August 20, 2019

Today’s digest includes the gut microbiome of sea turtles, microbes on a guyot in the Pacific Ocean, and a review of microbiome animal models. Enjoy!

General microbiome

Review: Simple animal models for microbiome research – Douglas – Nature Reviews Microbiology

Review: An Ecological Loop: Host Microbiomes across Multitrophic Interactions – Liu – Trends in Ecology & Evolution

Review: The antibody/microbiota interface in health and disease – Sterlin – Mucosal Immunology

Pregnancy and early life

Early-life gut microbiome modulation reduces the abundance of antibiotic-resistant bacteria – Casaburi – Antimicrobial Resistance & Infection Control

Human skin microbiome

The prevalence of the culturable human skin aerobic bacteria in Riyadh, Saudi Arabia – Shami – BMC Microbiology

Animal experiments

Oral Administration of Clinically Relevant Antimalarial Drugs Does Not Modify the Murine Gut Microbiota – Denny & Schmidt – Scientific Reports

Animal microbiome

New insights into the gut microbiome in loggerhead sea turtles Caretta caretta stranded on the Mediterranean coast – Arizza – PLoS One

Outcomes of a low birth weight phenotype on piglet gut microbial composition and intestinal transcriptomic profile – Fouhse – Canadian Journal of Animal Science

Plant, root, and soil microbiome

Deciphering rhizosphere microbiome assembly of wild and modern common bean (Phaseolus vulgaris) in native and agricultural soils from Colombia – Pérez-Jaramillo – Microbiome

Preprint: Exploring the microbial diversity in oil-contaminated mangrove sediments using 16S rRNA metagenomics – Ghanbari – BioRxiv

Plant-microorganisms interaction promotes removal of air pollutants in Milan (Italy) urban area – Franzetti – Journal of Hazardous Materials

Effects of natural vegetative restoration on soil fungal and bacterial communities in bare patches of the southern Taihang Mountains – Zhao – Ecology and Evolution

Water and extremophile microbiome

The differentiation of iron-reducing bacterial community and iron-reduction activity between riverine and marine sediments in the Yellow River estuary – Zhang – Marine Life Science & Technology

Bacterial Community on a Guyot in the Northwest Pacific Ocean Influenced by Physical Dynamics and Environmental Variables – Liu – JGR: Biogeosciences

Microdiversity ensures the maintenance of functional microbial communities under changing environmental conditions – García-García – ISME

Built environment

Seasonal diversity of the bacterial communities associated with petroglyphs sites from the Negev Desert, Israel – Nir – Annals of Microbiology

Antibiotic fermentation residue for biohydrogen production using different pretreated cultures: Performance evaluation and microbial community analysis – Yang – Bioresource Technology

Bioinformatics

Metagenomic approaches: effective tools for monitoring the structure and functionality of microbiomes in anaerobic digestion systems – Carabeo-Pérez – Applied Microbiology and Biotechnology

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August 1, 2019

Happy Thursday! Today’s digest includes fungi abundance in paddy fields, the microbial quality of treated wastewater, and the oral microbiome of cats. Enjoy!

Animal microbiome

The feline cutaneous and oral microbiota are influenced by breed and environment – Older – PLoS One

Microbial community modulates growth of symbiotic fungus required for stingless bee metamorphosis – Paludo – PLoS One

Preprint: Effects of the copper IUD on composition of the vaginal microbiota in the olive baboon – Eastman – bioRxiv

Plant, root, and soil microbiome

Nitrogen fertilization altered arbuscular mycorrhizal fungi abundance and soil erosion of paddy fields in the Taihu Lake region of China – Zhang – Environmental Science and Pollution Research

Reconciling disparate responses to grazing in the arbuscular mycorrhizal symbiosis – van Der Heyde – Rhizosphere

Redox-driven shifts in soil microbial community structure in the drawdown zone after construction of the Three Gorges Dam – Wang – Soil Ecology Letters

Water and extremophile microbiome

Biomarker Profiling of Microbial Mats in the Geothermal Band of Cerro Caliente, Deception Island (Antarctica): Life at the Edge of Heat and cold – Lezcano – Astrobiology

Microbial diversity analysis and screening for novel xylanase enzymes from the sediment of the Lobios Hot Spring in Spain – Knapik – Scientific Reports

Built environment

How does urban wastewater treatment affect the microbial quality of treated wastewater? – Lopez – Process Safety and Environmental Protection

Identifying microbial community evolution in membrane bioreactors coupled with anaerobic side-stream reactor, packing carriers and ultrasonication for sludge reduction by linear discriminant analysis – Zheng – Bioresource Technology

Food microbiology

Preprint: Deep microbial community profiling along the fermentation process of pulque, a major biocultural resource of Mexico – Rocha-Arriaga – bioRxiv

Bioinformatics

Preprint: µbialSim: constraint-based dynamic simulation of complex microbiomes – Popp and Centler – bioRxiv

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 27, 2019

This Thursday, read about the well-to-well contamination in microbiome research, antibiotic resistance gene pool in avian microbiomes, a novel robust taxonomic framework (AutoTax), and more. Happy reading!

General microbiome

*Quantifying and Understanding Well-to-Well Contamination in Microbiome Research – Jeremiah J. Minich – mSystems

Controlling for Contaminants in Low-Biomass 16S rRNA Gene Sequencing Experiments – Lisa Karstens – mSystems

Skin microbiome

The impact of skin care products on skin chemistry and microbiome dynamics – Amina Bouslimani – BMC Biology

Animal microbiome

*Meta-transcriptomics reveals a diverse antibiotic resistance gene pool in avian microbiomes – Vanessa R. Marcelin – BMC Biology

Soil microbiome

Defoliation management and grass growth habits modulated the soil microbial community of turfgrass systems – Qing Xia – PlosOne

Comparative overview of red kidney bean (Phaseolus valgaris) rhizospheric bacterial diversity in perspective of altitudinal variations – Deep Chandra Suyal – Biologia

Animal experiments

Puerarin prevents high-fat diet-induced obesity by enriching Akkermansia muciniphila in the gut microbiota of mice – Lei Wang – PlosOne

Water and extremophile microbiome

The anaerobic digestion microbiome: a collection of 1600 metagenome-assembled genomes shows high species diversity related to methane production – Stefano Campanaroa – bioRxiv

In situ transformation of ethoxylate and glycol surfactants by shale-colonizing microorganisms during hydraulic fracturing – Morgan V. Evans – ISME Journal

Bioinformatics

*Comprehensive ecosystem-specific 16S rRNA gene databases with automated taxonomy assignment (AutoTax) provide species-level resolution in microbial ecology – Morten Simonsen Dueholm – bioRxiv

June 24, 2019

Happy Monday! In today’s Digest, you’ll find a primer on metabolomics, a description of the fungal and bacterial communities involved in coffee fermentation, and several studies on extremophile communities.

General Microbiome
Staring into the void: Demystifying microbial metabolomics – Cynthia M Grim – FEMS Microbiology Letters

Bacterial metabolism-inspired molecules to modulate antibiotic efficacy – Yuan Liu – Journal of Antimicrobial Chemotherapy

Deterministic processes structure bacterial genetic communities across an urban landscape – J. M. Hassell – Nature Communications

Gut Microbiome
Bifidobacterium dentium Fortifies the Intestinal Mucus Layer via Autophagy and Calcium Signaling Pathways – Melinda A. Engevik – mBio

Lipopolysaccharides modulate intestinal epithelial permeability and inflammation in a species-specific manner – Matthew Stephens – Gut Microbes

Fecal Microbiome Data Distinguish Liver Recipients with Normal and Abnormal Liver Function from Healthy Controls – Hai-feng Lu – Frontiers in Microbiology

Human Microbiota and Personalized Cancer Treatments: Role of Commensal Microbes in Treatment Outcomes for Cancer Patients – Stephen Gately – Precision Medicine in Cancer Therapy

Animal Experiments
Intervening Effects of Total Alkaloids of Corydalis saxicola Bunting on Rats With Antibiotic-Induced Gut Microbiota Dysbiosis Based on 16S rRNA Gene Sequencing and Untargeted Metabolomics Analyses – Xi Liu – Frontiers in Microbiology

Animal Microbiome
Gestation alters the gut microbiota of an oviparous lizard – Brian K Trevelline – FEMS Microbiology Ecology

Diversity of deep-water coral associated bacteria and comparison across depth gradients – Sigmund Jensen – FEMS Microbiology Ecology

Plant, Root, and Soil Microbiome
Bacterial and archaeal spatial distribution and its environmental drivers in an extremely haloalkaline soil at the landscape scale – Martha Adriana Martínez-Olivas – PeerJ

The microbial community in an alkaline saline sediment of a former maar lake bed – Claudia L. Ibarra-Sánchez – Journal of Soils and Sediments

Impacts on soil microbial characteristics and their restorability with different soil disinfestation approaches in intensively cropped greenhouse soils – Tianzhu Meng – Applied Microbiology and Biotechnology

Nonylphenol causes shifts in microbial communities and nitrogen mineralization in soil microcosms – Stefania Mattana – Ecotoxicology and Environmental Safety

Changes in Plant Rhizosphere Microbial Communities under Different Vegetation Restoration Patterns in Karst and Non-karst Ecosystems – Zhouzhou Fan – Scientific Reports

Water and Extremophile Microbiome
Culture independent bacterial diversity of Changme Khang and Changme Khangpu glaciers of North Sikkim, India – Mingma Thundu Sherpa – Environmental Sustainability

Selection of a Microbial Community in the Course of Formation of Acid Mine Drainage – V. V. Kadnikov – Microbiology

Thermophilic Bacteria in Lake Baikal Bottom Sediments Associated with Hydrocarbon Discharge – O. N. Pavlova – Microbiology

Bacterial alkylquinolone signaling contributes to structuring microbial communities in the ocean – Kristen E. Whalen – Microbiome

Food Microbiology
First description of bacterial and fungal communities in Colombian coffee beans fermentation analysed using Illumina-based amplicon sequencing – Ana C. de Oliveira Junqueira – Scientific Reports

Techniques
Functional Gene Array-Based Ultrasensitive and Quantitative Detection of Microbial Populations in Complex Communities – Zhou Shi – mSystems

June 4, 2019

General microbiome
Rigorous Statistical Methods for Rigorous Microbiome Science – Amy D. Willis – mSystems

Understanding microbial community dynamics to improve optimal microbiome selection – Robyn J. Wright – Microbiome

Toward a Better Understanding of Species Interactions through Network Biology – Ryan S. McClure – mSystems

Human respiratory microbiome
Nasal commensal Staphylococcus epidermidis enhances interferon-λ-dependent immunity against influenza virus – Hyun Jik Kim – Microbiome

Human gut microbiome
A Multi-omics Approach to Unraveling the Microbiome-Mediated Effects of Arabinoxylan Oligosaccharides in Overweight Humans – Alfonso Benítez-Páez – mSystems

Gut microbiome identifies risk for colorectal polyps – Ezzat Dadkhah – BMJ Open Gastroenterology

Yogurt improves insulin resistance and liver fat in obese women with nonalcoholic fatty liver disease and metabolic syndrome: a randomized controlled trial – Yang Chen – American Journal of Clinical Nutrition

Preprint: Chemical Impacts of the Microbiome Across Scales Reveal Novel Conjugated Bile Acids – Robert A Quinn – bioRxiv

Animal models
Ruminal microbiome-host crosstalk stimulates the development of the ruminal epithelium in a lamb model – Limei Lin – Microbiome

Missing Links: the Role of Primates in Understanding the Human Microbiome – Katherine R. Amato – mSystems

Plant, root, and soil microbiome
Collaborative involvement of woody plant roots and rhizosphere microorganisms in the formation of pedogenetic clays – Frank Reith – Annals of Botany

Water and extremophile microbiome
Effects of sulfamethoxazole and sulfamethoxazole-degrading bacteria on water quality and microbial communities in milkfish ponds – Bea-Ven Chang – Environmental Pollution

Preprint: Temporal dynamics of Bacteria, Archaea and protists in equatorial coastal waters – Caroline Chénard – bioRxiv

Built environment
Concurrent measurement of microbiome and allergens in the air of bedrooms of allergy disease patients in the Chicago area – Miles Richardson – Microbiome

Phages and viruses
Preprint: The human gut virome is highly diverse, stable and individual-specific – Andrey Shkoporov – bioRxiv

Bioinformatics
NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language – Luis Pedro Coelho – Microbiome

Science, publishing, and career
Preprint: The Mastery Rubric for Bioinformatics: supporting design and evaluation of career-spanning education and training – Rochelle E. Tractenberg – bioRxiv

Alyson’s non-microbiology picks
Why Your Metro Commute Is So Insanely Windy – Julie Bogen – The Atlantic

The 2019 Wellcome photography prize: close focus on the human condition – Sean O’Hagan – The Guardian

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