Today’s Digest features a report that different types of tobacco products can cause oral microbial dysbiosis, an update on fecal microbiome transplant, and exploration into Westernization and evolution of gut microbiota. Enjoy reading!

General microbiology

Alterations of Salmonella Typhimurium Antibiotic Resistance under Environmental Pressure – Mengfei Peng et al. – Applied and Environmental Microbiology

Preprint: Experimental demonstration that screening can enable the environmental recruitment of a defensive microbiome – Tabitha Innocent et al. – bioRxiv

Human oral microbiome

Chicken or the Egg: Microbial Alterations in Biopsy Samples of Patients with Oral Potentially Malignant Disorders – Gabor Decsi et al. – Pathology & Oncology Research

** Types of tobacco consumption and the oral microbiome in the United Arab Emirates Healthy Future (UAEHFS) Pilot Study – Yvonne Vallès et al. – Scientific Reports

Human respiratory microbiome

Decreased microbiome diversity in the HIV small airway epithelium – Stella Xu et al. – Respiratory Research

Human gut microbiome

Antibiotic Exposure and Reduced Short Chain Fatty Acid Production after Hematopoietic Stem Cell Transplant – Lindsey ERomick-Rosendale et al. – Biology of Blood and Marrow Transplantation

** Review: Fecal Microbiota Transplantation: Current Status in Treatment of GI and Liver Disease – Byron P.Vaughn et al. – Clinical Gastroenterology and Hepatology

The association between the incidence of intestinal graft-versus-host disease and antibiotic use after allogeneic hematopoietic stem cell transplantation – Daisuke Hidaka et al. – Clinical Transplantation

Ecological effects of cefepime use during antibiotic cycling on the Gram-negative enteric flora of ICU patients – Carola Venturini et al. – Intensive Care Medicine Experimental

** Gut microbiota is associated with obesity and cardiometabolic disease in a population in the midst of Westernization – Jacobo de la Cuesta-Zuluaga et al. – Scientific Reports

A diverse range of human gut bacteria have the potential to metabolise the dietary component gallic acid – María Esteban-Torres et al. – Applied and Environmental Microbiology

Metagenomic analysis of gut microbial communities from a Central Asian population – Almagul Kushugulova et al. – BMJ Open

Animal experiments

Early cellular responses of germ-free and specific-pathogen-free mice to Francisella tularensis infection – ZuzanaKrocova et al. – Microbial Pathogenesis

Rat: Gut microbiota modulation accounts for the neuroprotective properties of anthocyanins – Cláudia Marques et al. – Scientific Reports

Mouse: Complementary intestinal mucosa and microbiota responses to caloric restriction – Kalina Duszka et al. – Scientific Reports

Greater Microbial Translocation and Vulnerability to Metabolic Disease in Healthy Aged Female Monkeys – Quentin N. Wilson et al. – Scientific Reports

Medicinal Mushrooms Supplements Alter Chicken Intestinal Microbiome – Janelle Robinson et al. – International Journal of Medicinal Mushrooms

Review: Standardization in host-microbiota interaction studies: challenges, gnotobiology as a tool, and perspective – Catherine Mooser et al. – Current Opinion in Microbiology

Animal microbiome

Review: Where in the serotonergic system does it go wrong? Unravelling the route by which the serotonergic system affects feather pecking in chickens – Elske N.de Haas & Jerine A.J.van der Eijk – Neuroscience & Biobehavioral Reviews

Exploring the pathology of an epidermal disease affecting a circum-Antarctic sea star – Laura Núñez-Pons et al. – Scientific Reports

Assessment of rumen microbiota from a large cattle cohort reveals the pan and core bacteriome contributing to varied phenotypes – Mingyuan Xue et al. – Applied and Environmental Microbiology

Preprint: Whole genome screen reveals a novel relationship between Wolbachia and Drosophila host translation – Yolande Grobler et al. – bioRxiv

Food microbiology

Dynamics and biodiversity of bacterial and yeast communities during the fermentation of cocoa beans – Jatziri Mota-Gutierrez et al. – Applied and Environmental Microbiology

Plant, root and soil microbiome

Alternate life history phases of a common seaweed have distinct microbial surface communities – Matthew A Lemay et al. – Molecular Ecology

Diversity of bacterial microbiota of coastal halophyte Limonium sinense and amelioration of salinity stress damage by symbiotic plant growth-promoting actinobacterium Glutamicibacter halophytocola KLBMP 5180 – Sheng Qin et al. – Applied and Environmental Microbiology

Bacterial microbiota protect an invasive bark beetle from a pine defensive compound – Chihang Cheng et al. – Microbiome

Structural inflexibility of the rhizosphere microbiome in mangrove plant Kandelia obovata under elevated CO2 – Panqing Yin et al. – Marine Environmental Research

Mutualistic fungus Phomopsis liquidambari increases root aerenchyma formation through auxin-mediated ethylene accumulation in rice (Oryza sativa L.) – Li-Yan Hu et al. – Plant Physiology and Biochemistry

Characteristics of archaea and bacteria in rice rhizosphere along a mercury gradient – Ming Ma et al. – Science of The Total Environment

Isolation and diversity of culturable rhizobacteria associated with economically important crops and uncultivated plants in Québec, Canada – Di Fan et al. – Systematic and Applied Microbiology

Phages and viruses

Hordes of Phages in the Gut of the Tilapia Sarotherodon melanotheron – Yvan Bettarel et al. – Scientific Reports

Bioinformatics

Joint Analysis of Long and Short Reads Enables Accurate Estimates of Microbiome Complexity – Anton Bankevich & Pavel A.Pevzner – Cell Systems

Microbes in the news

Gut bacteria can protect against Salmonella infections – Press Trust of India – Business Standard