July 3, 2019

Today’s Digest is short with a few articles from Scientific Reports and bioRxiv, spanning six areas, with two highlights added. Enjoy!

General microbiology

Preprint: Single Nanoparticle Tracking Reveals Efficient Long-Distance Undercurrent Transport above Swarming Bacteria – Jingjing Feng et al. – bioRxiv

Human gut microbiome

Preprint (correlation not causation): Parkinson’s disease-associated alterations of the gut microbiome can invoke disease-relevant metabolic changes – Federico Baldini et al. – bioRxiv

Plant, root and soil microbiome

Effect of Straw and Straw Biochar on the Community Structure and Diversity of Ammonia-oxidizing Bacteria and Archaea in Rice-wheat Rotation Ecosystems – Hanlin Zhang et al. – Scientific Reports

Water and extremophile microbiome

Diversity and extracellular enzyme activities of heterotrophic bacteria from sediments of the Central Indian Ocean Basin – Vijayshree S. Gawas et al. – Scientific Reports

Preprint: Energetic and Environmental Constraints on the Community Structure of Benthic Microbial Mats in Lake Fryxell, Antarctica – Megan Dillon et al. – bioRxiv

** Isolation and characterization of a thermophilic sulfur- and iron-reducing thaumarchaeote from a terrestrial acidic hot spring – Shingo Kato et al. – The ISME Journal

Phages and viruses

** Review: Phage Therapy in the Twenty-First Century: Facing the Decline of The Antibiotic Era; Is it Finally Time for The Age of the Phage? – Shayla Hesse and Sankar Adhya – Annual Review of Microbiology

Education

Preprint: Developing critical thinking in STEM education through inquiry-based writing in the laboratory classroom – Ah Jung Jeon et al. – bioRxiv

Preprint: Genetic research at the intersection of gender identity, sexual orientation, and mental health: community attitudes and recommendations for researchers – Taylor R Thomas et al. – 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

July 1, 2019

Today’s Monday digest is about microbiome changes in diseases such as Parkinson’s disease, schizophrenia, colorectal cancer and inflammatory bowel disease; review on importance of pig microbiota and impact of fecal storage protocols on microbial diversity and composition.

General microbiome

The pig microbiota and the potential for harnessing the power of the microbiome to improve growth and health – Nirosh D Aluthge – Journal of Animal Science

Microbial genes and pathways in inflammatory bowel disease – Melanie Schirmer – Nature Reviews Microbiology

Human microbiome

Changes in Gut Microbiome after Bariatric Surgery Versus Medical Weight Loss in a Pilot Randomized Trial – Clare J. Lee – Obesity Surgery

Microbiome Signatures Associated with Steatohepatitis and Moderate to Severe Fibrosis in Children With Nonalcoholic Fatty Liver Disease – Jeffrey B. Schwimmer – Gastroenterology

Altered gut microbiota and mucosal immunity in patients with schizophrenia – Ruihuan Xu – Brain Behavior and Immunity

Patients Eligible for Trials of Microbe-based Therapeutics do not Represent the Population With Recurrent Clostridioides difficile Infection – Colleen R. Kelly – Clinical Gastoenterology and Hepatology

A role for the mammalian female reproductive tract microbiome in pregnancy outcomes – Babiche A. Heil – Physiological Genomics

Altered intestinal microbiota associated with colorectal cancer – Hong Zhang – Frontiers of Medicine

Gut microbiota is associated with adiposity markers and probiotics may impact specific genera – Aline Corado Gomes – European Journal of Nutrition

Consistent alterations in faecal microbiomes of patients with primary sclerosing cholangitis independent of associated colitis – Malte Ruhlemann – Alimentary Pharmacology and Therapeutics

Altered gut microbiota and inflammatory cytokine responses in patients with Parkinson’s disease – Chin-Hsien Lin – Journal of Neuroinflammation

Animal experiments

Hypergravity disrupts murine intestinal microbiota – Corentine Alauzet – Scientific Reports

Dietary fructose-induced gut dysbiosis promotes mouse hippocampal neuroinflammation: a benefit of short-chain fatty acids – Jian-Mei Li – Microbiome

Gut microbiota depletion from early adolescence alters adult immunological and neurobehavioral responses in a mouse model of multiple sclerosis – Maryam Zeraati – Neuropharmacology

Enrichment of intestinal Lactobacillus by enhanced secretory IgA coating alters glucose homeostasis in P2rx7−/− mice – Lisa Perruzza – Scientific Reports

Plant, root, soil microbiome

Higher stochasticity of microbiota composition in seedlings of domesticated wheat compared to wild wheat – Ezgi Özkurt – BioRxiv

Emphasis on the deep or shallow parts of the tree provides a new characterization of phylogenetic distances – Julia Fukuyama – Genome Biology

Techniques

Assessment of the impact of different fecal storage protocols on the microbiota diversity and composition: a pilot study – Shirin Moossavi – BMC Mirobiology

Microbes and the market

Microbiome Sequencing Market players include: Biolog Inc., CosmosID Inc., Illumina Inc., Metabiomics and Oxford Nanopore Technologies Ltd – News Exterior

Global Microbiome Drugs Market NEWS 2019 By Types Probiotics, Prebiotics, Small Molecules, Biological Drugs – Market Reports