This digest has a study on the human hair microbiome, lots of animal studies and experiments, the normal long list of soil/plant publications, some water/extremophile studies, and a few interesting bioinformatics articles. Enjoy!
Events and jobs
There were some very cool events to check out from my employer, GENEWIZ, this past month. Every year here there is a celebration with a number of different events called GENEWIZ Week. Check out this past set of events below:
GENEWIZ Webinars – definitely check these cool talks out. You can access past talks, like mine on Metagenomics from 2017, at GENEWIZ Webinars Archive and my past webinar here: Metagenomics for Biomarker Discovery: Precision Medicine Applications
General microbiome
[pre-print] Free-living Bacterial Communities Are Mostly Dominated by Oligotrophs – Yingnan Gao – bioxRiv
Pregnancy and early life
Pilot assessment of probiotics for pregnant women in Rwanda – Amy McMillan – PLOS ONE
Human respiratory microbiome
* The respiratory virome in chronic obstructive pulmonary disease – Marian Garcia-Nuñez – Future Medicine
TRANSPLANTING THE PULMONARY VIROME: DYNAMICS OF TRANSIENT POPULATIONS – Alicia B Mitchell – The Journal of Heart and Lung Transplantation
Human skin microbiome
** Spatial and Environmental Variation of the Human Hair Microbiota – Lauren Brinkac – Scientific Reports
Human oral microbiome
Denture-Associated Oral Microbiome and Periodontal Disease Causing an Anaerobic Pyogenic Liver Abscess in an Immunocompetent Patient: A Case report and Review of the Literature – Muhammad Bader Hammami – Gastroenterology Research
Human gut microbiome
Changes in Gastric Microbiota during Gastric Carcinogenesis – Sun-Young Lee – KoreaMed Synapse
ADTU-05 Gut microbial composition in the migrant south-asian IBD population in UK – Mohammed Quraishi – BMJ Journals (Gut)
Gut Microbiota Dysbiosis and Diarrhea in Kidney Transplant Recipients – Lee JR – American Journal of Transplantation
The microbiome in autoimmune diseases – Fabrizio De Luca – Clinical and Experimental Immunology
Suppression of IL-17F, but not of IL-17A, provides protection against colitis by inducing Treg cells through modification of the intestinal microbiota – Ce Tang – Nature Immunology
* Characteristics of the bacterial microbiome in association with common intestinal parasites in irritable bowel syndrome – Laura Rindom Krogsgaard – Clinical and Translational Gastroenterology
Fecal microbiota transplantation for recurrent Clostridium difficile infection – Susy S. Hota – CMAJ
(not just human) The Expensive-Tissue Hypothesis in Vertebrates: Gut Microbiota Effect, a Review – Chun Hua Huang – International Journal of Molecular Sciences
Mediterranean Diet Score: Associations with Metabolic Products of the Intestinal Microbiome, Carotid Plaque Burden, and Renal Function – Michael Pignanelli – Nutrients
Animal experiments
Rumen Microbial Community of Saanen Goats Adapted to a High‐Fiber Diet in the Northeast of Iran – S.H. Ebrahimi – Iranian Journal of Applied Animal Science
Humic substances alter ammonia production and the microbial populations within a RUSITEC fed a mixed hay – concentrate diet – Stephanie A. Terry – Frontiers in Microbiology
Intestinal Microbiota Ecological Response to Oral Administrations of Hydrogen-Rich Water and Lactulose in Female Piglets Fed a Fusarium Toxin-Contaminated Diet – Weijiang Zheng – Toxins
Animal microbiome
Archaeal and bacterial diversity and community composition from 18 phylogenetically divergent sponge species in Vietnam – Ton That Huu Dat – PeerJ Microbiology
Gut bacterial and fungal communities of the domesticated silkworm (Bombyx mori) and wild mulberry-feeding relatives – Bosheng Chen – The ISME Journal
Gut bacterial and fungal communities of the domesticated silkworm (Bombyx mori) and wild mulberry-feeding relatives – Bosheng Chen – The ISME Journal
Aetiological Characterization of the Cutaneous Ulcer Syndrome in Papua New Guinea using Shotgun Metagenomics – Marc Noguera-Julian – Clinical Infectious Diseases
Inter-population variation in the Atlantic salmon microbiome reflects environmental and genetic diversity – Tamsyn M. Uren Webster – Applied and Environmental Microbiology
Plant, root, and soil microbiome
Influence of Belowground Herbivory on The Dynamics of Root and Rhizosphere Microbial Communities – Morgane Ourry – Frontiers of Ecological Evolution
* Plant species and heavy metals affect biodiversity of microbial communities associated with metal-tolerant plants in metalliferous soils – Sławomir Borymski – Frontiers in Microbiology
Functional Microbial Features Driving Community Assembly During Seed Germination and Emergence – Torres-Cortés Gloria – Frontiers in Plant Science
Influence of the Chemical Form of Antimony on Soil Microbial Community Structure and Arsenite Oxidation Activity – Kataoka T – Europe PMC
Recognizing Patterns: Spatial Analysis of Observed Microbial Colonization on Root Surfaces – Hannes Schmidt – Frontiers in Environmental Science
Microbial diversity of tobacco rhizosphere soil in different growth stages of marigold-tobacco intercropping system – Xia TiYuan – Editorial Department of Southwest China Journal of Agricultural Sciences
Differences in rice rhizosphere bacterial community structure by application of lignocellulolytic plant-probiotic bacteria with rapid composting traits – Thounaojam Nevita – Ecological Engineering
Data on molecular identification, phylogeny and in vitro characterization of bacteria isolated from maize rhizosphere in Cameroon – Tchuisseu Tchakounté Gylaine Vanissa – Data in Brief
[pre-print] A comprehensive mycofloral diversity of pedosphere, phyllosphere and aerosphere of Som. (Persea bombycina Kost.) -Manjit Kumar Ray – bioRxiv
Rhizosphere Microbiomes Modulated by Pre-crops Assisted Plants in Defense Against Plant-Parasitic Nematodes – Ahmed Elhady – Frontiers in Microbiology
The culturable endophytic fungal communities of switchgrass grown on a coal-mining site and their effects on plant growth – Ye Xia – PLOS ONE
Arbuscular mycorrhizal fungi stimulate organic phosphate mobilization associated with changing bacterial community structure under field conditions – Lin Zhang – Environmental Microbiology
Water and extremophile microbiome
Metagenomic insights into diazotrophic communities across Arctic glacier forefields – Maisie V. Nash – FEMS Microbiology Ecology
Microbial community shifts in response to acid mine drainage pollution within a natural wetland ecosystem – Oscar E. Aguinaga – Frontiers in Microbiology
Heterogeneity of interactions of microbial communities in regions of Taihu Lake with different nutrient loadings: A network analysis – Xinyi Cao – Scientific Reports
Diversity and functionality of archaeal, bacterial and fungal communities in deep Archaean bedrock groundwater – Lotta Purkamo – FEMS Microbial Ecology
Reduced arsenic availability and plant uptake and improved soil microbial diversity through combined addition of ferrihydrite and Trichoderma asperellum SM-12F1 – Hongxiang Zhang – Environmental Science and Pollution Research
Fungi from Admiralty Bay (King George Island, Antarctica) Soils and Marine Sediments – Lia Costa Pinto Wentzel – Microbial Ecology
Bioinformatics
When old metagenomic data meet newly sequenced genomes, a case study – Xin Li – PLOS ONE
PERFect: PERmutation Filtering test for microbiome data – Ekaterina Smirnova – Biostatistics
Ed’s non-microbiology picks
Photochemistry beyond the red limit in chlorophyll f–containing photosystems – Dennis J. Nürnberg – Science
Research Finds Tipping Point for Large-scale Social Change
LACK OF PAID SICK LEAVE INCREASES POVERTY
Toxic toads could devastate Madagascar’s biodiversity – Science
Effects of 8-hour time restricted feeding on body weight and metabolic disease risk factors in obese adults: A pilot study – Kelsey Gabel – Nutrition and Healthy Aging
Forget in a Flash: A Further Investigation of the Photo-Taking-Impairment Effect – Julia S. Soares – Journal of Applied Research in Memory and Cognition
New discovery about the brain’s water system may prove beneficial in stroke
DNA repair processes are critical mediators of p53-dependent tumor suppression – Ana Janic – Nature Medicine
Astronomers find a galaxy unchanged since the early universe
Microbiome Digest - Bik's Picks 