July 27, 2019

Have a nice weekend! Today, in this Digest, it is worth to remark a study in mice showing the impact of microbiome composition on muscle loss, in addition to a paper presenting the new version of QIIME, one of the most utilized microbiome analysis software available. 

 

Human and General Microbiome

Pearls: Microbiome evolution during host aging – Francisco Daniel Davila Aleman – PLOS Pathogens

Review: The structure and function of the human small intestinal microbiota: Current understanding and future directions – Arthur J. Kastl, Jr – Cellular and Molecular Gastroenterology and Hepatology

Review: The impact of tumor and gut microbiotas on cancer therapy; Beneficial or detrimental? – Yalda Hekmatshoar – Life Sciences 

Review: Gut Microbiota in Phytopharmacology: A Comprehensive Overview Of Concepts, Reciprocal Interactions, Biotransformations And Mode Of Actions – Priyankar Dey – Pharmacological Research

Review: The role of the skin microbiota in acne pathophysiology – S. Ramasamy – British Journal of Dermatology

Review: Study Insights into Gastrointestinal Cancer through the Gut Microbiota – Fanli Kong – BioMed Research International

Review: Contribution of Aging, Obesity, and Microbiota on Tumor Immunotherapy Efficacy and Toxicity – Regina E. M. Baiden-Amissah – International Journal in Molecular Sciences

TARgeting the cutaneous microbiota in atopic dermatitis by coal tar via AHR-dependent induction of antimicrobial peptides – Jos P.H. Smits – Journal of Investigative Dermatology

The Gut Microbiota in Collagenous Colitis Shares Characteristics With Inflammatory Bowel Disease-Associated Dysbiosis – Adam Carstens – Clinical and Translational Gastroenterology

Changes in oral microbial profiles associated with oral squamous cell carcinoma vs leukoplakia – Kengo Hashimoto – Journal of Investigative and Clinical Dentistry

Probiotics modulate the gut microbiota composition and immune responses in patients with atopic dermatitis: a pilot study – Zhifeng Fang – European Journal of Nutrition

Role of Bile Acids in Dysbiosis and Treatment of Nonalcoholic Fatty Liver Disease –  – Caihua Wang – Mediators of Inflammation

Rectal Swabs from Critically Ill Patients Provide Discordant Representations of the Gut  Microbiome Compared to Stool Samples – Katherine Fair – mSphere 

Measurement of gut microbial metabolites in cardiometabolic health and translational research – Wei‐Kai Wu – Rapid Communications in Mass Spectrometry

 

Animal Microbiome and Animal Experiments

The gut microbiota influences skeletal muscle mass and function in mice – Shawon Lahiri – Science Translational Science

Intestinal Clostridium species lower host susceptibility to enterohemorrhagic Escherichia coli O157:H7 infection – Yukako Koyanagi – Pathogens and Disease

Preparation and characterization of selenium enriched-Bifidobacterium longum DD98, and its repairing effects on antibiotic-induced intestinal dysbacteriosis in mice – Hui Zhu – Food and Function 

The Ruminal Microbiome and Metabolome Alterations Associated with Diet-Induced Milk Fat Depression in Dairy Cows – Hongbo Zeng – Metabolites

 

Water Microbiome

Insights into the antibiotic resistance dissemination in a wastewater effluent microbiome:  bacteria, viruses and vesicles matter – Lucia Maestre‐Carballa – Environmental Microbiology

 

Built Environment Microbiome

Identification of city specific important bacterial signature for the MetaSUB CAMDA challenge microbiome data – Alejandro R. Walker – Biology Direct 

 

Plant Microbiome

Genome Evolution and Host Microbiome Shifts Correspond with Intraspecific Niche Divergence within Harmful Algal Bloom-Forming Microcystis aeruginosa – Sara L. Jackrel – Molecular Ecology

Novel insights into plant-associated archaea and their functioning in arugula (Eruca sativa Mill.) – Julian Taffner – Journal of Advanced Research

Seeds of native alpine plants host unique microbial communities embedded in cross-kingdom networks – Birgit Wassermann – Microbiome

 

Bioinformatics

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2 – Evan Bolyen – Nature Biotechnology

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July 2, 2019

This Tuesday, read about the fecal microbial transplantation for cardiometabolic syndrome treatment, oral microbiome of early stage Parkinson’s disease, Finnish Health and Early Life Microbiota (HELMi) project, and more. Happy reading!

General microbiome

Review: Defining Division of Labour in Microbial Communities – Samir Giri – JMB

Review: Selective pressures during chronic infection drive microbial competition and cooperation – Jiwasmika Baishya & Catherine A. Wakeman – Biofilms and Microbiomes

Gut microbiome

*Review: Fecal Microbial Transplantation and Its Potential Application in Cardiometabolic Syndrome – Avner Leshem – Frontiers in Immunology

Review: The Microbiome and Irritable Bowel Syndrome – A Review on the Pathophysiology, Current Research and Future Therapy – Pei Pei Chong – Frontiers in Microbiology

Alterations of the bile microbiome in primary sclerosing cholangitis – Timur Liwinski – BMJ Gut Microbiota

Selective and suppressive effects of antibiotics on donor and recipient bacterial strains in gut microbiota determine transmission efficiency of blaNDM-1-bearing plasmids – Lianwei Ye – Journal of Antimicrobial Chemotherapy

Pregnancy and early life

Contributions to human breast milk microbiome and enteromammary transfer of Bifidobacterium breve – Kattayoun Kordy – bioRxiv

Experimental support for multidrug resistance transfer potential in the preterm infant gut microbiota – Mari Hagbø – Paediatric research

*Cohort profile: Finnish Health and Early Life Microbiota (HELMi) longitudinal birth cohort – Katri Korpela – BMJ Paediatrics

Oral microbiome

*The oral microbiome of early stage Parkinson’s disease and its relationship with functional measures of motor and non-motor function – Dragos Mihaila – PlosOne

Phages and viruses

What is (not) known about the dynamics of the human gut virome in health and disease – Leen Beller Jelle Matthijnssens – Current Opinion in Virology

Water and extremophile microbiome

Characterization of indigenous bacteria from radon-rich groundwater and their tolerance to physicochemical stress – T. Nayak – International Journal of Environmental Science and Technology

Sewage effluent from an Indian hospital harbors novel carbapenemases and integron-borne antibiotic resistance genes – Nachiket P. Marathe – Microbiome

Techniques

Primer-free FISH probes from metagenomics/metatranscriptomics data permit the study of uncharacterised taxa in complex microbial communities – Shi Ming Tan – Biofilms and microbiomes

Bioinformatics

Use and abuse of correlation analyses in microbial ecology – Alex Carr – ISME Journal

Education

From trainees to trainers to instructors: Sustainably building a national capacity in bioinformatics training – Annette McGrath – Plos Computational Biology

Ten quick tips for effective dimensionality reduction – Lan Huong Nguyen and Susan Holmes – Plos Computational Biology

June 10, 2019

This Monday, read about the precision of microbiome wording, cryopreservation of the human gut microbiota, water infrastructure microbiomes, and more. Happy reading!

General microbiome

Determining Microbial Roles in Ecosystem Function: Redefining Microbial Food Webs and Transcending Kingdom Barriers – Kim M. Handley – mSystems

Digitalizing the Microbiome for Human Health – Kirti Nath and Christoph A. Thaiss – mSystems

New Approaches to Microbiome-Based Therapies – Andrea C. Wong and Maayan Levy – mSystems

Benefits and Costs of Animal Virulence for Microbes – Arturo Casadevall and Liise-anne Pirofski – mSystems

*Language, numeracy and logic in microbiome science – Fergus Shanahan and Colin Hill – Nature Reviews Gastroenterology & Hepatology

Gut microbiome

*Cryopreservation of the human gut microbiota: current state and perspectives – Daria V.Smirnovaa – International Journal of Medical Microbiology

Metaproteomics of the human gut microbiota: challenges and contributions to other OMICS – Ngom Issa Isaac – Clinical Mass Spectrometry

Mapping human microbiome drug metabolism by gut bacteria and their genes – Michael Zimmermann – Nature

MinION Sequencing of colorectal cancer tumour microbiomes – a comparison with amplicon-based and RNA-Sequencing – William S Taylor – bioRxiv

Assessment of Causal Direction Between Gut Microbiota-Dependent Metabolites and Cardiometabolic Health: Abi-Directional Mendelian Randomisation Analysis – Jinzhu Jia – Diabetes

Metagenomic and metabolomic analyses reveal distinct stage-specific phenotypes of the gut microbiota in colorectal cancer – Shinichi Yachida – Nature Medicine

Dysbiosis of gut microbiota in a selected population of Parkinson’s patients – Daniele Pietrucci – Parkinsonism & Related Disorders

Animal experiment

Heterochronic faecal transplantation boosts gut germinal centres in aged mice – Marisa Stebegg – Nature communications

High fat diet alters gut microbiota but not spatial working memory in early middle-aged Sprague Dawley rats – Nikita Girish Deshpande – PlosOne

Animal microbiome

Fibre digestion by rumen microbiota – a review of recent metagenomic and metatranscriptomic studies – Stephanie A Terry – Canadian Journal of Animal Science

Correlation between Disease Severity and the Intestinal Microbiome in Mycobacterium tuberculosis-Infected Rhesus Macaques – Sivaranjani Namasivayam – mBio

Water microbiome

*Integrating biotechnology and microbial ecology in urban water infrastructure through a microbiome continuum viewpoint – Lutgarde Raskin and Per Halkjær Nielsen – Current Opinion in Biotechnology

Techniques

MOBN: an interactive database of multi-omics biological networks – Cheng Zhang – bioRxiv

May 28, 2019

Today’s digest is about metaproteomics in microbial communities, infant and child microbiome and association with diseases, coral ecosphere, microbial biospherics and updates on new techniques to analyze microbiome sequencing data.

General microbiome

Metaproteomics: Much More than Measuring Gene Expression in Microbial Communities – Manuel Kleiner – mSystems

Associational effects in the microbial neighborhood – Anja Worrich – ISME Journal

Uncovering complex molecular networks in host–pathogen interactions using systems biology – Joshua M. Peters – Emerging Topics in Life Sciences

Human microbiome

The skin microbiome of vertebrates – Ashley A. Ross – Microbiome

Patterns in the longitudinal oropharyngeal microbiome evolution related to ventilator-associated pneumonia – Rami Sommerstein – Antimicrobial Resistance & Infection Control

Microbial composition of the human nasopharynx varies according to influenza virus type and vaccination status – Tao Ding -BioRxiv

Cytometric fingerprints of gut microbiota predict Crohn’s disease state – Peter Rubbens – BioRxiv

Dynamic colonization of microbes and their functions after fecal microbiota transplantation for inflammatory bowel disease – Nathaniel D. Chu – BioRxiv

Pregnancy and infant microbiome

Paediatrician’s perspective of infant gut microbiome research: current status and challenges – Paul MacDaragh Ryan – Archives of Disease in Childhood

The Salivary Microbiome Is Altered in Children With Eosinophilic Esophagitis and Correlates With Disease Activity – Hiremath Girish – Clinical and Translational Gastroenterology

Influence of own mother’s milk and different proportions of formula on intestinal microbiota of very preterm newborns – Adriana Zanella – PlosOne

Influence of a Serratia marcescens outbreak on the gut microbiota establishment process in low-weight preterm neonates – Esperanza Escribano – PlosOne

Reviewing the evidence on breast milk composition and immunological outcomes – Alba Boix-Amorós – Nutrition Reviews

Characterization of Stool Virome in Children Newly Diagnosed With Moderate to Severe Ulcerative Colitis – Rafal Tokarz – Inflammatory Bowel Diseases

Animal experiments

Effect of intestinal tapeworms on the gut microbiota of the common carp, Cyprinus carpio – Pei P. Fu – Parasites and Vectors

Comparison of Bacterial Populations in the Ceca of Swine at Two Different Stages and their Functional Annotations – Himanshu Kumar – Genes

Toll‐like receptor 2 and toll‐like receptor 4 responses regulate neutrophil infiltration into the junctional epithelium and significantly contribute to the composition of the oral microbiota – Ana M. Chang – Journal of Periodontology

Plant, root, soil microbiome

Mediterranean grassland soil C–N compound turnover is dependent on rainfall and depth, and is mediated by genomically divergent microorganisms – Spencer Diamond – Nature Microbiology

Rhizosphere microbiomes diverge among Populus trichocarpa plant-host genotypes and chemotypes, but it depends on soil origin – Allison M. Veach – Microbiome

Microbial community drivers of PK/NRP gene diversity in selected global soils – Chiara Borsetto – Microbiome

Decreased temporary turnover of bacterial communities along soil depth gradient during a 35-year grazing exclusion period in a semiarid grassland – Chao Zhang – Geoderma

Soil bacterial community dynamics following surfactant addition and bioaugmentation in pyrene-contaminated soils – D.C.Wolf – Chemosphere

Structural and Functional Responses of Soil Microbial Communities to Biodegradable Plastic Film Mulching in Two Agroecosystems – Sreejata Bandopadhyay – BioRxiv

Ecological and genomic attributes of novel bacterial taxa that thrive in subsurface soil horizons – Tess E. Brewer – BioRxiv

Water microbiome and extremophiles

The coral ecosphere: A unique coral reef habitat that fosters coral–microbial interactions – Laura Weber – Limnology and Oceanography

Tide driven microbial dynamics through virus-host interactions in the estuarine ecosystem – Xiaowei Chen – Water Research

Microbial biofilm formation and community structure on low-density polyethylene microparticles in lake water microcosms – Mengting Gong – Environmental Pollution

Diversity and relative abundance of ammonia- and nitrite-oxidizing microorganisms in the offshore Namibian hypoxic zone – Evan Lau – PlosOne

Consistent metagenome-derived metrics verify and define bacterial species boundaries – Matthew R. Olm – BioRxiv

Techniques

Competitive interaction with keystone taxa induced negative priming under biochar amendments – Lijun Chen – Microbiome

Strengthening Insights in Microbial Ecological Networks from Theory to Applications – Xiaofei Lv – mSystems

Microbial biospherics: The experimental study of ecosystem function and evolution Matthias C. Rillig – PNAS

NUFEB: A Massively Parallel Simulator for Individual-based Modelling of Microbial Communities – Bowen Li – BioRxiv

Detecting interaction networks in the human microbiome with conditional Granger causality – Kumar Mainali – Plos Computational Biology

M1CR0B1AL1Z3R—a user-friendly web server for the analysis of large-scale microbial genomics data – Oren Avram – Nucleic Acids Research

End-to-end assessment of fecal bacteriome analysis: from sample processing to DNA sequencing and bioinformatics results – Ana Paula Christoff – BioRxiv

Microbiome in news

Antibiotics may help curb Alzheimer’s symptoms – Medical News Today

SANISCALP®, to preserve the Microbiome for a soothed and healthy scalp! – Cosmetics desgin.com – Mamamia

Mother Dirt Expands Biome-Friendly Skincare Range With New Body Care Line – Mid Daily News

Microbes and the market

Global Microbiome Drugs Market Forecast 2019-2025: MaaT Pharma, Pfizer, Second Genome, Seres Therapeutics – Technology Market

Microbiome Therapeutics Market 2019 – By Future Growth, Trends Plans, Top Key Players, Business Opportunities, Region, Pricing Analysis, Opportunities and Forecast to 2024 – Norwalk Daily

Global Human Microbiome Modulators Market Report 2019: Trends and Opportunities for the Business Prediction over 2024 – Current News Magazine

Microbiome Sequencing Services Market 2019 Report Shows the Competitive Situation Among the Top Manufacturers, With Sales, Revenue and Share – Augusta Observer

 

May 2, 2019

In today’s digest read about variations in milk and infant fecal microbiome (Ethiopia, Gambia, USA, Ghana, Kenya, Peru, Spain, and Sweden), the microbiome, metabolome, and lipidome of obese and non-obese horses (USA), and Bacteroides fragilis adaptive evolution (Western countries and China). Happy reading!

Pregnancy and birth

*What’s normal? Microbiomes in human milk and infant feces are related to each other but vary geographically: the INSPIRE study – Kimberly A. Lackey – Frontiers in Nutrition

Progesterone Increases Bifidobacterium Relative Abundance during Late Pregnancy – Meital Nuriel-Ohayon – Cell Reports

Gut microbiome

Neonatal Vitamin A Supplementation and Vitamin A Status Are Associated with Gut Microbiome Composition in Bangladeshi Infants in Early Infancy and at 2 Years of Age – M Nazmul Huda – The Journal of nutrition

Fungi form interkingdom microbial communities in the primordial human gut that develop with gestational age – Kent A. Willis – bioRxiv

*Adaptive Evolution within Gut Microbiomes of Healthy People – Shijie Zhao – Cell Host & Microbe

Small intestinal microbial dysbiosis underlies symptoms associated with functional gastrointestinal disorders – George B. Saffouri – Nature Communications

Oral microbiome

Review: The Role of Exopolysaccharides in Oral Biofilms – C. Cugini – Journal of Dental Research

Human Salivary Amylase Gene Copy Number Impacts Oral and Gut Microbiomes – Angela C. Poole – Cell Host & Microbe

Animal microbiome

*Comparison of the microbiome, metabolome, and lipidome of obese and non-obese horses – Michelle C. Coleman – PlosOne

Utilizing the fecal microbiota to understand foal gut transitions from birth to weaning – Ubaldo De La Torre – PlosOne

Microbiome characterization of poultry products based on the poultry part and production label – Sang In Lee – FEMS Microbiology Letters

Metagenomic analysis of isolation methods of a targeted microbe, Campylobacter jejuni, from chicken feces with high microbial contamination – Junhyung Kim – Microbiome

Invited review: Advances and challenges in application of feedomics to improve dairy cow production and health – H.Z.Sun – Journal of Dairy Science

Characterization of pig saliva as the major natural habitat of Streptococcus suis by analyzing oral, fecal, vaginal, and environmental microbiota – Kazunori Murase – PlosOne

Insight into the microbial world of Bemisia tabaci cryptic species complex and its relationships with its host – Hua-Ling Wang – Scientific Reports

Water and extremophile microbiome

The Plastisphere – Uncovering tightly attached plastic “specific” microorganisms – Inga Vanessa Kirstein – PlosOne

The cooling tower water microbiota: Seasonal dynamics and co-occurrence of bacterial and protist phylotypes – Han-Fei Tsao – Water Research

Modular Assembly of Polysaccharide-Degrading Marine Microbial Communities – Tim N.Enke – Current Biology

Impact of a river flood on marine water quality and planktonic microbial communities – Annamaria Zoppini – Estuarine, Coastal and Shelf Science

Microbial ecological processes in MBBR biofilms for biological phosphorus removal from wastewater – Knut Rudi – Water Science & Technology

Highly diverse fungal communities in carbon-rich aquifers of two contrasting lakes in Northeast Germany – Anita Perkins – bioRxiv

Plant/root/soil microbiome

The rice leaf microbiome has a conserved community structure controlled by complex host-microbe interactions – Veronica Roman-Reyna – bioRxiv

Spatial vs. temporal controls over soil fungal community similarity at continental and global scales – Colin Averil – The ISME Journal

Metabolomics Reveal that Engineered Nanomaterial Exposure in Soil Alters Both Soil Rhizosphere Metabolite Profiles and Maize Metabolic Pathways – Lijuan Zhao – Environmental Science: Nano

High-throughput sequencing reveals the diversity and community structure of rhizosphere fungi of Ferula Sinkiangensis at different soil depths – Tao Zhang – Scientific Reports

Microplastics can change soil properties and affect plant performance – Anderson Abel de Souza Machado – Environmental Science and Technology

April 29, 2019

Today’s Monday morning digest is about correlations of human gut microbiome with circulating metabolites, coronary artery disease severity; microbial communities in biogas plants, and proteomic profiling of gut microbiota-associated bile salt hydrolase activity.

Human gut microbiome

Correlation of Gut Microbiome Between ASD Children and Mothers and Potential Biomarkers for Risk Assessment – Ning Li – Genomics, Proteomics & Bioinformatics

Neonatal Vitamin A Supplementation and Vitamin A Status Are Associated with Gut Microbiome Composition in Bangladeshi Infants in Early Infancy and at 2 Years of Age – M Nazmul Huda – Journal of Nutrition

Diversification and evolution of vancomycin-resistant Enterococcus faecium during intestinal domination – Krista A. Dubin – Infection and Immunity

Microbiota as a cornerstone in the development of primary sclerosing cholangitis: paving the path for translational diagnostic and therapeutic approaches – Catherine Mooser – Gut

Alterations in the gut microbiome and metabolism with coronary artery disease severity – Honghong Liu – Microbiome

Deciphering the complex interplay between microbiota, HPV, inflammation and cancer through cervicovaginal metabolic profiling – Zehra Esra Ilhan – EBio Medicine

Relationship between gut microbiota and circulating metabolites in population-based cohorts – Dina Vojinovic – BioRxiv

Animal experiments

Antibiotics-induced perturbations in gut microbial diversity influence metabolic phenotypes in a murine model of high-fat diet-induced obesity – Dongmin Liu – Applied Microbiology and Biotechnology

Composition, diversity and function of gastrointestinal microbiota in wild red-billed choughs (Pyrrhocorax pyrrhocorax) – Wen Wang – International Microbiology

Plant, root, soil microbiome

Antioxidant activity changes of exopolysaccharides with different carbon sources from Lactobacillus plantarum LPC-1 and its metabolomic analysis – Xin Cheng – World Journal of Microbiology and Biotechnology

Effects of grassland afforestation on structure and function of soil bacterial and fungal communities – Kaibo Wang – Science of the Total Environment

Water microbiome and extremophiles

Effect of applied voltage and temperature on methane production and microbial community in microbial electrochemical anaerobic digestion systems treating swine manure – Jaecheul Yu – Journal of Industrial Microbiology & Biotechnology

Metaproteome analysis reveals that syntrophy, competition, and phage-host interaction shape microbial communities in biogas plants – R. Heyer – Microbiome

Techniques

Improving Assignment of Microbial Genetic Polymorphisms Assignments in Complex Samples by Bayesian Estimation – Jiarui Li – Genomics, Proteomics & Bioinformatics

Accounting for Biological Variation With Linear Mixed-effects Modelling Improves the Quality of Clinical Metabolomics Data – Kwanjeera Wanichthanarak – Computational and Structural Biotechnology Journal

Chemoproteomic Profiling of Gut Microbiota-Associated Bile Salt Hydrolase Activity – Bibudha Parasar – ACS Central Science

Microbiome in news

Human Microbiome Therapeutics Market Research Methodology- Prominent Players Enterome Bioscience, Yakult Honsha Co. Ltd., DuPont – The Market Bureau

The Week That Wasn’t: See-Through Skulls, Fecal Soup, Microbiome Pill – Medscape

Non-Microbiology Picks

The incretin system in healthy humans: the role of GIP and GLP-1 – Jens Juul Holst – Metabolism

April 1, 2019

In today’s digest read about covert pathogenesis in urinary tract, microbial fuel cells in treatment of organic acid fermentation wastewater, gut microbial metabolism in weanling pigs, and more. Enjoy!

Urinary microbiome

*Covert pathogenesis: Transient exposures to microbes as triggers of disease – Nicole M. Gilbert, Amanda L. Lewis – PlosPathogens

Evaluation of antibacterial efficacy of sulfur nanoparticles alone and in combination with antibiotics against multidrug-resistant uropathogenic bacteria – Priti Paralikar – Journal of Environmental Science and Health, Part A

Review: A Comprehensive Review of Overactive Bladder Pathophysiology: On the Way to Tailored Treatment – Benoit Peyronnet – European Urology

Vaginal microbiome

Effect of progesterone on Candida albicans biofilm formation under acidic conditions: a transcriptomic analysis – Bruna Gonçalves – bioRxiv

Skin microbiome

Cutibacterium acnes antibiotic production shapes niche competition in the human skin microbiome – Jan Claesen – bioRxiv

Neutral Processes Drive Seasonal Assembly of the Skin Mycobiome – Xinzhao Tong – mSystems

Gut Microbiome

The Perturbation of Infant Gut Microbiota Caused by Cesarean Delivery Is Partially Restored by Exclusive Breastfeeding – Yu Liu – Frontiers in Microbiology

Gut Microbiome Functional and Taxonomic Diversity within an Amazonian semi-nomadic hunter-gatherer group – Liliane Costa Conteville – bioRxiv

Risk of inflammatory bowel disease after Campylobacter jejuni and Campylobacter concisus infection: a population-based cohort study – Hans Mittle Nielsen – Scandinavian Journal of Gastroenterology

Unilateral ureteral obstruction causes gut microbial dysbiosis and metabolome disorders contributing to tubulointerstitial fibrosis – Lin Chen – Experimental & Molecular Medicine

Oral microbiome

Polymicrobial synergy within oral biofilm promotes invasion of dendritic cells and survival of consortia members – Ahmed El-Awady – Biofilms and Microbiomes

Animal microbiome

*Metagenomic reconstructions of gut microbial metabolism in weanling pigs – Weilan Wang – Microbiome

Probiotics/Prebiotics

Strain-level diversity of commercial probiotic isolates of Bacillus, Lactobacillus, and Saccharomyces species illustrated by molecular identification and phenotypic profiling – Juliana M. Ansari – PlosOne

Biosurfactant Production by Lactic Acid Bacterium Pediococcus dextrinicus SHU1593 Grown on Different Carbon Sources: Strain Screening Followed by Product Characterization – Abouzar Ghasemi – Scientific Reports

Phages and viruses

Bacteriophage adherence to mucus mediates preventive protection against pathogenic bacteria – Gabriel MF Almeida – bioRxiv

Review: The gut virome: the ‘missing link’ between gut bacteria and host immunity? – Indrani Mukhopadhya – Therapeutic Advances in Gastroenterology

Soil microbiome

Shift of the microbial communities from exposed sandstone rocks to forest soils during pedogenesis – Yaping Liu – International Biodeterioration & Biodegradation

Water and extremophile microbiome

Startup, performance, and microbial communities of an anammox reactor inoculated with indigenous sludge for the treatment of high-salinity and mesophilic underground brine – Nobuyuki Yokota – Clean Technologies and Environmental Policy

*Power generation and microbial community analysis in microbial fuel cells: A promising system to treat organic acid fermentation wastewater – Tian Xia – Bioresource Technology

Techniques

Cultivating in situ triggers growth of previously uncultivated microorganisms via a growth initiation factor in nature – Dawoon Jung – bioRxiv

Bioinformatics

Library preparation and sequencing platform introduce bias in metagenomics characterisation of microbial communities – Casper S. Poulse – bioRxiv