February 8, 2017

A dense Digest today, a lot of reviews on the human gut microbiome, a plethora of papers on plant, soil and water microbiomes, and an alarmingly high rate of multi-drug resistant bacteria from human fecal samples in China


Teaching and Learning Fellow in Microbiome Data Analysis – University of British Columbia

Microbiology Quality Technician II – CR Bard

Postdoctoral Research Assistant on the Social Dimensions of the Microbiome – University of Oxford

General microbiology

Transcriptional characterization of Vibrio fischeri during colonization of juvenile Euprymna scolopes – Luke R. Thompson – Environmental Microbiology

Effect of antibiotics on bacterial populations: a multi-hierachical selection process – José Luis Martínez – F1000 Research

Plant growth promoting potential and phylogenetic characteristics of a lichenized nitrogen fixing bacterium, Enterobacter cloacae – Chidanandamurthy Thippeswamy Swamy – Journal of Basic Microbiology

*High rates of human faecal carriage of mcr-1-positive multi-drug resistant isolates emerge in China in association with successful plasmid families – Lan-Lan Zhong – bioRxiv

Assessing the genome level diversity of Listeria monocytogenes from contaminated ice cream and environmental samples linked to a listeriosis outbreak in the United States – Yi Chen – PLoS One

Human skin microbiome

Significant disparities in allergy prevalence and microbiota between the young people in Finnish and Russian Karelia – Lasse Ruokolainen – Clinical & Experimental Allergy

Beyond Cell Division: the Ecological Roles of Autolysins in Oral Biofilm Communities – Nyssa Cullin – Current Oral Health Reports

Human lung microbiome

Longitudinal assessment of sputum microbiome by sequencing of the 16S rRNA gene in non-cystic fibrosis bronchiectasis patients – Michael J. Cox – PLoS One

Human gut microbiome

Review: Intestinal Microbiota: Facts and Fiction – M Kverka – Digestive Diseases

Review: Evolutionary and ecological forces that shape the bacterial communities of the human gut – J S Messer – Mucosal Immunology

Review: Dietary Fiber and Prebiotics and the Gastrointestinal Microbiota – Hannah D. Holscher – Gut Microbes

Review: The Fungal Mycobiome and Its Interaction with Gut Bacteria in the Host – Qi Hui Sam – International Journal of Molecular Sciences

Review: The Gut Microbiome in Irritable Bowel Syndrome and Other Functional Bowel Disorders – Yehuda Ringel – Gastroenterology Clinics of North America

Many more human gut microbiome reviews available from the March Issue of the Gastroenterology Clinics of North America

Human gut-microbiome-brain axis

Editorial: Tightening the Case for Gut Microbiota in Autism-Spectrum Disorder – Jonathan Braun – CMGH Cellular and Molecular Gastroenterology and Hepatology

Review: The Microbiome-Gut-Brain Axis in Health and Disease – Timothy G. Dinan – Gastroenterology Clinics of North America


Review: Mixing omics: combining genetics and metabolomics to study rheumatic diseases – Cristina Menni – Nature Reviews Rheumatology

Review: Emerging Approaches to Tuberculosis Drug Development: At Home in the Metabolome – Robert S. Jansen – Trends in Pharmacological Sciences

Rats Urinary Metabolome Reveals for the Potential Role of Functional Foods and Exercise in Obesity Management – Mohammed Farag – Food and Function

Untargeted metabolomics approach for unraveling robust biomarkers of nutritional status in fasted gilthead sea bream (Sparus aurata) – Ruben Gil-Solsona – PeerJ

Animal experiments

Mouse: Sex-Specific Effects of Organophosphate Diazinon on the Gut Microbiome and Its Metabolic Functions – Bei Gao – Environmental Health Perspectives

Metagenomics approach to the study of the gut microbiome structure and function in zebrafish Danio rerio fed with gluten formulated diet – Hyunmin Koo – Journal of Microbiological Methods

Commentary: Zebrafish screens for new colitis treatments – a bottom-up approach – Jou A. Lee – The FEBS Journal

Mouse: Resistant starch can improve insulin sensitivity independently of the gut microbiota – Laure B. Bindels – Microbiome

Animal microbiome

Invited review: Large-scale indirect measurements for enteric methane emissions in dairy cattle: A review of proxies and their potential for use in management and breeding decisions – E. Negussie – Journal of Dairy Science

Variation of the microbiota and metabolome along the canine gastrointestinal tract – Julia B. Honneffer – Metabolomics

Effects of Organic Amendments on Microbiota Associated with the Culex nigripalpus Mosquito Vector of the Saint Louis Encephalitis and West Nile Viruses – Dagne Duguma – mSphere

Review: Progress in fish gastrointestinal microbiota research – An R. Wang – Reviews in Aquaculture

Diversity and functions of the sheep faecal microbiota: a multi-omic characterization – Alessandro Tanca – Microbial Biotechnology

Microbial shifts in the porcine distal gut in response to diets supplemented with Enterococcus Faecalis as alternatives to antibiotics – Pinghua Li – Scientific Reports

Plant, root and soil microbiome

Fungi from Brazilian Savannah and Atlantic rainforest show high antibacterial and antifungal activity – Paula de Paula Menezes Barbosa – Biocatalysis and Agricultural Biotechnology

Impact of Elevated CO2 and/or Temperature on the AM Fungal Diversity in Groundnut Rhizosphere under Open Top Chamber facility – HN Asha – International Journal of Current Microbiology and Applied Sciences

Seed-coating fenugreek with Burkholderia rhizobacteria enhances yield in field trials and can combat Fusarium wilt – Harish Kuma – Rhizosphere

Changes at the Rhizosphere Microbiota of the Sunflower–Orobanche cumana Wallr Pathosystem – TH Hristev – International Journal of Current Microbiology and Applied Sciences

Review: Phosphate Solubilizing Microbes: An Overview – KP Ingle – International Journal of Current Microbiology and Applied Sciences

Draft Genome Sequence of Plant Growth-Promoting Drought-Tolerant Bacillus sp. Strain CMAA 1363 Isolated from the Brazilian Caatinga Biome – Vanessa Nessner Kavamura – Genome Announcements

Effects of Garlic/Cucumber Relay Intercropping on Soil Enzyme Activities and the Microbial Environment in Continuous Cropping – Lantian Du – HortScience

Characterization of bacterial communities from Masseiras, a unique Portuguese greenhouse agricultural system – Cristina Becerra-Castro – Antonie van Leeuwenhoek

Soil microbial community responses to long-term land use intensification in subtropical grazing lands – Sutie Xu – Geoderma

The impact of salinity on the microbial response to drying and rewetting in soil – Kristin M. Rath

The influence of different concentrations of bio-organic fertilizer on cucumber Fusarium wilt and soil microflora alterations – Nan Huang – PLoS One

Cowpea Nodules Harbor Non-rhizobial Bacterial Communities that Are Shaped by Soil Type Rather than Plant Genotype – Jakson Leite – Frontiers in Plant Science

Microbial Interactions in the Phyllosphere Increase Plant Performance under Herbivore Biotic Stress – Muhammad Saleem – Frontiers in Microbiology

Water and extremophile microbiome

Complete Genome Sequence of Thermus thermophilus TMY, Isolated from a Geothermal Power Plant – Yasuhiro Fujino – Genome Announcements

Marine Microbes as a Potential Source of Cellulolytic Enzymes – N. Trivedi – Chapter 2 of Advances in Food and Nutrition Research, Vol. 79

Genetic toolbox for controlled expression of functional proteins in Geobacillus spp. – Ivan Pogrebnyakov – PLoS One

Coupled Effects of Electrical Stimulation and Antibiotics on Microbial Community in Three-Dimensional Biofilm-Electrode Reactors – Hai-Liang Song – Water, Air, & Soil Pollution

Do biofilm communities respond to the chemical signatures of fracking? A test involving streams in North-central Arkansas – Wilson H. Johnson – BMC Microbiology

Effects of chemical cleaning on RO membrane inorganic, organic and microbial foulant removal in a full-scale plant for municipal wastewater reclamation – Tong Yu – Water Research

Microbial nitrification, denitrification and respiration in the leached cinnamon soil of the upper basin of Miyun Reservoir – Wen Xu – Scientific Reports

Microbes in space

The Effects of HZE Particles, γ and X-ray Radiation on the Survival and Genetic Integrity of Halobacterium salinarum NRC-1, Halococcus hamelinensis, and Halococcus morrhuae – Leuko Stefan – Astrobiology

Survival, DNA Integrity, and Ultrastructural Damage in Antarctic Cryptoendolithic Eukaryotic Microorganisms Exposed to Ionizing Radiation – Pacelli Claudia – Astrobiology

Phages and viruses

Genomic sequence of ‘Candidatus Liberibacter solanacearum’ haplotype C and its comparison with haplotype A and B genomes – Jinhui Wang – PLoS One


Microbial Typing by Machine Learned DNA Melt Signatures – Nadya Andini – Scientific Reports


From Culture to High-Throughput Sequencing and Beyond: A Layperson’s Guide to the “Omics” and Diagnostic Potential of the Microbiome – Paul W. O’Toole – Gastroenterology Clinics of North America

Microbes in the news

2017 sneak peek: What the new year holds for science – Elizabeth Gibney – Nature

Is It the “Terrible Twos”? Or Is It a Disrupted Gut Microbiome? – Chris Kresser

Microbes on the market

Human Microbiome Market : Global Market Snapshot by 2020 – Persistence Market Research

6 thoughts on “February 8, 2017

    • Thanks for the feedback, CC. This article was actually not that bad; even had citations from scientific papers. I do hope you enjoyed the dozens of other great links in this post. – Elisabeth Bik


  1. My issue isn’t the quality of his writing! Kresser’s blogs help him drum up business for his consultation business. That’s fine, that’s his business model, good for him. My objection is that linking to his post could be seen as some sort of endorsement from microbiome digest. The articles referenced could have been posted here without a link to his website and name. It’s not like he wrote the articles himself, right? It’s just weird because microbiome digest doesn’t usually link to commercial products or websites (apart from the colgate thing a few weeks back). I don’t know if I communicated what I wanted to say. I wasn’t trying to be snarky – it’s just weird to see commercial stuff linked to here when it’s usually just links to papers.


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