Today’s digest features a lot of great “gut microbiome papers”, with a focus on precision medicine.
Events and jobs
Scientist, Computational Biology – Flagship Pioneering, VL45 Company LocationCambridge, Massachusetts
Human gut microbiome
** Microbiota Accessible Carbohydrates Facilitate Clearance of Clostridium difficile – Andrew J Hryckowian – bioRxiv **
** Precision medicine using microbiota – Christian Jobin – Science
Highlights three articles, including:
* The commensal microbiome is associated with anti-PD-1 efficacy in metastatic melanoma patients – Vyara Matson – Science
* Gut microbiome influences efficacy of PD-1–based immunotherapy against epithelial tumors – Bertrand Routy – Science
* Gut microbiome modulates response to anti–PD-1 immunotherapy in melanoma patients – V. Gopalakrishnan – Science **
Exploring Gut Microbiota Composition as an Indicator of Clinical Response to Dietary FODMAP Restriction in Patients with Irritable Bowel Syndrome – Jørgen Valeur – Digestive Diseases And Sciences
Mucus Microbiome of Anastomotic Tissue During Surgery Has Predictive Value for Colorectal Anastomotic Leakage – Jasper B van Praagh – Annals Of Surgery
Review: Local Acetaldehyde-An Essential Role in Alcohol-Related Upper Gastrointestinal Tract Carcinogenesis – Mikko T Nieminen – Cancers
Review: The Gut-Brain Axis and the Microbiome: Clues to Pathophysiology and Opportunities for Novel Management Strategies in Irritable Bowel Syndrome (IBS). – Eamonn M M Quigley – Journal Of Clinical Medicine
Animal experiments
** Precision editing of the gut microbiota ameliorates colitis – Wenhan Zhu – Nature **
Polystyrene microplastics induce microbiota dysbiosis and inflammation in the gut of adult zebrafish – Yuanxiang Jin – Environmental Pollution
Profiling the lymphoid-resident T cell pool reveals modulation by age and microbiota – Aurélie Durand – Nature Communications
Cultivable anaerobic and aerobic bacterial communities in the fermentation chambers of Holotrichia parallela (coleoptera: scarabaeidae) larvae – Zhen-Yu Zhang – Plos One
The effect of DNA degradation bias in passive sampling devices on metabarcoding studies of arthropod communities and their associated microbiota – Henrik Krehenwinkel – Plos One
The evaluation of the quality of Feng Huang Oolong teas and their modulatory effect on intestinal microbiota of high-fat diet-induced obesity mice model – Yuhui Chen – International Journal Of Food Sciences And Nutrition
Animal microbiome
Host contributes to longitudinal diversity of fecal microbiota in swine selected for lean growth – Duc Lu – Microbiome
Review: Recent insights into the tick microbiome gained through next-generation sequencing – Telleasha L Greay – Parasites & Vectors
Plant, root, and soil microbiome
Responses of soil bacterial community after seventh yearly applications of composted tannery sludge – Ana Roberta Lima Miranda – Geoderma
Assessment of Cu applications in two contrasting soils—effects on soil microbial activity and the fungal community structure – Katharina M. Keiblinger – Ecotoxicology
Microorganisms reveal what plants do not: wheat growth and rhizosphere microbial communities after Azospirillum brasilense inoculation and nitrogen fertilization under field conditions – Luciana P. Di Salvo – Plant and Soil
16S rRNA analysis of diversity of manure microbial community in dairy farm environment – Pramod Pandey – Plos One
Agricultural constraints on microbial resource use and niche breadth in drainage ditches – Ellard R Hunting – Peerj
Water and extremophile microbiome
Accessing chemical diversity from the uncultivated symbionts of small marine animals – Thomas E Smith – Nature Chemical Biology
Macroalgal-bacterial interactions: Role of dimethylsulfoniopropionate in microbial gardening by Ulva (Chlorophyta) – Ralf W. Kessler – Molecular Ecology
Bacterial Recycling of Archaeal Biomass as a New Strategy for Extreme Life in the Dead Sea Deep Sediment – Camille Thomas – EarthArXiv
Unravelling the identity, metabolic potential, and global biogeography of the atmospheric methane-oxidising Upland Soil Cluster α – Jennifer Pratscher – Environmental Microbiology
Book: Optimization and Applicability of Bioprocesses – Hemant J. Purohit and other editors
Articles of interest include:
* Microbial CO2 Fixation Bioprocesses and Desert as Future Carbon Sink – Leena Agarwal
* Biofilm Microenvironments: Modeling Approach – Saheli Ghosh
* Visualization of Microorganisms in Bioprocesses – Tsuyoshi Yamaguchi
Built environment
The effect of temperature on airborne filamentous fungi in the indoor and outdoor space of a hospital – Fariba Abbasi – Environmental Science and Pollution Research
Probiotics / prebiotics / antibiotics
Cross-feeding modulates antibiotic tolerance in bacterial communities – Elizabeth M Adamowicz – bioRxiv
Review: Immune-Mediated Mechanisms of Action of Probiotics and Synbiotics in Treating Pediatric Intestinal Diseases – Julio Plaza-Díaz – Nutrients
Review: How Sweet Are Our Gut Beneficial Bacteria? A Focus on Protein Glycosylation in Lactobacillus. – Dimitrios Latousakis – International Journal Of Molecular Sciences
Phages and viruses
Review: Interactions between Enteric Bacteria and Eukaryotic Viruses Impact the Outcome of Infection – Angela K Berger – Viruses
Bioinformatics
Techniques
News Feature: Can microbes keep time for forensic investigators? – Carolyn Beans – PNAS
Profiling soil microbial communities with next-generation sequencing: the influence of DNA kit selection and technician technical expertise – Taha Soliman – Peerj
Microbes in the news
Caltech breakthrough: Bacteria engineered with ‘sonar’ can track, fight disease – Eric Rosenbaum – CNBC
Microbes on the market
Can’t sleep? It could be your microbiome, says this Cambridge startup – Max Stendahl – Boston Business Journal
Rebiotix and CoreBiome Collaborate on Evaluating Microbiomes of Patients Treated with Microbiota Restoration Therapy™ – Markets Insider
Seres Therapeutics Reports SER-287 Phase 1b Microbiome Analyses that Provide Mechanistic Support for Clinical Efficacy in Ulcerative Colitis – PipelineReview.com