adaptation to scavenging – Marie Lisandra Zepeda Mendoza, Acta Veterinaria Scandinavica

Animal experiments 

Fecal Microbiota Transplantation Beneficially Regulates Intestinal Mucosal Autophagy and Alleviates Gut Barrier Injury – Saisai Cheng, mSystems

Host genetics and the rumen microbiome jointly associate with methane emissions in dairy cows – Gareth Frank Difford, Plos Genetics

Inhibitory effects of dietary soy isoflavone and gut microbiota on contact hypersensitivity in mice – Takao Nagano, Food Chemistry

Lichen microbiome

Plasticity of a holobiont: desiccation induces fasting-like metabolism within the lichen microbiota – Tomislav Cernava, ISME

Plant, root, and soil microbiome

Short-term effect of Eucalyptusplantations on soil microbial communities and soil-atmosphere methane and nitrous oxide exchange – Caroline A. Cuer, Scientific Reports

Microbial community structure and functional potential of lava-formed Gotjawal soils in Jeju, Korea – Jong-Shik Kim, Plos One

Diversity of fungi and bacteria in species-rich grasslands increases with plant diversity in shoots but not in roots and soil – Diana Navrátilová, FEMS Microbiology Ecology

Variation in ectomycorrhizal fungal communities associated with Silver linden (Tilia tomentosa) within and across urban areas – Maarten Van Geel, FEMS Microbiology Ecology

Influence of triazole pesticides on tillage soil microbial populations and metabolic changes – Praveen Satapute, Science of The Total Environment

Soil Nutrient Status and Microbial Communities as Influenced by Bio-Fuel Trees Plantation – Agnes Imoya P. O., Environment and Ecology

Various Phyllosphere and Soil Bacterial Communities of Natural Grasses and the Impact Factors in a Copper Tailings Dam – Tong Jia, Current Microbiology

Effects of wine-cap Strophariacultivation on soil nutrients and bacterial communities in forestlands of northern China – Sai Gong, PeerJ

Effect of pH and temperature on microbial community structure and carboxylic acid yield during the acidogenic digestion of duckweed – Ozgul Calicioglu, Biotechnology for Biofuels

Trichoderma harzianum T-22 and BOL-12QD inhibit lateral root development of Chenopodium quinoa in axenic co-culture – Oscar M. Rollano-Peñaloza, Cogent Biology

Water, wastewater, and extremophile microbiome

Microbial communities in the nepheloid layers and hypoxic zones of the Canary Current upwelling system – Stefan Thiele, Microbiology Open

The effects of litter quality and living plants on the home-field advantage of aquatic macrophyte decomposition in a eutrophic urban lake, China – Van Biak Luai, Science of The Total Environment

The microbiome and antibiotic resistance in integrated fishfarm water: Implications of environmental public health – Gary Klase, Science of The Total Environment

Changes in the drinking water microbiome: effects of water treatments along the flow of two drinking water treatment plants in a urbanized area, Milan (Italy) – Antonia Bruno, Frontiers in Microbiology

Organic particles: heterogeneous hubs for microbial interactions in aquatic ecosystems – Mina Bizic-Ionescu, Frontiers in Microbiology

Importance of denitrification driven by the relative abundances of microbial communities in coastal wetlands – Yan Zhang, Environmental Pollution

A nearly uniform distributional pattern of heterotrophic bacteria in the Mariana Trench interior – Jiwei Tian, Deep Sea Research Part I: Oceanographic Research Papers

Patterns of permissiveness towards broad host range plasmids in microbial communities across the urban water cycle in Europe – Arnaud Dechesne, Abstract from 17th International Symposium on Microbial Ecology

Biodegradation of sulfamethoxazole by a bacterial consortium of Achromobacter denitrificans PR1 and Leucobacter sp. GP – Ana C. Reis, Applied Microbiology and Biotechnology

Molecular and microbiological insights on the enrichment procedures for the isolation of petroleum degrading bacteria and fungi – Giulia Spini, Frontiers in Microbiology

Microbial Ecology of South Florida Surface Waters: Examining the Potential for Anthropogenic Influences – Chase P. Donnelly, HCNSO Student Theses and Dissertations

Antarctic heterotrophic bacterium Hymenobacter nivis P3Tdisplays light‐enhanced growth and expresses putative photoactive proteins – Mia Terashima, Environmental Microbiology Reports

Microbial genomics

Comprehensive analysis of intra- and interpatient evolution of enterovirus D68 by whole-genome deep sequencing – Robert Dyrdak, bioRxiv

Leveraging single-cell genomics to expand the fungal tree of life – Steven R. Ahrendt, Nature Microbiology

Microbes in space

Transcriptomic responses of Serratia liquefaciens cells grown under simulated Martian conditions of low temperature, low pressure, and CO2-enriched anoxic atmosphere – Patricia Fajardo-Cavazos, Scientific Reports

Food microbiology

Metagenomic analysis and the functional profiles of traditional fermented pork fat ‘sa-um’ of Northeast India – Surajit De Mandal, AMB Express

Probiotics / prebiotics

Gut microbiome modulation during treatment of mucositis with the dairy bacterium Lactococcus lactis and recombinant strain secreting human antimicrobial PAP – Rodrigo Carvalho, Scientific Reports

In Vitro Fermentation of Selected Prebiotics and Their Effects on the Composition and Activity of the Adult Gut Microbiota – Sophie Fehlbaum, International Journal of Molecular Sciences

Techniques

Assessing the ratio of Bacillus spores and vegetative cells by shotgun proteomics – Charlotte Mappa, Environmental Science and Pollution Research

 

October 11, 2018

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The effects of chronic ethanol ingestion on the fruit fly microbiota, engineering the mosquito microbiota to produce an antiplasmodial effector, how temperature change affects an ecosystems biodiversity and function.

General microbiome

Changes in temperature alter the relationship between biodiversity and ecosystem functioning – Francisca C García – PNAS

Human respiratory microbiome

Respiratory Microbiota Predicts Clinical Disease Course of Acute Otorrhea in Children With Tympanostomy Tubes – Wing Ho Man – The Pediatric Infectious Disease Journal

Human oral microbiome

Carious status and supragingival plaque microbiota in hemodialysis patients – Qi Yue – PLOS ONE

Human gut microbiome

Review: Fecal Microbiota Transplantation for the Management of Clostridium difficile Infection – Raghavendra Paknikar – Surgical Infections

Review: Diet, gut microbiome and indoxyl sulphate in chronic kidney disease patients – Chih-Yu Yang – Nephrology

Animal experiments

Risks Related to High-Dosage Recombinant Antimicrobial Peptide Microcin J25 in Mice Model: Intestinal Microbiota, Intestinal Barrier Function and Immune Regulation – Haitao Yu – Journal of Agricultural and Food Chemistry

Microbial Changes and Host Response in F344 Rat Colon Depending on Sex and Age Following a High-Fat Diet – Sun Min Lee – Frontiers in Microbiology

Animal microbiome

Pre-print: Chronic ethanol ingestion impairs Drosophila melanogaster health in a microbiome-dependent manner – James Angus Chandler – bioRxiv

Blood meal-induced inhibition of vector-borne disease by transgenic microbiota – Jackie L Shane – Nature Communications

Plant, root, and soil microbiome

Friends or foes in the rhizosphere: traits of fluorescent Pseudomonas that hinder Azospirillum brasilense growth and root colonization – Guillermo A Maroniche – FEMS Microbiology Ecology

Water and extremophile microbiome

Seasonal variation of extracellular enzymatic activity in marine snow-associated microbial communities and their impact on the surrounding water – Ingrid Ivančić – FEMS Microbiology Ecology

Food microbiology

Comparative evaluation of spoilage-related bacterial diversity and metabolite profiles in chilled beef stored under air and vacuum packaging – Ahmad Rois Mansur – Food Microbiology

Assessment of the non-lactic acid bacteria microbiota in fresh cucumbers and commercially fermented cucumber pickles brined with 6% NaCl – Ilenys M Pérez-Díaz – Food Microbiology

Bioinformatics

Bayesian Inference of Microbial Community Structure from Metagenomic Data Using BioMiCo – Katherine A Dunn – Microbiome Analysis (Book)

Metabolomics

Targeted Metabolic Profiling Indicates Apple Rootstock Genotype-Specific Differences in Primary and Secondary Metabolite Production and Validate Quantitative Contribution From Vegetative Growth – Rachel Leisso – Frontiers in Plant Science

Techniques

Analyzing Metabolic Pathways in Microbiomes – Mobolaji Adeolu – Microbiome Analysis (Book)

More microbes

Prevalence of Yersinia Species in the Ileum of Crohn’s Disease Patients and Controls – Guillaume Le Baut – Frontiers in Cellular and Infection Microbiology

October 10, 2018

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Microbiota conservation and diversity in butterfly species, air and waterborne microbiota of a pharmaceutical plant, the a study on the oral microbiota of rugby players.

General microbiome

Preserving microbial diversity – Maria G Dominguez Bello – Science

Pregnancy and early life

Evaluation of patient- versus provider-collected vaginal swabs for microbiome analysis during pregnancy – Kristine M Wylie – BMC Research Notes

Human skin microbiome

The microbiome of the “sterile” pustules in palmoplantar pustulosis – Kana Masuda-Kuroki – Experimental Dermatology

Human oral microbiome

Oral health and microbiota status in professional rugby players: A case-control study – Matthieu Minty – Journal of Dentistry

Oral Bacteriome Compositions Identified by 16S rRNA Metagenomics in a Randomly Selected “Healthy” Nigerian Male and Female Subjects – Kingsley C Anukam – International Journal of Research and Reports in Dentistry

Human gut microbiome

Review: The Gut-Brain Axis and the Microbiome: Mechanisms and Clinical Implications – Vadim Osadchiy – Clinical Gastroenterology and Hepatology

Animal experiments

Replication Study: Intestinal inflammation targets cancer-inducing activity of the microbiota – Kathryn Eaton – eLIFE

Animal microbiome

Pre-print: Conserved microbiota among young Heliconius butterfly species – Bas van Schooten – PeerJ

Gastrointestinal Microbial Flora in Wild and Captive Olive Baboons (Papio anubis) – Senelwa Davis Lugano – American Journal of Infectious Diseases and Microbiology

Plant, root, and soil microbiome

Rhizosphere microbiome structure alters to enable wilt resistance in tomato – Min-Jung Kwak – Nature Biotechnology

Apple rootstocks of different nitrogen tolerance affect the rhizosphere bacterial community composition – Xiaofen Chai – Journal of Applied Microbiology

Effects of consecutive monoculture of sweet potato on soil bacterial community as determined by pyrosequencing – Huan Li – Journal of Basic Microbiology

Ectomycorrhizal fungi may not act as a barrier inhibiting host plant absorption of heavy metals – Yangze Tang – Chemosphere

Pre-print: Co-occurrence patterns of litter decomposing communities in mangroves indicate a robust community resistant to disturbances – Rodrigo G Taketani – PeerJ

Water and extremophile microbiome

Structure of Microbial Mats in the Mramornaya Bay (Crimea) Coastal Areas – NV Pimenov – Microbiology

Pangenomic comparison of globally distributed Poribacteria associated with sponge hosts and marine particles – Sheila Powell – The ISME Journal

High diversity of thermophilic cyanobacteria in Rupite hot spring identified by microscopy, cultivation, single-cell PCR and amplicon sequencing – Otakar Strunecky – Extremophiles

Built environment

Air and waterborne microbiome of a pharmaceutical plant provide insights on spatiotemporal variations and community resilience after disturbance – Filippo Pacchioni – BMC Microbiology

Food microbiology

Review: The Effect of Gluten-Free Diet on Health and the Gut Microbiota Cannot Be Extrapolated from One Population to Others – Jose F Garcia-Marzcorro – Nutrients

Phages and viruses

Characterization of dog serum virome from Northeastern Brazil – MN Weber – Virology

Bioinformatics

‘NetShift’: a methodology for understanding ‘driver microbes’ from healthy and disease microbiome datasets – Bhusan K Kuntal – The ISME Journal

Techniques

A Simple In Vitro Gut Model for Studying the Interaction between Escherichia coli and the Intestinal Commensal Microbiota in Cecal Mucus – Matthew E Mokszycki – Applied and Environmental Microbiology

Science, career, and publishing

Inoculating science against potential pandemics and information hazards – Kevin M Esvelt – PLOS Pathogens

October 8, 2018

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The Digest is back with a lot of plant and soil microbiome papers. Highlights include how nematodes may alter microbial communities to benefit the host, a review on host-microbe interactions affecting acne, and a common garden study on causal relationship between plant phenotype and its rhizosphere microbiome.

General microbiology

A Candida auris Outbreak and Its Control in an Intensive Care Setting – David W. Eyre et al. – New England Journal of Medicine

** Diplogastrellus nematodes are sexually transmitted mutualists that alter the bacterial and fungal communities of their beetle host – Cristina C. Ledón-Rettig et al. – PNAS

Cross-talk between MarR-like transcription factors coordinates the regulation of motility in uropathogenic Escherichia coli – Courtney L. Luterbach & Harry L.T. Mobley – Infection and Immunity

Antibiotic resistance

Environmental dimensions of antibiotic resistance: Assessment of basic science gaps – Kornelia Smalla et al. – FEMS Microbiology Ecology

Human skin microbiome

** Host-microbiome interactions and recent progress into understanding the biology of acne vulgaris – Alan M. O’Neill & Richard L. Gallo – Microbiome

Human oral microbiome

Molecular analysis of oral microflora in patients with primary Sjögren’s syndrome by using high-throughput sequencing – Zhifang Zhou et al. – PeerJ

Human repiratory microbiome

Genomics, Microbiomics, Proteomics, and Metabolomics in Bronchopulmonary Dysplasia – Charitharth Vivek Lal et al. – Seminars in Perinatology

Human gut microbiome

Association of metformin administration with gut microbiome dysbiosis in healthy volunteers – Ilze Elbere et al. – PLoS One

Oral probiotic combination of Lactobacillus and Bifidobacterium alters the gastrointestinal microbiota during antibiotic treatment for Clostridium difficile infection – T. J. De Wolfe et al. – PLoS One

Review: Impact of the gut microbiota on chemical risk assessment – Tine Rask Licht & Martin Iain Bahl – Current Opinion in Toxicology

Alterations in gut bacterial and fungal microbiomes are associated with bacterial Keratitis, an inflammatory disease of the human eye – Rajagopalaboopathi Jayasudha et al. – Journal of Biosciences

The Microbiome and Radiation Induced-Bowel Injury: Evidence for Potential Mechanistic Role in Disease Pathogenesis – Tomoko Kumagai et al. – Nutrients

Impact of Agaricus bisporus Mushroom Consumption on Gut Health Markers in Healthy Adults – Julie Hess et al. – Nutrients

Animal experiments

Effect of probiotic treatment on the clinical course, intestinal microbiome, and toxigenic Clostridium perfringens in dogs with acute hemorrhagic diarrhea – Anna-Lena Ziese et al. – PLoS One

Caloric restriction promotes functional changes involving short-chain fatty acid biosynthesis in the rat gut microbiota – Alessandro Tanca et al. – Scientific Reports

Animal microbiome

Evidence for Gut-Associated Serratia symbiotica in Wild Aphids and Ants Provides New Perspectives on the Evolution of Bacterial Mutualism in Insects – François Renoz et al. – Microbial Ecology

Plant, root and soil microbiome

Vertical stratification of bacteria and the chemical compounds in crude oil-contaminated soil layers of the semi-deserted Dzungharian Basin – Jiang-Ke Yang et al. – PLoS One

Dynamics of Changes in Microbiological Composition of Stored Sediments – Aleksandra Sałata et al. – Journal of Ecological Engineering

Review: Nano-scale undead drivers of microbial life, biogeochemical turnover and ecosystem functions – Yakov Kuzyakov & Kyle Mason-Jones – Soil Biology and Biochemistry

Response of microbial communities to different organochlorine pesticides (OCPs) contamination levels in contaminated soils – Yu Du et al. – Chemosphere

Changes in the soil microbial communities of alpine steppe at Qinghai-Tibetan Plateau under different degradation levels – Heng Zhou et al. – Science of The Total Environment

Responses of the endophytic bacterial communities of Juncus acutus to pollution with metals, emerging organic pollutants and to bioaugmentation with indigenous strains – Evdokia Syranidou et al. – Frontiers in Plant Science

Desert and steppe soils exhibit lower autotrophic microbial abundance but higher atmospheric CO2 fixation capacity than meadow soils – Kang Zhao et al. – Soil Biology and Biochemistry

Bacterial microbiota and metabolic character of traditional sour cream and butter in Buryatia, Russia – Jie Yu et al. – Frontiers in Microbiology

Interactions between soil properties, soil microbes and plants in remnant-grassland and old-field areas: a reciprocal transplant approach – Monique E. Smith et al. – Plant and Soil

Exploration of the Biosynthetic Potential of the Populus Microbiome – Patricia M. Blair et al. – mSystems

Soil microbial community structure in the rhizosphere of Robinia pseudoacacia L. seedlings exposed to elevated air temperature and cadmium-contaminated soils for 4  years – X. Jia et al. – Science of The Total Environment

** Plant Phenotypic Traits Eventually Shape Its Microbiota：A Common Garden Test – Yunshi Li et al. – Frontiers in Microbiology

Soil Type-Dependent Interactions of P-Solubilizing Microorganisms with Organic and Inorganic Fertilizers Mediate Plant Growth Promotion in Tomato – Isaac Kwadwo Mpanga et al. – Agronomy

Water and extremophile microbiome

Distinct community structure and microbial functions of biofilms colonizing microplastics – Lingzhan Miao et al. – Science of The Total Environment

Mature biofilm communities on synthetic polymers in seawater – Specific or general? – Inga V. Kirstein et al. – Marine Environmental Research

Phages and viruses

Virome definition in cerebrospinal fluid of patients with neurological complications after hematopoietic stem cell transplantation – C. Pou et al. – Journal of Clinical Virology

Metagenomic sequencing from mosquitoes in China reveals a variety of insect and human viruses – Pengpeng Xiao et al. – Frontiers in Cellular and Infection Microbiology

Technology

Review: Practical considerations for sampling and data analysis in contemporary metagenomics-based environmental studies – Christopher Staley & Michael J. Sadowsky –

Bioinformatics

Postnovo: Post-Processing Enables Accurate and FDR-Controlled De Novo Peptide Sequencing – Samuel E. Miller et al. – Journal of Proteome Research

October 1, 2018

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To kick off October, we have a Microbiome Digest filled with ecological approaches to microbial communities and techniques for analysis. Plus: what the Nobels are doing to encourage diversity, and what ecstasy does to octopuses. Happy reading!

General Microbiome
Neutral and selective dynamics in a synthetic microbial community. – Nate J. Cira – PNAS

Microbiomes as Metacommunities: Understanding Host-Associated Microbes through Metacommunity Ecology. – Elizabeth Theresa Miller – Trends in Ecology and Evolution

Clinician Guide to Microbiome Testing – Christopher Staley – Digestive Diseases and Sciences

Human Urinary Microbiome
NMR-based metabonomic approach reveals changes in the urinary and fecal metabolome caused by resveratrol. – Gabriela Torres Santiago – Journal of Pharmaceutical and Biomedical Analysis

Urinary microbes and postoperative urinary tract infection risk in urogynecologic surgical patients – Krystal J. Thomas-White – International Urogynecology Journal

Human Gut Microbiome
Metagenomic insights into resistant starch degradation by human gut microbiota. – Marius Vital – Applied and Environmental Microbiology

Pathogenic functions of host microbiota. – Silke Rath – Microbiome

Prebiotics and Probiotics in Digestive Health – Eamonn M.M. Quigley – Clinical Gastroenterology and Hepatology

Animal Experiments
Isolation and characterization of the Bacillus cereus BC7 strain, which is capable of zearalenone removal and intestinal flora modulation in mice. – Yue Wang – Toxicon

Sulfated Polysaccharide from Sea Cucumber and its Depolymerized Derivative Prevent Obesity in Association with Modification of Gut Microbiota in High‐Fat Diet‐Fed Mice – Zhenjun Zhu – Molecular Nutrition and Food Research

Animal Microbiome
Cultivable microbiome and its resistance to antimicrobials isolated from Zaprionus indianus – Graziele Aparecida Fernandes da Cruz – Environmental Monitoring and Assessment

Plant, root, and soil microbiome
Impact of weather conditions, leaf age and irrigation water disinfection on the major epiphytic bacterial genera of baby spinach grown in an open field – Pilar Truchado – Food Microbiology

Influence of light on plant – phyllosphere interaction – Sofia D. Carvalho – Frontiers in Plant Science

Techniques
PCR-based quantification of taxa-specific abundances in microbial communities: Quantifying and avoiding common pitfalls. – Fabian Bonk – Journal of Microbiological Methods

Genomes from uncultivated prokaryotes: a comparison of metagenome-assembled and single-amplified genomes. – Johannes Alneberg – Microbiome

Progress of analytical tools and techniques for human gut microbiome research – Eun-Ji Song – Journal of Microbiology

Preprint: Dynamic interaction network inference from longitudinal microbiome data – Jose Lugo-Martinez – bioRxiv

Science, Publishing, and Career
What the Nobels are — and aren’t — doing to encourage diversity – Elizabeth Gibney -Nature

Alyson’s Non-Microbiology Pick
What Ecstasy Does to Octopuses – Ed Yong – The Atlantic

September 30, 2018

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General microbiome

Multi-omics integrative analysis with genome-scale metabolic model simulation reveals global cellular adaptation of Aspergillus niger under industrial enzyme production condition – Hongzhong Lu, Scientific Reports

Botulinum Neurotoxin-Producing Bacteria. Isn’t It Time that We Called a Species a Species? – Theresa Smith, mBio

Sizing Up the Uncultured Microbial Majority – Laura A. Hug, mSystems

Pregnancy and early life

TLR Activation and Allergic Disease: Early Life Microbiome and Treatment – Kathryn R. Michels, Current Allergy and Asthma Reports

Human gut microbiome

Lifestyle Factors Affecting the Gut Microbiota’s Relationship with Type 1 Diabetes – Elke Gülden, Current Diabetes Reports

Animal experiments

MAVS deficiency induces gut dysbiotic microbiota conferring a proallergic phenotype – Emilie Plantamura, PNAS

Assessing microbial contamination and antibiotic resistant bacteria using zebra mussels (Dreissena polymorpha) – Maria Alexandra Bighiu, Science of The Total Environment

Plant, root, and soil microbiome

Use of sugarcane–soybean intercropping in acid soil impacts the structure of the soil fungal community – Tengxiang Lian, Scientific Reports

Aphid infestation in the phyllosphere affects primary metabolic profiles in the arbuscular mycorrhizal hyphosphere – Carmina Cabral, Scientific Reports

Antioxidative response in leaves and allelochemical changes in root exudates of Ricinus communis under Cu, Zn, and Cd stress – Shuifeng Wang, Environmental Science and Pollution Research

Biochemical and microbiological activity of soil contaminated with o-cresol and biostimulated with Perna canaliculus mussel meal – Magdalena Zaborowska, Environmental Monitoring and Assessment

Assessment of Soil Microbial Status under Different Land Use Systems in North Western Zone of Kashmir – Fozia Shafiq Wani, International Journal of Current Microbiology and Applied Sciences

Culturable Foliar Fungal Endophytes of Mangrove Species in Bicol Region, Philippines – Jonathan Jaime G. Guerrero, Philippine Journal of Science

Developmental stage has a greater effect than Cry1Ac expression in transgenic cotton on the phyllosphere mycobiome – Jiangang Pan, Canadian Journal of Microbiology

Interaction of Brassicaceae seed meal soil amendment and apple rootstock genotype on microbiome structure and replant disease suppression – Likun Wang, Phytopathology

Response of soil micro-ecology to different levels of cadmium in alkaline soil – Bin Wu, Ecotoxicology and Environmental Safety

Variation of soil bacterial communities along a chronosequence of Eucalyptusplantation – Jiayu Li, PeerJ

Long-term nitrogen fertilization elevates the activity and abundance of nitrifying and denitrifying microbial communities in an upland soil: implications for nitrogen loss from intensive agricultural systems – Fenghua Wang, Frontiers in Microbiology

Comparative assessment of autochthonous bacterial and fungal communities and microbial biomarkers of polluted agricultural soils of the Terra dei Fuochi – Valeria Ventorino, Scientific Reports

Genome guided investigation of antibiotics producing actinomycetales strain isolated from a Macau mangrove ecosystem – Dini Hu, Scientific Reports

Water and extremophile microbiome

Community Structure, Dynamics and Interactions of Bacteria, Archaea and Fungi in Subtropical Coastal Wetland Sediments – Man Kit Cheung, Scientific Reports

Discovering novel hydrolases from hot environments – Roland Wohlgemuth, Biotechnology Advances

Microbes in space

Meta-analysis of data from spaceflight transcriptome experiments does not support the idea of a common bacterial “spaceflight response” – Michael D. Morrison, Scientific Reports

Food microbiology

The effect of sulfur dioxide addition at crush on the fungal and bacterial communities and the sensory attributes of Pinot gris wines – Sydney C. Morgan, International Journal of Food Microbiology

Waste microbiome

Bioelectrochemical enhancement of methane production in anaerobic digestion of food waste – Jae-Min Choi, International Journal of Hydrogen Energy

Performance and Microbial Community Analysis of Bioaugmented Activated Sludge System for Indigo Production from Indole – Xuwang Zhang, Applied Biochemistry and Biotechnology

Probiotics / prebiotics

Bifidobacterium pseudocatenulatum CECT 7765 supplementation improves inflammatory status in insulin-resistant obese children – Jesús Sanchis-Chordà, European Journal of Nutrition

Bioinformatics

Design and implementation of semester long project and problem based bioinformatics course – Geetha Saarunya, F1000 Research

Techniques

NMR-Based Metabolomic Approach To Elucidate the Differential Cellular Responses during Mitigation of Arsenic(III, V) in a Green Microalga – Neha Arora, ACS Omega

September 28, 2018

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Happy Friday! Today we have a long Digest with several interesting reviews and preprints. Learn about the fallopian tube microbiome, the bacterial communities in Icelandic volcanic deposits, the effect of ammonia on anaerobic digesters, skin defense peptides that modulate a frog’s resistance to a pathogen, and a new tool for constructing pan-genomes from shotgun metagenomic data. Enjoy!

General Microbiome
The mammalian mycobiome: A complex system in a dynamic relationship with the host
– Ghee Chuan Lai – WIREs Systems Biology and Medicine

Niche and fitness differences determine invasion success and impact in laboratory bacterial communities. – Shao-peng Li – ISMEJ

Pregnancy and Early Life
Fallopian tube microbiota: evidence beyond DNA. -Elise S Pelter – Future Microbiology

Human Oral Microbiome
Titanium as a modifier of the peri‐implant microbiome structure – Diane Daubert – Clinical Implant Dentistry and Related Research

Human Gut Microbiome
Linking gut microbiota, metabolic syndrome and economic status based on a population-level analysis. – Yan He – Microbiome

Metagenomic analysis of intestinal mucosa revealed a specific eukaryotic gut virome signature in early-diagnosed inflammatory bowel disease – Federica Ungaro – Gut Microbes

Obesity-Linked Gut Microbiome Dysbiosis Associated with Derangements in Gut Permeability and Intestinal Cellular Homeostasis Independent of Diet. – Ravinder Nagpal – Journal of Diabetes Research

Preprint: Social relationships, social isolation, and the human gut microbiota – Kimberly Dill-McFarland – bioRxiv

Review: Gut Microbiota: IgA Protects the Pioneers – Whitman B. Schofield – Current Biology

Review: The Gut Microbiota and Dysbiosis in Autism Spectrum Disorders. – Heather K. Hughes – Current Neurology and Neuroscience Reports

Animal Experiments
Modulation of Pulmonary Microbiota by Antibiotic or Probiotic Aerosol Therapy: A Strategy to Promote Immunosurveillance against Lung Metastases. – Valentino Le Noci – Cell Reports

Nod2 Deficiency in mice is Associated with Microbiota Variation Favouring the Expansion of mucosal CD4+ LAP+ Regulatory Cells – A. Butera – Scientific Reports

Fermented Astragalus in diet altered the composition of fecal microbiota in broiler chickens – Hongxing Qiao – AMB Express

Chronic nonbacterial prostate inflammation in a rat model is associated with changes of gut microbiota that can be modified with a galactoglucomannan‐rich hemicellulose extract in diet – Yvonne Konkol – BJU International

Animal Microbiome
Microbiota and skin defense peptides may facilitate coexistence of two sympatric Andean frog species with a lethal pathogen. – Sandra V. Flechas – ISMEJ

Green forage and fattening duration differentially modulate cecal microbiome of Wanxi white geese. – Xingyong Chen – PLoS One

Plant, root, and soil microbiome
Succession and diversity of microbial communities in landfills with depths and ages and its association with dissolved organic matter and heavy metals. – Si-jia Liu – Science of The Total Environment

Characterization of the bacterial communities on recent Icelandic volcanic deposits of different ages.– Bo Byloos – BMC Microbiology

Linking microbial co-occurrences to soil ecological processes across a woodland-grassland ecotone. – Samiran Banerjee – Ecology and Evolution

Water and Extremophile Microbiome
Independent and interactive effects of reduced seawater pH and oil contamination on subsurface sediment bacterial communities – António Louvado – Environmental Science and Pollution Research

Effects of nutrient enrichment on surface microbial community gene expression in the oligotrophic North Pacific Subtropical Gyre – J. C. Robidart – ISMEJ

Food and Industrial Microbiology
Lacto-fermented sauerkraut improves symptoms in IBS patients independent of product pasteurisation – a pilot study – Elsa Sandberg Nielsen – Food & Function

Relationship between microbial community, operational factors and ammonia inhibition resilience in anaerobic digesters at low and moderate ammonia background concentrations. – Y. Lu – New Biotechnology

Microbial Community Enhances Biodegradation of Bisphenol A Through Selection of Sphingomonadaceae. – Seungdae Oh – Microbial Ecology

Bioinformatics
MSPminer: abundance-based reconstitution of microbial pan-genomes from shotgun metagenomic data. – Florian Plaza Oñate – Bioinformatics

Preprint: A unified framework for unconstrained and constrained ordination of microbiome read count data – Stijn Hawinkel – bioRxiv

September 26, 2018

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Today’s mid-week short digest includes articles on integrating human genetics and the gut microbiome to find potent risk factors in cardiovascular disease; comparison of bariatric surgery techniques on the gut microbiota; transmission of antibiotic resistance genes from mothers to infants and importance of breastfeeding. News updates on growth prediction of human microbiome based diagnostics and first rapid test to determine Bifidobacteria in infant gut!

Human gut microbiome

Individual variations in cardiovascular-disease-related protein levels are driven by genetics and gut microbiome – Daria V. Zhernakova – Nature Genetics

Maternal gut and breast milk microbiota affect infant gut antibiotic resistome and mobile genetic elements – Katariina Pärnänen – Nature Communications

Multidrug-resistant Gram-negative bacteria from patients, hospital environment and healthcare workers: a six-month cross-sectional study – Aline Fernanda Rodrigues Sereia – bioRxiv

Microbiota stability in healthy individuals after single-dose lactulose challenge – a randomized controlled study – Sandra Y Wotzkas – bioRxiv

Laparoscopic Roux-en-Y gastric bypass profoundly changes gut microbiota compared to laparoscopic sleeve gastrectomy: a metagenomic comparative analysis – William Farin – bioRxiv

Subgingival microbiome of rheumatoid arthritis patients in relation to their disease status and periodontal health – Kathrin Beyer – PlosOne

Profiling of microorganism-binding serum antibody specificities in professional athletes – Rajna Minić – PlosOne

Animal experiments

Human Breast-Milk Feeding Enhances the Humoral and Cell-Mediated Immune Response in Neonatal Piglets – John J Miklavcic – The Journal of Nutrition

Glyphosate perturbs the gut microbiota of honey bees – Erick V. S. Motta – PNAS

Water and extremophile microbiome 

Microbiome profiling in extremely acidic soils affected by hydrothermal fluids: the case of Solfatara Crater (Campi Flegrei, southern Italy) – Crognale Simona – Fems Microbiology Ecology

Techniques

The Smallest Intestine (TSI) – a low volume in vitro model of the small intestine with increased throughput – T Cieplak – FEMS microbiology Letters

Microbes in the news

First-Ever Rapid Response Test for Levels of Bifidobacterium in Baby’s Gut Microbiome – Microbiome Times

Human Microbiome Market will Likely to expanding at a CAGR of 9.8% during the forecast period from 2018 to 2026 – Business Analyst

Puppies spread antibiotic-resistant infections to 118 people, CDC reports – CBS News

Non-microbiology picks

The best of intentions: Prenatal breastfeeding intentions and infant health – Kerri M. Raissian – SSM Population Health

 

September 24, 2018

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General microbiology

Frequency- and Amplitude-Dependent Microbial Population Dynamics during Cycles of Feast and Famine – Jason Merritt, PHYSICAL REVIEW LETTERS

Small at Size, Big at Impact: Microorganisms for Sustainable Development – Nasib Singh, Microbial Bioprospecting for Sustainable Development

Population Genomics of Archaea: Signatures of Archaeal Biology from Natural Populations – David J. Krause, Population Genomics

Pregnancy and early life

Sharing of human milk oligosaccharides degradants within bifidobacterial communities in faecal cultures supplemented with Bifidobacterium bifidum – Aina Gotoh, Scientific Reports

Multi-site human microbiome

Gut–Liver Axis: How Do Gut Bacteria Influence the Liver? – Peter Christopher Konturek, Medical Sciences

Subgingival microbiome of rheumatoid arthritis patients in relation to their disease status and periodontal health – Kathrin Beyer, Plos One

Optimal immunosuppressor induces stable gut microbiota after liver transplantation – Jian-Wen Jiang, World Journal of Gastroenterology

Human respiratory microbiome

The Microbiome and Tuberculosis: Early Evidence for Cross Talk – Sivaranjani Namasivayam, mBio

Trans-maternal Helicobacter pylori exposure reduces allergic airway inflammation in offspring through regulatory T-cells – Andreas Kyburz, Journal of Allergy and Clinical Immunology

Human oral microbiome

Comparison of initial oral microbiomes of young adults with and without cavitated dentin caries lesions using an in situbiofilm model – Stefan Rupf, Scientific Reports

Human gut microbiome

In silico Identification of Metagenomic Signature Describing Neurometabolic Potential of Normal Human Gut Microbiota – A. S. Kovtun, Russian Journal of Genetics

Gut microbiota modulates drug pharmacokinetics – Juanhong Zhang, Drug Metabolism Reviews

Active Site Flexibility Revealed in Crystal Structures of Parabacteroides merdae β‐Glucuronidase from the Human Gut Microbiome – Michael S. Little, Protein Science

Structural and Functional Analysis of the Gut Microbiome for Toxicologists – Robert G. Nichols, Current Protocols in Toxicology

Altered intestinal antibacterial gene expression response profile in irritable bowel syndrome is linked to bacterial composition and immune activation – Sean M. P. Bennet, Neurogastroenterology and Motility

Animal experiments

Response of goose intestinal microflora to the source and level of dietary fiber – Haizhu Zhou, Poultry Science

Microbiota modulation by eating patterns, dietary and macronutrient composition; impact on food intake – Elizabeth A. Klingbeil, American Journal of Physiology

Water and extremophile microbiome

Accounting for bacterial overlap between raw water communities and contaminating sources improves the accuracy of signature-based microbial source tracking – Moa Hägglund, Frontiers in Microbiology

Bacterial community structure in a sympagic habitat expanding with global warming: brackish ice brine at 85–90 °N – Beatriz Fernández-Gómez, ISME

Single-cell genomics uncover Pelagibacter as the putative host of the extremely abundant uncultured 37-F6 viral population in the ocean – Francisco Martinez-Hernandez, ISME

Microbial Community Function in Electroactive Biofilm-based Constructed Wetlands – Ramírez Vargas, Biogeosciences

Fungal endophyte‐infected leaf litter alters in‐stream microbial communities and negatively influences aquatic fungal sporulation – Emily R. Wolfe, Synthesising Ecology

Salt marsh denitrification is impacted by oiling intensity six years after the Deepwater Horizon oil spill – Corianne Tatariw, Environmental Pollution

Wastewater used for urban agriculture in West Africa as a reservoir for antibacterial resistance dissemination – Blaise P. Bougnom, Environmental Research

Plant, root, and soil microbiome

Phosphate solubilizing bacteria with glucose dehydrogenase gene for phosphorus uptake and beneficial effects on wheat – Muhammad Suleman, Plos One

Multiple ecological processes jointly drive the soil microbial community assembly in subalpine coniferous forests – Pengyu Zhao, PeerJ

Aphid Colonization Affects Potato Root Exudate Composition and the Hatching of a Soil Borne Pathogen – Grace A. Hoysted, Frontiers in Plant Sciences

Root inoculation with Azotobacter chroococcum 76A enhances tomato plants adaptation to salt stress under low N conditions – Michael James Van Oosten, BMC Plant Biology

Variation of bacterial biodiversity from saline soils and estuary sediments present near the Mediterranean Sea coast of Camargue (France) – Jorge R. Osman, Antonie van Leeuwenhoek

Plant roots alter microbial functional genes supporting root litter decomposition – Shengjing Shi, Soil Biology and Biochemistry

Bacterial community response to a preindustrial‐to‐future CO2 gradient is limited and soil‐specific in Texas Prairie grassland – Swastika Raut, Global Change Biology

Built environment

Houseplants as home health monitors – C. Neal Stewart Jr., SYNTHETIC BIOLOGY

Characterization of Aspergillus niger Isolated from the International Space Station – Jillian Romsdahl, mSystems

Food microbiology

Microbiological Changes during Ripening of Chihuahua Cheese Manufactured with Raw Milk and Its Seasonal Variations – Cristina Sánchez-Gamboa, Foods

Supplementation in mushroom crops and its impact on yield and quality – Jaime Carrasco, AMB Express

Aronia (Aronia melanocarpa) Polyphenols Modulate Microbial Community in Simulator of the Human Intestinal Microbial Ecosystem (SHIME®) and Decrease Secretion of Pro‐Inflammatory Markers in a Caco‐2/endothelial Cell Co‐Culture Model – Ting Wu, Molecular Nutrition and Food Research

Techniques

A critical evaluation of the use of gas chromatography- and high performance liquid chromatography-mass spectrometry techniques for the analysis of microbial metabolites in human urine after consumption of orange juice – José Luis Ordóñez, Journal of Chromatography A

Recovering cellular biomass from fluids using chemical flocculation – Paul A. Kenward, Environmental Microbiology Reports

Influence of support media supplementation to reduce the inhibition of anaerobic digestion by phenol and ammonia: Effect on degradation performances and microbial dynamics – Simon Poirier, Data in Brief

A resourceful methodology to profile indolic auxins produced by rhizo-fungi using spectrophotometry and HPTLC – Dhavalkumar Patel, Biotech

Bioinformatics

Computational Tools and Databases of Microbes and Its Bioprospecting for Sustainable Development – Dipannita Hazra, Microbial Bioprospecting for Sustainable Development

Metabolomics

Paradoxes in leaky microbial trade – Yoav Kallus, Nature Communications

Antibiotics

Amycomicin is a potent and specific antibiotic discovered with a targeted interaction screen – Gleb Pishchany, PNAS

Microbes in the news

Subculture show converts Storefront for Art and Architecture into living lab – The Architects Newspaper, Ali Oriaku