Today’s digest has quite a few reviews in “Human Gut Microbiome” section and quite interesting news: what killed Aztecs, the womb might not be sterile, while surfers might be spreading antibiotic-resistant bacteria. Check as well an interesting blog post on “How can academia kick its addiction to the impact factor?” and news about “Dimensions” – new science search engine. Dimensions not only indexes papers and their citations, but also – uniquely among scholarly databases – connects publications to their related grants, funding agencies, patents and clinical trials.
General microbiome
Conserved collateral susceptibility networks in diverse clinical strains of Escherichia coli – Nicole L Podnecky – bioRxiv
Interactions between species introduce spurious associations in microbiome studies – Rajita Menon – PLOS Computational Biology
Antimicrobial resistant Klebsiella pneumoniae carriage and infection in specialized geriatric care wards linked to acquisition in the referring hospital – Claire L Gorrie – Clinical Infectious Diseases
Microbiological and molecular characterization of thermophilic Streptomycesvariabilis with antimicrobial activity – Ramy Fikry – Journal of Basic and Environmental Sciences
Population level evidence for seasonality of the human microbiome – Christina Korownyk – Chronobiology International
Metagenomic analysis of microbial communities yields insight into impacts of nanoparticle design – Jacob W. Metch – Nature Nanotechnology
Microbial Competition of Rhodotorula mucilaginosa UANL-001L and E. coli increase biosynthesis of Non-Toxic Exopolysaccharide with Applications as a Wide-Spectrum Antimicrobial – Augusto Vazquez-Rodriguez – Scientific Reports
Pregnancy and early life
Perturbations of the gut microbiome genes in infants with atopic dermatitis according to feeding type – Min-Jung Lee – Journal of Allergy and Clinical Immunology
Overweight and obesity status in pregnant women are related to intestinal microbiota and serum metabolic and inflammatory profiles – Noora Houttu – Clinical Nutrition
Human respiratory microbiome
Give me a sample of air and I will tell which species are found from your region – molecular identification of fungi from airborne spore samples – Nerea Abrego – Molecular Ecology Resources
Fungi stabilize connectivity in the lung and skin microbial ecosystems – Laura Tipton – BMC Microbiome
Oral microbiome
Microbiome associated with denture malodour – S Yitzhaki – Journal of Breath Research
High-resolution microbiome profiling uncovers Fusobacterium nucleatum, Lactobacillus gasseri/johnsonii, and Lactobacillus vaginalis associated to oral and oropharyngeal cancer in saliva from HPV positive and HPV negative patients treated with surgery and chemo-radiation – Rafael Guerrero-Preston – Oncotarget
Location-Specific Oral Microbiome Possesses Features Associated With CKD – Jianzhong Hu – Kidney International Reports
Oral microbiota reduce wound healing capacity of epithelial monolayers, irrespective of the presence of 5-fluorouracil – Eline Vanlancker – Experimental Biology and Medicine
An experimental study for rapid detection and quantification of endodontic microbiota following photo-activated disinfection via new multiplex real-time PCR assay – Maryam Pourhajibagher – Photodiagnosis and Photodynamic Therapy
Review: Genome analysis and clinical implications of the bacterial communities in early biofilm formation on dental implants restored with titanium or zirconia abutments – Flávia Correa Raffaini – Biofueling
Human skin microbiome
Association of Disease Severity With Skin Microbiome and Filaggrin Gene Mutations in Adult Atopic Dermatitis – Maja-Lisa Clausen – JAMA Dermatology
Human nearly-sterile sites
The Microbiome and Neurologic Disease: Past and Future of a 2-Way Interaction – Javier Ochoa-Repáraz – Neurotherapeutics
Human gut microbiome
Mini Review: Beneficial actions of microbiota-derived tryptophan metabolites – J. J. Galligan – Neurogastroenterology & Motility
Review: Gut microbiome influences on anastomotic leak and recurrence rates following colorectal cancer surgery – S. Gaines – BJS
Review: Microbiota Signaling Pathways that Influence Neurologic Disease – Laura M. Cox – Neurotherapeutics
Review: How mass spectrometric approaches applied to bacterial identification have revolutionized the study of human gut microbiota – Grégory Dubourg – Expert Review of Proteomics
Concise Review: Gut microbiota and probiotics: novel immune system modulators in myasthenia gravis? – Elena Rinaldi – Annals of the New York Academy of Science
Research Highlights: Gut microbiota: Targeting of specific microbial species mitigates colitis – Hugh Thomas – Nature Reviews Gastroenterology and Hepatology
Research Highlights: Gut microbiota: Filling up on fibre for a healthy gut – Katrina Ray – Nature Reviews Gastroenterology and Hepatology
Stachyose Improves Inflammation Through Modulating Gut Microbiota of High-Fat Diet / Streptozotocin Induced Type 2 Diabetes in Rats – Guimei Liu – Molecular Nutrition & Food Research
Analysis of fecal microbiota in patients with functional constipation undergoing treatment with synbiotics – Lin Sheng Huang – European Journal of Clinical Microbiology & Infectious Diseases
The microbiota metabolite indole inhibits Salmonella virulence: Involvement of the PhoPQ two-component system – Nandita Kohli – PLOS
Metatranscriptome of human faecal microbial communities in a cohort of adult men – Galeb S. Abu-Ali – Nature Microbiology
Early-life gut microbial colonization shapes Th1/Th2 balance in asthma model in BALB/c mice – Li-Juan Qian –
Animal experiments
Impact of Trans-Fats on Heat-Shock Protein Expression and the Gut Microbiota Profile of Mice – Gessika Cristina Borges Castro Carvalho – Journal of Food Science
Animal microbiome
The impact of depuration on mussel hepatopancreas bacteriome composition and predicted metagenome – J. A. Rubiolo – Antonie van Leeuwenhoek
The Sarda Sheep Host Fecal Proteome – Antonio Palomba – Proteomics
Interactions Between Parasites and the Bacterial Microbiota of Chickens – Rüdiger Hauck – Avian Diseases
Plant, root, and soil microbiome
Cropping practices manipulate abundance patterns of root and soil microbiome members paving the way to smart farming – Kyle Hartman – BMS Microbiome
Saving seed microbiomes – Gabriele Berg – The ISME
Rice Crop Growth and Rhizospheric Microbial Dynamics in Heavy Metals Contaminated Inceptisol – Manoj Shrivastava – Water Quality Management
Cropping practices manipulate abundance patterns of root and soil microbiome members paving the way to smart farming – Kyle Hartman – BMC Microbiome
Water and extremophile microbiome
Diverse spatial organization of photosynthetic membranes among purple nonsulfur bacteria – Breah LaSarre – bioRxiv
Homologous recombination and transposon propagation shapes the population structure of an organism from the deep subsurface with minimal metabolism – Alexander J Probst – bioRxiv
Cultivation and genomics of the first freshwater SAR11 (LD12) isolate – Michael Winslow Henson -bioRxiv
Data Descriptor: The reconstruction of 2,631 draft metagenome-assembled genomes from the global oceans – Benjamin J. Tully – Scientific Data
Survey of sulfur-oxidizing bacterial community in the Pearl River water using soxB, sqr, and dsrA as molecular biomarkers – Jianfei Luo – 3 Biotech
Cultivable fungi present in Antarctic soils: taxonomy, phylogeny, diversity, and bioprospecting of antiparasitic and herbicidal metabolites – Eldon C. Q. Gomes – Extremophiles
Taxonomical Resolution and Distribution of Bacterioplankton Along the Vertical Gradient Reveals Pronounced Spatiotemporal Patterns in Contrasted Temperate Freshwater Lakes – J. Keshri – Microbial Ecology
Coral physiology and microbiome dynamics under combined warming and ocean acidification – Andréa G. Grottoli – PLOS
Crenothrix are major methane consumers in stratified lakes – Kirsten Oswald – The ISME
Food microbiology
Review: Modern perspectives on the health benefits of kefir in next generation sequencing era: improvement of the host gut microbiota – Dong-Hyeon Kim – Critical Reviews in Food Science and Nutrition
Probiotics / prebiotics
Lactobacillus acidophilus Improves Intestinal Inflammation in an Acute Colitis Mouse Model by Regulation of Th17 and Treg Cell Balance and Fibrosis Development – Park Jin-Sil – Journal of Medicinal Food
Phages and viruses
Interferons: Reprogramming the Metabolic Network against Viral Infection – Kavita Raniga – Viruses
Bioinformatics
FastViromeExplorer: a pipeline for virus and phage identification and abundance profiling in metagenomics data – Saima Sultana Tithi – PeerJ
VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data – Jie Ren – BMC Microbiome
Techniques
In-depth resistome analysis by targeted metagenomics – Val F. Lanza – BMC Microbiome
Microbes in the news
500 years later, scientists discover what probably killed the Aztecs
Could baby’s first bacteria take root before birth?
Robotic baby helps researchers understand how biological dust develops immunity in crawling babies
Surfers May Be Spreading Antibiotic-Resistant Bacteria From Swallowing Poop-Laced Water
Microbes and Art
Artist Hunter Cole Presents Exhibit Featuring Photos of Bacteria That Create Their Own Light
Science, publishing, and career
Science search engine links papers to grants and patents
How can academia kick its addiction to the impact factor?
