Happy Thanksgiving, everyone! NCBI’s Pubmed nor Google Alerts did not take any holiday, so here is a post stuffed (pun intended) with new papers. For today, I got the microbiome of turkey, red wine, and coprolites. And strain-level variation in human-associated bacteria, cat periodontitis, and historical penguin activity too!
General microbiome
Nurturing the microbiome field: It is exciting to see the nucleus of a grand vision for the field, but we must make the fundamentals of the scientific method central to our mission – Pat Schloss – Science
Book: Microbial Endocrinology: Interkingdom Signaling in Infectious Disease and Health
Chapters include:
- Effects of Stress on Commensal Microbes and Immune System Activity
- Psychological Stress, Immunity, and the Effects on Indigenous Microflora
- Microbiome to Brain: Unravelling the Multidirectional Axes of Communication
- The Role of the Microbiome in the Relationship of Asthma and Affective Disorders
Pregnancy and birth
Preterm gut microbiota and metabolome following discharge from intensive care – Christopher J. Stewart – Scientific Reports
The role of gut microbiota in fetal methylmercury exposure: Insights from a pilot study – Toxicology Letters
Assessing the Intestinal Microbiota in the SHINE Trial – Ethan K. Gough – Clinical Infectious Diseases
Gravidas with Class III Obesity: Evaluating the Abdominal Skin Microbiota Above and Below the Panniculus – Rodney K Edwards – The Journal of Maternal-Fetal & Neonatal Medicine
Review: A Review of Antibiotic Use in Pregnancy – P. Brandon Bookstaver – Pharmacotherapy
Review: On the origin of species: Factors shaping the establishment of infant’s gut microbiota – Niels van Best – Birth Defects Research Part C: Embryo Today: Reviews
Review: Molecular characterization of the human microbiome from a reproductive perspective – Amir Mor – Fertility and Sterility
Review: Reproductive tract microbiome in assisted reproductive technologies – Jason M. Franasiak – Fertility and Sterility
Review: Gynecologic health and disease in relation to the microbiome of the female reproductive tract – Katherine A. Green – Fertility and Sterility
Human skin microbiome
Genetic associations and shared environmental effects on the skin microbiome of Korean twins – Jiyeon Si – BMC Genomics
Human respiratory microbiome
The Sputum Microbiome in Chronic Obstructive Pulmonary Disease Exacerbations
Yvonne J. Huang – Annals of the American Thoracic Society
Review: Clinical Insights into Pulmonary Exacerbations in Cystic Fibrosis from the Microbiome. What Are We Missing? – Fiona J. Whelan – Annals of the American Thoracic Society
Human oral microbiome
Microbiome of titanium and zirconia dental implants abutments – Cássio do Nascimento – Dental Materials
Human gut microbiome
Microbiota and food residues including possible evidence of pre-mammalian hair in Upper Permian coprolites from Russia – Piotr Bajdek – Lethaia
Red wine polyphenols modulate fecal microbiota and reduce markers of the metabolic syndrome in obese patients – Moreno-Indias Isabel – Food & Function
The human gut microbial ecology associated with overweight and obesity determines ellagic acid metabolism – María V. Selma – Food & Function
The severity of NAFLD is associated with gut dysbiosis and shift in the metabolic function of the gut microbiota – Jérôme Boursier – Hepatology
Differences of microbiota in small bowel and faeces between irritable bowel syndrome patients and healthy subjects – Chen-Shuan Chung – Scandinavian Journal of Gastroenterology
Methodology, Not Concept of Fecal Microbiota Transplantation, Affects Clinical Findings – Bota Cui – Gastroenterology
The Gut-Liver Axis in Primary Sclerosing Cholangitis – Bertus Eksteen – Clinics in Liver Disease
Animal models
Anticancer immunotherapy by CTLA-4 blockade relies on the gut microbiota – Marie Vétizou – Science
Antepartum Antibiotic Treatment Increases Offspring Susceptibility to Experimental Colitis: A Role of the Gut Microbiota – Peris Mumbi Munyaka – PLOS ONE
Metabolomic study on the faecal extracts of atherosclerosis mice and its application in a Traditional Chinese Medicine – Feng Tian – Journal of Chromatography B
Animal microbiome
Temporal Relationships Exist Between Cecum, Ileum, and Litter Bacterial Microbiomes in a Commercial Turkey Flock, and Subtherapeutic Penicillin Treatment Impacts Ileum Bacterial Community Establishment – Jessica L. Danzeisen – Frontiers in Veterinary Science
A Pyrosequencing Investigation of Differences in the Feline Subgingival Microbiota in Health, Gingivitis and Mild Periodontitis – Stephen Harris – PLOS ONE
Phylogenetic and ecological factors impact the gut microbiota of two Neotropical primate species – Katherine R. Amato – Oecologia
Plant, root, and soil microbiome
Bacterial diversity is strongly associated with historical penguin activity in an Antarctic lake sediment profile – Renbin Zhu – Scientific Reports
Elk, sagebrush, and saprotrophs: indirect top-down control on microbial community composition and function – Anna R. Peschel – Ecology
Effect of soil salinity and nutrient levels on the community structure of the root-associated bacteria of the facultative halophyte, Tamarix ramosissima, in southwestern United States – Takeshi Taniguchi – Journal of General and Applied Microbiology
Metagenomic insights into communities, functions of endophytes, and their associates with infection by root-knot nematode, Meloidogyne incognita, in tomato roots – Bao-Yu Tia – Scientific Reports
Effect of rice straw application on microbial community and activity in paddy soil under different water status – Fuxia Pan – Environmental Science and Pollution Research
Mapping the Centimeter-Scale Spatial Variability of PAHs and Microbial Populations in the Rhizosphere of Two Plants – Amélia Bourceret – PLOS ONE
Diversity of bacterial endophytes in 3 and 15 year-old grapevines of Vitis vinifera cv. Corvina and their potential for plant growth promotion and phytopathogen control – Marco Andreolli – Microbiological Research
Review: Functions, mechanisms and regulation of endophytic and epiphytic microbial communities of plants – Charles W. Bacon – Symbiosis
Review: Culture-independent discovery of natural products from soil metagenomes – Micah Katz – Journal of Industrial Microbiology & Biotechnology
Built environment microbiology
ISS: Extracellular Lipase and Protease Production from a Model Drinking Water Bacterial Community Is Functionally Robust to Absence of Individual Members – Graham G. Willsey – PLOS ONE
Food microbiology
Bacterial Ecology of Fermented Cucumber Rising pH Spoilage as Determined by Nonculture-Based Methods – Eduardo Medina – Journal of Food Science
Microbial Ecology
Complete nitrification by Nitrospira bacteria – Holger Daims – Nature
Does Microbial Diversity Confound General Predictions? – Marie Duhamel – Trends in Plant Science
Metagenomics and bioinformatics
Population genetic analyses of metagenomes reveal extensive strain-level variation in prevalent human-associated bacteria – Stephen Nayfach – BioRxiv
Techniques
Robust and effective methodologies for cryopreservation and DNA extraction from anaerobic gut fungi – Kevin V. Solomon – Anaerobe
Collecting Fecal Samples for Microbiome Analyses in Epidemiology Studies – Rashmi Sinha – Cancer Epidemiology, Biomarkers & Prevention
Microbes in the news
Is Double-Dipping Okay? CFUs in 4 types of dips after double dipping – Digg
New Research Reveals Bacteria Associated With Feline Gum Disease for the First Time – PR Newswire
Mission space food: Sugar-growing bacteria go into orbit – Clare Wilson – New Scientist
Your Coffee Machine Is a Breeding Ground for Caffeine-Resistant Bacteria – Matthew Braga – Motherboard
Your Poop Knows Best–New Study Shows Microbiome Can Help Predict Health Responses to Certain Foods – Patrick Mustain – Scientific American
Science, publishing, and career
China pursues fraudsters in science publishing – Mara Hvistendahl – Science
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