Today’s rich Digest features a report on how persister pathogens can spread antibiotic resistant plasmids, a study on how diet might alleviate Alzheimer’s, and a screen for the effect of microbiome on diabetes drug efficacy. Other highlights include the evolution and ecology of animal gut microbial communities, microbial communities in soils with radioactive contamination, and free microbiome standards by Zymo Research. Happy reading!
General microbiology
The horizontal gene transfer of Agrobacterium T-DNAs into the series Batatas (Genus Ipomoea) genome is not confined to hexaploid sweetpotato – Dora G. Quispe-Huamanquispe et al. – Scientific Reports
Simulations reveal challenges to artificial community selection and possible strategies for success – Li Xie et al. – PLoS Biology
Primer: Artificially selecting microbial communities: If we can breed dogs, why not microbiomes? – Flor I. Arias-Sánchez et al. – PLoS Biology
Antimicrobial resistance
** Salmonella persisters promote the spread of antibiotic resistance plasmids in the gut – Erik Bakkeren et al. – Nature
Pregnancy and early life
Prenatal antibiotics exposure and the risk of autism spectrum disorders: A population-based cohort study – Amani F. Hamad et al. – PLoS One
Visualization of microbes by 16S in situ hybridization in term and preterm placentas without intraamniotic infection – Maxim D. Seferovic et al. – AJOG
Fetal exposure to the maternal microbiota in humans and mice – Noelle Younge et al. – JCI Insight
Fungi form interkingdom microbial communities in the primordial human gut that develop with gestational age – Kent A. Willis et al. – FASEB J.
Human oral and esophageal microbiome
In vitro: The inhibitory effect of quaternary ammonium salt on bacteria in root canal – Sanjay Kumar Tiwari et al. – Scientific Reports
Alterations to the Esophageal Microbiome Associated with Progression from Barrett’s Esophagus to Esophageal Adenocarcinoma – Erik J. Snider et al. – Cancer Epidemiology, Biomarkers & Prevention
Human respiratory microbiome
Review: The microbiome in bronchiectasis – Hollian Richardson et al. – European Respiratory Review
Human gut microbiome
Gut microbiota alterations associated with reduced bone mineral density in older adults – Mrinmoy Das et al. – Rheumatology
Press: Confounding factors in the effect of gut microbiota on bone density – Rajeev Aurora – Rheumatology
Characterization of Proximal Small Intestinal Microbiota in Patients With Suspected Small Intestinal Bacterial Overgrowth – Andrea S. Shin et al. – Clinical and Translational Gastroenterology
Gut microbiota shifts in patients with gastric cancer in perioperative period – Liang, Weiren et al. – Medicine
Human gut-microbiome-brain axis
** Modified Mediterranean-ketogenic diet modulates gut microbiome and short-chain fatty acids in association with Alzheimer’s disease markers in subjects with mild cognitive impairment – Ravinder Nagpal et al. – EBioMedicine
Press: Diet’s effect on gut bacteria could play role in reducing Alzheimer’s risk – Science Daily
Systemic review and meta-analysis of alcohol induced gut dysbiosis and the resulting behavioral impact – Nayab Qamar et al. – Behavioral Brain Research
Review: The Microbiota-Gut-Brain Axis – John F. Cryan et al. – Physiological Reviews
Human multi-site microbiome
Prosthetic joint infections present diverse and unique microbial communities using combined whole-genome shotgun sequencing and culturing methods – Abigail A. Weaver et al. – Journal of Medical Microbiology
Metabolomics
Metabolic switches from quiescence to growth in synchronized Saccharomyces cerevisiae – Jinrui Zhang et al. – Metabolomics
Animal experiments
Dietary inulin alters the gut microbiome, enhances systemic metabolism and reduces neuroinflammation in an APOE4 mouse model – Jared D. Hoffman et al. – PLoS One
Beneficial roles of probiotics on the modulation of gut microbiota and immune response in pigs – Donghyun Shin et al. – PLoS One
Effects of antibacterial peptides on rumen fermentation function and rumen microorganisms in goats – Zhihua Ren et al. – PLoS One
** Host-Microbe-Drug-Nutrient Screen Identifies Bacterial Effectors of Metformin Therapy – Rosina Pryor et al. – Cell
Press: An Elegan(t) screen shows how the microbiome improves drug efficacy – MRC Research News
Rat: Variation in the gut microbial community is associated with the progression of liver regeneration – Qiongling Bao et al. – Hepatology Research
Animal microbiome
The Pacific harbor seal gut microbiota in Mexico: Its relationship with diet and functional inferences – Arlette Pacheco-Sandoval et al. – PLoS One
Gut microbiota features associated with Clostridioides difficile colonization in puppies – Alexander S. F. Berry et al. – PLoS One
Gut microbiota and their putative metabolic functions in fragmented Bengal tiger population of Nepal – Dibesh Karmacharya et al. – PLoS One
Cadmium and selenate exposure affects the honey bee microbiome and metabolome, and bee-associated bacteria show potential for bioaccumulation – Jason A. Rothman et al. – Applied and Environmental Microbiology
* Review: Evolutionary and Ecological Consequences of Gut Microbial Communities – Nancy A. Moran et al. – Annual Reviews of Ecology, Evolution & Systemactics
Defining the distinct skin and gut microbiomes of the northern pike (Esox lucius) – Elizabeth M. Reinhart et al. – Frontiers in Microbiology
Predicting the unpredictable: How host specific is the mycobiota of bark and ambrosia beetles? – Kirsten E. Miller et al. – Fungal Ecology
Plant, root and soil microbiome
Preprint: The microbiome as a biosensor: functional profiles elucidate hidden stress in hosts – Avihai Zolti et al. – bioRxiv
Soil indigenous microbiome and plant genotypes cooperatively modify soybean rhizosphere microbiome assembly – Fang Liu et al. – BMC Microbiology
* Community structure and functional genes in radionuclide contaminated soils in Chernobyl and Fukushima – Carolina Hoyos-Hernandez et al. – FEMS Microbiology Letters
Microalgae and phototrophic purple bacteria for nutrient recovery from agri-industrial effluents: Influences on plant growth, rhizosphere bacteria and putative carbon and nitrogen cycling genes – Somayeh Zarezadeh et al. – Frontiers in Plant Science
Shifts and recovery of soil microbial communities in a 40-year field trial under mineral fertilization – Jiří Čuhel et al. – Pedobiologia
Water and extremophile microbiome
Identification of soluble microbial products (SMPs) from the fermentation and methanogenic phases of anaerobic digestion – C. Kunacheva et al. – Science of the Total Environment
Review: Microbial mercury methylation in the cryosphere: Progress and prospects – Prakriti Sharma Ghimire et al. – Science of the Total Environment
Rapid Colonization of Uranium Mining-Impacted Waters, the Biodiversity of Successful Lineages of Phytoplankton Extremophiles – Beatriz Baselga-Cervera – Microbial Ecology
Relationship between microbial community and environmental conditions in a constructed wetland system treating greywater – F.S.Bernardes et al. – Ecological Engineering
Built environment microbiome
Microbial Exchange via Fomites and Implications for Human Health – Brent Stephens et al. – Current Pollution Reports
Phages and viruses
Faecal Virome Analysis of Wild Animals from Brazil – Matheus A. Duarte et al. – Viruses
Bioinformatics
Accurate estimation of microbial sequence diversity with Distanced – Timothy J Hackmann – Bioinformatics
Microbes in the news
Researchers reveal how bacteria behind hospital infections block out antibiotics – Dumbarton and Vale of Leven Reporter
Using mouthwash could reduce benefits of exercise – Dumbarton and Vale of Leven Reporter
* A comprehensive catalogue of human digestive tract bacteria – Anne Trafton – MIT News
No poop required: Researchers devise blood test for gut microbiome diversity using data from defunct startup Arivale – James Thorne – Geek Wire
* Zymo Research Distributes Free Microbiome Standards and Controls – PR Newswire
Top List: Trending in microbiome: From comprehensive culture workflows, to novel biotherapeutics, and microbial characterization – Select Science
APC Researcher Awarded Global Grant For Gut Health – APC Microbiome Ireland
* Poop-testing startup uBiome was once valued at $600 million by Silicon Valley’s top VCs. It just filed for bankruptcy – Erin Brodwin & Emma Court – Business Insider
Gut feeling: How a healthy microbiome helps beat stress and lift mood – Scott Anderson – New Scientist
HLA Alleles With Risk for Ankylosing Spondylitis, Rheumatoid Arthritis Affect Gut Microbiome – Hannah Dellabella – Rheumatology Advisor
How the microbiome movement can be beneficial to you overall health – KUSI Newsroom
No microbiome is an island, survey reveals – Elizabeth Pennisi – Science
Microbes on the market
Metagenomic Analysis of the Human Microbiome – Technology Networks
Update note: Added additional pregnancy/neonatal microbiome papers – Sept 15, @kentmd
Microbiome Digest - Bik's Picks 