August 23, 2017

Today, a short Digest but with interesting features: effects of intestinal cleanout on microbiota, changes in K vitamin derivatives in human, reviews about Streptococcus group B and effect of FMT on Clostridium difficile, and more.

Human microbiome

Multidomain analyses of a longitudinal human microbiome intestinal cleanout perturbation experiment – Julia Fukuyama – PLoS Computational Biology

Research Highlight: Gut microbiota: Gas-induced GLP1 release – David Holmes – Nature Reviews Endocrinology

Maternal obesity is associated with gut microbial metabolic potential in offspring during infancy – Tomás Cerdó – Journal of Physiology and Biochemistry

Fecal concentrations of bacterially derived vitamin K forms are associated with gut microbiota composition but not plasma or fecal cytokine concentrations in healthy adults – J Philip Karl – The American Journal of Clinical Nutrition

Temporal Stability of the Healthy Human Skin Microbiome Following Dead Sea Climatotherapy – Michael Brandwein – Acta Dermato-Venereologica

Review: Intrinsic Maturational Neonatal Immune Deficiencies and Susceptibility to Group B Streptococcus Infection – Michelle L. Korira – Clinical Microbiological Reviews

Systematic review: Faecal microbiota transplantation for Clostridium difficile infection: a multicentre study of non-responders – Paul Moayyedi – Medical Journal of Australia

Forensic microbiome

Daily thanatomicrobiome changes in soil as an approach of postmortem interval estimation: An ecological perspective – Joe Adserias Garriga – Forensic Science International

Animal microbiome

Correlations of age and growth rate with microbiota composition in Atlantic cod (Gadus morhua) larvae – Ly T. T. Trinh – Scientific Reports

Microbial community composition along the digestive tract in forage- and grain-fed bison – Gaddy T. Bergmann – BMC Veterinary Research

The effect of storage at ambient temperature on the feline fecal microbiota – Moran Tal – BMC Veterinary Research

Performance, biochemical and haematological responses, and relative organ weights of laying hens fed diets supplemented with prebiotic, probiotic and synbiotic – Shirley Gee Hoon Tang – BMC Veterinary Research

Mosapride Stabilizes Intestinal Microbiota to Reduce Bacterial Translocation and Endotoxemia in CCl4-Induced Cirrhotic Rats – Hong Xu – Digestive Diseases and Sciences

Transition of the intestinal microbiota of cats with age – Hiroaki Masuoka – PLoS ONE

Pathogen research

Draft Genome Sequences of Two Enterobacter cloacae subsp. cloacae Strains Isolated from Australian Hematology Patients with Bacteremia – Lex E. X. Leonga – Genome Announcements

The impact of the Staphylococcus aureus virulome on infection in a developing country: a cohort study – Marthe Lebughe – Frontiers in Microbiology

Bioactive compounds

Regulative effects of curcumin spice administration on gut microbiota and its pharmacological implications – Liang Shen – Food & Nutrition Research

Identification of Secondary Metabolite Gene Clusters in the Pseudovibrio Genus Reveals Encouraging Biosynthetic Potential toward the Production of Novel Bioactive Compounds – Lynn M. Naughton – Frontiers in Microbiology

Other

Characterizing a thermostable Cas9 for bacterial genome editing and silencing – Ioannis Mougiakos – BioRxiv

Determination of geochemical bio-signatures in Mars-like basaltic environments – Karen Olsson-Francis – Frontiers in Microbiology

August 18, 2017

Posted on August 18, 2017 by JP Cardenas

Human Microbiome: Gut

Worse inflammatory profile in omnivores than in vegetarians associates with the gut microbiota composition – Ana Carolina Franco-de-Moraes – Diabetology & Metabolic Syndrome (BMC)

News and views: Spondyloarthropathies: Ruminococcus on the horizon in arthritic disease – Lars Vereecke & Dirk Elewaut – Nature Reviews Rheumatology

Increased human intestinal barrier permeability plasma biomarkers zonulin and FABP2 correlated with plasma LPS and altered gut microbiome in anxiety or depression – Bruce R Stevens – Gut (BMJ)

Human Microbiome: Respiratory tract

Strain level Streptococcus colonization patterns during the first year of life – Meredith Wright – Frontiers in Microbiology

State of the art: The airway microbiota in early cystic fibrosis lung disease – Katherine B. Frayman – Pediatric Pulmonology (Wiley)

Human Microbiome: Mouth

The saliva microbiome profiles are minimally affected by collection method or DNA extraction protocols – Yenkai Lim – Scientific Reports

Built microbiome

Bacterial diversity among four healthcare-associated institutes in Taiwan – Chang-Hua Chen – Scientific Reports

Animal Microbiome

Host Ecology Rather Than Host Phylogeny Drives Amphibian Skin Microbial Community Structure in the Biodiversity Hotspot of Madagascar – Molly C. Bletz – Frontiers in Microbiology

Microbiota in the coelomic fluid of two common coastal starfish species and characterization of an abundant Helicobacter-related taxon – Satoshi Nakagawa – Scientific Reports

Stability in metabolic phenotypes and inferred metagenome profiles before the onset of colitis-induced inflammation – M. Glymenaki – Scientific Reports

Microbiome-mediated neutrophil recruitment via CXCR2 and protection from amebic colitis – Koji Watanabe – PLoS Pathogens

Gut microbiota of a long-distance migrant demonstrates resistance against environmental microbe incursions – Alice Risely – Molecular Ecology (Wiley)

Unraveling the Fecal Microbiota and Metagenomic Functional Capacity Associated with Feed Efficiency in Pigs – Hui Yang – Frontiers in Microbiology

Research Highlight: Tell me who you are and I’ll tell you what you eat – Irene Vacca – Nature Reviews Microbiology

Mucus organisation is shaped by colonic content; a new view – J. B. J. Kamphuis – Scientific Reports

Effect of barley supplementation on the fecal microbiota, caecal biochemistry, and key biomarkers of obesity and inflammation in obese db/db mice – Jose F. Garcia-Mazcorro – European Journal of Nutrition

Associations Between Nutrition, Gut Microbiome, and Health in A Novel Nonhuman Primate Model – Jonathan B. Clayton – BioRxiv

Milk microbiome and bacterial load following dry cow therapy without antibiotics in dairy cows with healthy mammary gland – Erika C. R. Bonsaglia – Scientific Reports

Space-type radiation induces multimodal responses in the mouse gut microbiome and metabolome – David Casero – Microbiome (BMC)

Probiotics, Prebiotics and Synbiotics

Secretome of intestinal bacilli: a natural guard against pathologies – Olga N. Ilinskaya – Frontiers in Microbiology

The Probiotic Combination of Bifidobacterium longum subsp. infantis CECT 7210 and Bifidobacterium animalis subsp. lactis BPL6 Reduces Pathogen Loads and Improves Gut Health of Weaned Piglets Orally Challenged with Salmonella Typhimurium – Emili Barba-Vidal – Frontiers in Microbiology

Bifidobacterium pseudocatenulatum LI09 and Bifidobacterium catenulatum LI10 attenuate D-galactosamine-induced liver injury by modifying the gut microbiota – Daiqiong Fang – Scientific Reports

Administration of two probiotic strains during early childhood does not affect the endogenous gut microbiota composition despite probiotic proliferation – Martin Frederik Laursen – BMC Microbiology

A randomized synbiotic trial to prevent sepsis among infants in rural India – Pinaki Panigrahi – Nature

Pathogen Research

High-Resolution Microbiome Profiling for Detection and Tracking of Salmonella enterica – Christopher J. Grim – Frontiers in Microbiology

In situ architecture, function, and evolution of a contractile injection system – Désirée Böck – Science

Bioactive compounds

Onion Peel Ethylacetate Fraction and Its Derived Constituent Quercetin 4`-O-Β-D Glucopyranoside Attenuates Quorum Sensing Regulated Virulence and Biofilm Formation – Hanan AlYousef – Frontiers in Microbiology

Promysalin is a salicylate-containing antimicrobial with a cell-membrane-disrupting mechanism of action on Gram-positive bacteria – Rahul D. Kaduskar – Scientific Reports

Bacteriophages

Selection of Functional Quorum Sensing Systems by Lysogenic Bacteriophages in Pseudomonas aeruginosa – Miguel-Angel Saucedo-Mora – Frontiers in Microbiology

Characterization and formulation into solid dosage forms of a novel bacteriophage lytic against Klebsiella oxytoca – Teagan L. Brown – PLoS ONE

Soil and Environmental Microbiology

Distinct Seasonal Patterns of Bacterioplankton Abundance and Dominance of Phyla α-Proteobacteria and Cyanobacteria in Qinhuangdao Coastal Waters Off the Bohai Sea – Yaodong He – Frontiers in Microbiology

The Rhizosphere Bacterial Microbiota of Vitis vinifera cv. Pinot Noir in an Integrated Pest Management Vineyard – Giorgia Novello – Frontiers in Microbiology

Perspective: How microbes survive in the open ocean – Jonathan P. Zehr – Science

Ecophysiology of freshwater Verrucomicrobia inferred from metagenome-assembled genomes – Shaomei He – BioRxiv

Impact of litter quantity on the soil bacteria community during the decomposition of Quercus wutaishanica litter – Quanchao Zeng – PeerJ preprints

Microbial phylogeny determines transcriptional response of resistome to dynamic composting processes – Cheng Wang – Microbiome (BMC)

Bioinformatics and Genomics

Abundance-based reconstitution of microbial pan-genomes from whole-metagenome shotgun sequencing data – Florian Plaza Oñate – BioRxiv

Evaluation of the impact of Illumina error correction tools on de novo genome assembly – Mahdi Heydari – BMC Bioinformatics

Non-microbiology picks

A pathology atlas of the human cancer transcriptome – Mathias Uhlen – Science

Increasing Symptoms in Irritable Bowel Symptoms With Ingestion of Galacto-Oligosaccharides Are Mitigated by α-Galactosidase Treatment – C J Tuck – The American Journal of Gastroenterology

Lessons from between the white lines for isolated data scientists – Benjamin S Baumer - PeerJ preprints

July 28, 2017

Posted on July 28, 2017 by JP Cardenas

Microbiome Research

High spatial and temporal variations of microbial community along the southern catfish gastrointestinal tract: insights into dynamic food digestion – Zhimin Zhang – Frontiers in Microbiology

Host ecology rather than host phylogeny drives amphibian skin microbial community structure in the biodiversity hotspot of Madagascar – Molly C. Bletz – Frontiers in Microbiology

A pilot study demonstrating the altered gut microbiota functionality in stable adults with Cystic Fibrosis – F. Fouhy – Scientific Reports

Research Highlight: Baby bugs can’t stop the thugs… – Yvonne Bordon – Nature Reviews Immunology

Chondroitin sulfate disaccharides modified the structure and function of the murine gut microbiome under healthy and stressed conditions – Fang Liu – Scientific Reports

Nasopharyngeal microbiome in premature infants and stability during rhinovirus infection – Geovanny F Perez – Journal of Investigative Medicine

Microbiomarkers in inflammatory bowel diseases: caveats come with caviar – Felix Sommer – Gut (BMJ)

Kynurenines: Tryptophan’s metabolites in exercise, inflammation, and mental health – Igor Cervenka – Science

Probiotics, Prebiotics and bioactive compounds

Protection mechanism of Clostridium butyricum against Salmonella enteritidis infection in broilers – Xiaonan Zhao – Frontiers in Microbiology

Isolation of human intestinal bacteria capable of producing the bioactive metabolite isourolithin A from ellagic acid – Maria V. Selma – Frontiers in Microbiology

Anti-obesity and anti-inflammatory effects of synthetic acetic acid vinegar and Nipa vinegar on high-fat-diet-induced obese mice – Boon Kee Beh – Scientific Reports

Antimicrobial activities of widely consumed herbal teas, alone or in combination with antibiotics: an in vitro study – Mayram Hacioglu – PeerJ

Food microbiology

Primary souring: a novel bacteria-free method for sour beer production – Kara Osburn – BioRxiv

Bioinformatics

PhaMers identifies novel bacteriophage sequences from thermophilic hot springs – Jonathan Deaton -BioRxiv

PinAPL-Py: A comprehensive web-application for the analysis of CRISPR/Cas9 screens – Philipp N. Spahn – BioRxiv

Pathogens

PyroTyping, a novel pyrosequencing-based assay for Mycobacterium tuberculosis genotyping – B. Molina-Moya – Scientific Reports

Vibrio cholerae genomic diversity within and between patients – Inès Levade – BioRxiv

Experimental evolution and genome data analysis of Candida albicans reveals cryptic bacteria in single yeast colonies – Danielle C. F. Bruno – BioRxiv

Comments and Opinion: The theory of disappearing microbiota and the epidemics of chronic diseases – Martin J. Blaser – Nature Reviews Immunology

Bactericidal and anti-biofilm effects of polyhexamethylene biguanide in models of intracellular and biofilm of Staphylococcus aureus isolated from bovine mastitis -Nor Fadhilah Kamaruzzaman – Frontiers in Microbiology

Clinicians should assess the benefits and risks of using bezlotoxumab for reducing the risk of recurrent Clostridium difficile infection – Habiba Hassouna – Evidence based Medicine

Whole RNA-sequencing and transcriptome assembly of Candida albicans and Candida africana under chlamydospore-inducing conditions – Domenico Giosa – Genome Biology and Evolution

Soil/Environmental Microbiome

The rhizosphere bacterial microbiota of Vitis vinifera cv. Pinot Noir in an integrated pest management vineyard – Giorgia Novello – Frontiers in Microbiology

Microbial Community Structure and the Persistence of Cyanobacterial Populations in Salt Crusts of the Hyperarid Atacama Desert from Genome-Resolved Metagenomics – Kari M. Finstad – Frontiers in Microbiology

Long term fertilization structures Bacterial and Archaeal communities along soil depth gradient in a paddy soil – Yunfu Gu – Frontiers in Microbiology

Drought and host selection influence bacterial community dynamics in the grass root microbiome – Dan Naylor – The ISME Journal

Other (Non-microbiology picks)

Comparative genomics of the tardigrades Hypsibius dujardini and Ramazzottius varieornatus – Yuki Yoshida – Plos Biology

July 25, 2017

Posted on July 25, 2017 by JP Cardenas

General Microbiome

Correcting for batch effects in case-control microbiome studies – Sean Gibbons – BioRxiv

Richer gut microbiota with distinct metabolic profile in HIV infected Elite Controllers – – Jan Vesterbacka – Scientific Reports (Nature)

Advantages of phylogenetic distance based constrained ordination analyses for the examination of microbial communities – V. Shankar – Scientific Reports (Nature)

Influence of the pneumococcal conjugate vaccines on the temporal variation of pneumococcal carriage and the nasal microbiota in healthy infants: a longitudinal analysis of a case–control study – Moana Mika – Microbiome (BMC)

Design and validation of a DNA-microarray for phylogenetic analysis of bacterial communities in different oral samples and dental implants – Carola Parolin – Scientific Reports (Nature)

Research Highlight: The innate immune receptor NLRP12 maintains intestinal homeostasis by regulating microbiome diversity – Jenny Moi-Fong Lau and Yvonne Dombrowski – Cellular & Molecular Immunology

Human Milk Microbial Community Structure Is Relatively Stable and Related to Variations in Macronutrient and Micronutrient Intakes in Healthy Lactating Women – Janet E Williams – The Journal of Nutrition

The Brain-Gut Axis Contributes to Neuroprogression in Stress-Related Disorders – Rea K. – Neuroprogression in Psychiatric Disorders

A nutritional approach for managing irritable bowel syndrome – Natalie Bhesania – Current Opinion in Pediatrics

Microbiota, metabolome, and immune alterations in obese mice fed a high fat diet containing type 2 resistant starch – Javad Barouei – Molecular Nutrition and Food Research

Diet Versus Phylogeny: a Comparison of Gut Microbiota in Captive Colobine Monkey Species – Vanessa L. Hale – Microbial ecology

Effects of oral florfenicol and azithromycin on gut microbiota and adipogenesis in mice – Rui Li – PlosOne

Probiotics

Review (Provisionally accepted): Bacillus as potential probiotics: status, concerns and future perspectives – Fouad M. F. Elshaghabee – Frontiers in Microbiology

Non-antibiotic Isotretinoin Treatment Differentially Controls Propionibacterium acnes on Skin of Acne Patients – Angela E. Ryan-Kewley – Frontiers in Microbiology

Effect of probiotics on the meat flavour and gut microbiota of chicken – Yan Wang – Scientific Reports (Nature)

Pathogens

Minireview: Insight Into the Origin and Evolution of the Vibrio parahaemolyticus Pandemic Strain – Romilio T. Espejo – Frontiers in Microbiology

Nitrate Sensing and Metabolism Inhibit Biofilm Formation in the Opportunistic Pathogen Burkholderia pseudomallei by Reducing the Intracellular Concentration of c-di-GMP – Mihnea R. Mangalea – Frontiers in Microbiology

Trehalose Polyphleates, External Cell Wall Lipids in Mycobacterium abscessus, Are Associated with the Formation of Clumps with Cording Morphology, Which Have Been Associated with Virulence – Marta Llorens-Fons – Frontiers in Microbiology

The resident pathobiont Staphylococcus xylosus in Nfkbiz-deficient skin accelerates spontaneous skin inflammation – Yeji Kim – Scientific Reports (Nature)

Inactivation Mechanism of Escherichia coli Induced by Slightly Acidic Electrolyzed Water – Zhangying Ye – Scientific Reports (Nature)

Targeting the permeability barrier and peptidoglycan recycling pathways to disarm Pseudomonas aeruginosa against the innate immune system – Gabriel Torrens – PlosOne

Environmental Microbiology

Modified Lipid Extraction Methods for Deep Subsurface Shale – Rawlings N. Akondi – Frontiers in Microbiology

The Cyanobacteria-Dominated Sponge Dactylospongia elegans in the South China Sea: Prokaryotic Community and Metagenomic Insights – Zhao-Ming Gao – Frontiers in Microbiology

Towards a highly efficient diversity census of the prokaryotic biosphere: a group testing approach – Bar Shalem – BioRxiv

Protocol: Rhizosphere Sampling Protocols for Microbiome (16S/18S/ITS rRNA) Library Preparation and Enrichment for the Isolation of Drought Tolerance-Promoting Microbes – Venkatachalam Lakshmanan – Methods in molecular biology

Endophytic fungal communities of Polygonum acuminatum and Aeschynomene fluminensis are influenced by soil mercury contamination – William Pietro-Souza – PlosOne

July 7, 2017

Posted on July 7, 2017 by JP Cardenas

Human Microbiome

Review: Altered molecular signature of intestinal microbiota in irritable bowel syndrome patients compared with healthy controls: A systematic review and meta-analysis – Liu et al. – Digestive and Liver Disease

Non-antibiotic Isotretinoin treatment differentially controls Propionibacterium acnes on skin of acne patients. – Ryan-Kewley et al. – Frontiers in Microbiology

Longitudinal profiling reveals a persistent intestinal dysbiosis triggered by conventional anti-tuberculosis therapy – Namasivayam et al. – Microbiome (BMC)

Research Highlights: Obesity: Gut microbiome and serum metabolome changes – Claire Greenhill – Nature Reviews Endocrinology

Research Highlights: Gut microbiota: Link between the gut and adipose tissues – Alan Morris – Nature Reviews Endocrinology

Review: The gut microbiome and liver cancer: mechanisms and clinical translation – Yu & Schwabe – Nature Reviews Gastroenterology and Hepatology

Pathogens

Reactive Oxygen Species-Dependent Essential Genes in Salmonella Typhimurium – Karash and Min Kwon – BioRxiv

Whole transcriptome sequencing of Pseudomonas syringae pv. actinidiae-infected kiwifruit plants reveals species-specific interaction between long non-coding RNA and coding genes – Wang et al – Scientific Reports (Nature)

Effects of different substrates/growth media on microbial community of saliva-derived biofilm – Li et al – FEMS Microbiology letters

Methods (including bioinformatics)

Selective imaging of Gram-negative and Gram-positive microbiotas in the mouse gut – Wang et al. – Biochemistry (ACS)

Methodology: VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data – Ren et al. – Microbiome (BMC)

Methodology: A novel ultra high-throughput 16S rRNA gene amplicon sequencing library preparation method for the Illumina HiSeq platform – de Muinck et al. – Microbiome (BMC)

Completing bacterial genome assemblies with multiplex MinION sequencing – Wick et al. – BioRxiv

Axe: rapid, competitive sequence read demultiplexing using a trie – Murray & Borevitz – BioRxiv

Water microbiome

Unraveling the microbial interactions and metabolic potentials in pre- and post-treated sludge from a wastewater treatment plant using metagenomic studies – Sidhu et al. – Frontiers in Microbiology

Nutrient dynamics and stream order influence microbial community patterns along a 2914 km transect of the Mississippi River – Henson et al. – BioRxiv

Extremophiles

Oxidative weathering and microbial diversity of an inactive seafloor hydrothermal sulfide chimney – Li et al. – Frontiers in Microbiology

Hidden biofilms in a far northern lake and implications for the changing Arctic – Mohit et al. – npj Biofilms and Microbiomes

Probiotics – Fermented Food

Amplicon sequencing of the slpH locus permits culture-independent strain typing of Lactobacillus helveticus in dairy products – Moser et al. – Frontiers in Microbiology

Probiotic Enterococcus mundtii Isolate Protects the Model Insect Tribolium castaneum against Bacillus thuringiensis – Grau et al. – Frontiers in Microbiology

Animal Microbiome

Regulation of gut luminal serotonin by commensal microbiota in mice – Hata et al. – PLoS ONE

News

News: How Gut Bacteria Tell Their Hosts What to Eat – Knvul Sheikh via Scientific American Mind (Nature)

News: Mind over Meal: Does Weight-Loss Surgery Rewire Gut-Brain Connections? – Bret Stetka via Scientific American Mind (Nature)

Fellowships

Post-Doctoral Research Fellow, Microbiome and Vaccine Induced Immunity – Seattle, WA, United States

Postdoctoral Fellow (Listeria monocytogenes research) – Dunedin, New Zealand

Other

The earth is flat (p > 0.05): significance thresholds and the crisis of unreplicable research – Amrhein et al. – PeerJ

June 23, 2017

Posted on June 23, 2017 by JP Cardenas

Human Microbiome

Genome reconstruction and characterisation of extensively drug-resistant bacterial pathogens through direct metagenomic sequencing of human faeces – Mu et al. – BioRxiv

Oropharyngeal and Sputum Microbiomes Are Similar Following Exacerbation of Chronic Obstructive Pulmonary Disease – Liu et al. – Frontiers in Microbiology

Segal’s Law, 16S rRNA gene sequencing, and the perils of foodborne pathogen detection within the American Gut Project – Pettengill & Rand – PeerJ

Unexplored diversity and strain-level structure of the skin microbiome associated with psoriasis – Tett et al. – npj Biofilms and Microbiomes

Rosacea and its association with enteral microbiota in Korean females – Nam et al. – Experimental Dermatology

Review: The role of microbiota, and probiotics and prebiotics in skin health – Maguire & Maguire – Archives of Dermatological Research

Human age and skin physiology shape diversity and abundance of Archaea on skin – Moissl-Eichinger et al. – Scientific Reports

Microbial Signatures Associated with Oropharyngeal and Oral Squamous Cell Carcinomas – Banerjee et al. – Scientific Reports

Animal Microbiome

Gut Dysbiosis and Adaptive Immune Response in Diet-induced Obesity vs. Systemic Inflammation – Pindjakova et al. – Frontiers in Microbiology

Characterization of the Microbiome along the Gastrointestinal Tract of Growing Turkeys – Wilkinson et al. – Frontiers in Microbiology

Diet-induced reconstruction of mucosal microbiota associated with alterations of epithelium lectin expression and regulation in the maintenance of rumen homeostasis – Shen et al. – Scientific Reports

Fatty acid composition and phospholipid types used in infant formulas modifies the establishment of human gut bacteria in germ-free mice – Guldhammer Nejrup et al. – Scientific Reports

Microbiota-derived butyrate suppresses group 3 innate lymphoid cells in terminal ileal Peyer’s patches – Kim et al. – Scientific Reports

Early-life gut microbial colonization shapes Th1/Th2 balance in asthma model in BALB/c mice – Qin et al. – BMC Microbiology

The development of lower respiratory tract microbiome in mice – Singh et al. – Microbiome (BMC)

Pathogen research

Genetic indicators of drug resistance in the highly repetitive genome of Trichomonas vaginalis – Bradic et al. – Genome Biology and Evolution

Metabolic and fitness determinants for in vitro growth and intestinal colonization of the bacterial pathogen Campylobacter jejuni – Gao et al. – PLoS Biology

Review: Periodontal diseases – Kinane et al. – Nature Reviews Disease Primer

Soil and Water Microbiome

Culture-Independent Analyses Reveal Novel Anaerolineaceae as Abundant Primary Fermenters in Anaerobic Digesters Treating Waste Activated Sludge – McIlroy et al. – Frontiers in Microbiology

Nitrogen enrichment impacts on boreal litter decomposition are driven by changes in soil microbiota rather than litter quality – Maaroufi et al. – Scientific Reports

Bioinformatics

CD-HIT-OTU-MiSeq, an Improved Approach for Clustering and Analyzing Paired End MiSeq 16S rRNA Sequences – Li et al. – BioRxiv

Divide and Conquer (DC) BLAST: fast and easy BLAST execution within HPC environments – Yim & Cushman – PeerJ

BGDMdocker: a Docker workflow for data mining and visualization of bacterial pan-genomes and biosynthetic gene clusters – Cheng et al. – PeerJ Preprints

Evolution

Phylogenetic Tracings of Proteome Size Support the Gradual Accretion of Protein Structural Domains and the Early Origin of Viruses from Primordial Cells – Nasir et al. – Frontiers in Microbiology

Pan-genome and phylogeny of Bacillus cereus sensu lato – Bazinet – BioRxiv

TreeTime: maximum likelihood phylodynamic analysis – Sagulenko et al. – BioRxiv

Other

Review: Fungal and Bacterial Pigments: Secondary Metabolites with Wide Applications – Morris et al. – Frontiers in Microbiology

A Highly Efficient CRISPR-Cas9-Mediated Large Genomic Deletion in Bacillus subtilis – So et al. – Frontiers in Microbiology

May 24, 2017

Posted on May 24, 2017 by JP Cardenas

Human Microbiome

Non-pylori Helicobacters (NHPHs) induce shifts in gastric microbiota in Helicobacter pylori-infected patients – Peng et al. – Frontiers in Microbiology

Association between body mass index and Firmicutes/Bacteroidetes ratio in an adult Ukrainian population – Koliada et al. – BMC Microbiology

The effect of heritability and host genetics on the gut microbiota and metabolic syndrome – Young Lim et al. – Gut (BMJ)

Fungal microbiota dysbiosis in IBD – Sokol et al. – Gut (BMJ)

A tale of two risks: smoking, diabetes and the subgingival microbiome – Ganesan et al. – The ISME Journal

Animal Microbiome

The Structural and Functional Capacity of Ruminal and Cecal Microbiota in Growing Cattle Was Unaffected by Dietary Supplementation of Linseed Oil and Nitrate – Popova et al. – Frontiers in Microbiology

Probiotics – Prebiotics

Gut Bacteria Missing in Severe Acute Malnutrition, Can We Identify Potential Probiotics by Culturomics? – Tidjani Alou et al – Frontiers in Microbiology

Detection and Physicochemical Characterization of Membrane Vesicles (MVs) of Lactobacillus reuteri DSM 17938 – Grande et al. – Frontiers in Microbiology

Review: Resistant Starch Regulates Gut Microbiota: Structure, Biochemistry and Cell Signalling – Yang et al. – Cellular Physiology and Biochemistry

Food Microbiology

A Functional Metagenomic Analysis of Tetracycline Resistance in Cheese Bacteria – Flórez et al. – Frontiers in Microbiology

Extensive Horizontal Gene Transfer in Cheese-Associated Bacteria – Bonham et al. – BioRxiv

Food Safety in the Age of Next Generation Sequencing, Bioinformatics, and Open Data Access – Taboada et al. – Frontiers in Microbiology

In vitro assessment of Pediococcus acidilactici Kp10 for its potential use in the food industry – Abbasiliasi et al. – BMC Microbiology

Pathogen Research

In-depth Profiling of MvfR-Regulated Small Molecules in Pseudomonas aeruginosa after Quorum Sensing Inhibitor Treatment – Allegretta et al. – Frontiers in Microbiology

Metabolic anticipation in Mycobacterium tuberculosis – Eoh et al. – Nature Microbiology

Predicting Drug Resistance Evolution: Antimicrobial Peptides Vs. Antibiotics – Yi et al. – BioRxiv

Environmental Microbiology

Undocumented Potential For Primary Productivity In A Globally-Distributed Bacterial Photoautotroph – Graham et al. – BioRxiv

Epibionts dominate metabolic functional potential of Trichodesmium colonies from the oligotrophic ocean – Frischkorn et al. – The ISME Journal

Bioinformatics

BSocial: Deciphering Social Behaviors within Mixed Microbial Populations – Purswani et al. – Frontiers in Microbiology

A Phylogenetic Method To Perform Genome-Wide Association Studies In Microbes That Accounts For Population Structure And Recombination – Collins and Didelot – BioRxiv

Association Mapping From Sequencing Reads Using K-mers – Rahman et al. – BioRxiv

MATAM: Reconstruction Of Phylogenetic Marker Genes From Short Sequencing Reads In Metagenomes – Pericard et al. – BioRxiv

Other

Perspective: Our path to better science in less time using open data science tools – Stewart Lowndes et al. – Nature Ecology & Evolution

Teaching genetics prior to teaching evolution improves evolution understanding but not acceptance – Mead et al. – PLoS Biology

Review: Adaptations of archaeal and bacterial membranes to variations in temperature, pH and pressure – Siliakus et al. – Extremophiles

May 19, 2017

Posted on May 19, 2017 by JP Cardenas

Microbiome research

Exploring a possible link between the intestinal microbiota and feed efficiency in pigs

Ursula M. McCormack et al., Applied and Environmental Microbiology

Modulation of the Gut Microbiota by Krill Oil in Mice Fed a High-Sugar High-Fat Diet

Chenyang Lu et al., Frontiers in Microbiology

Opinion: Gut microbiome as a clinical tool in gastrointestinal disease management: are we there yet?

Eamonn M. M. Quigley, Nature Reviews Gastroenterology & Hepatology (Online since March 30, 2017; however this has not been pointed out here before)

Pathogen microbiology

Mini review: The Role of Ribonucleases and sRNAs in the Virulence of Foodborne Pathogens

Rute G. Matos et al., Frontiers in Microbiology

Pathogenic Characteristics of Staphylococcus aureus Endovascular Infection Isolates from Different Clonal Complexes

Dafne Pérez-Montarelo et al., Frontiers in Microbiology

Pseudomonas aeruginosa Exolysin promotes bacterial growth in lungs, alveolar damage and bacterial dissemination

Stéphanie Bouillot et al., Scientific Reports (Nature)

Intrinsic Toxin-Derived Peptides Destabilize and Inactivate Clostridium difficile TcdB

Jason L. Larabee et al., mBio

Probiotics – Prebiotics

Vaginal Lactobacillus Inhibits HIV-1 Replication in Human Tissues Ex Vivo

Rogers A. Ñahui Palomino et al., Frontiers in Microbiology

Assessing the Risk of Probiotic Dietary Supplements in the Context of Antibiotic Resistance

Min Zheng et al., Frontiers in Microbiology

Review: Lactic Acid Bacteria and Bifidobacteria with Potential to Design Natural Biofunctional Health-Promoting Dairy Foods

Daniel M. Linares et al., Frontiers in Microbiology

In silico Prediction, in vitro Antibacterial Spectrum, and Physicochemical Properties of a Putative Bacteriocin Produced by Lactobacillus rhamnosus Strain L156.4

Letícia de C. Oliveira et al., Frontiers in Microbiology

Health benefit of vegetable/fruit juice-based diet: Role of microbiome

Susanne M. Henning et al., Scientific Reports (Nature)

Characterization of bile salt hydrolase from Lactobacillus gasseri FR4 and demonstration of its substrate specificity and inhibitory mechanism using molecular docking analysis

Rizwana Parveen Rani et al., Frontiers in Microbiology

Lactobacillus johnsonii ameliorates intestinal, extra-intestinal and systemic pro-inflammatory immune responses following murine Campylobacter jejuni infection

Stefan Bereswill et al., Scientific Reports (Nature)

News and Views: Paediatrics: Are human milk oligosaccharides the magic bullet for necrotizing enterocolitis?

Michael S. Caplan, Nature Reviews Gastroenterology & Hepatology

Assessing the Challenges in the Application of Potential Probiotic Lactic Acid Bacteria in the Large-Scale Fermentation of Spanish-Style Table Olives

Francisco Rodríguez-Gómez et al., Frontiers in Microbiology

Antimicrobials

A broad-spectrum bactericidal lipopeptide with anti-biofilm properties

Ohad Meir et al., Scientific Reports (Nature)

The anticancer peptide TAT-RasGAP317-326 exerts broad antimicrobial activity

Mathieu Heulot et al., Frontiers in Microbiology

Genomics

Revealing genome-scale transcriptional regulatory landscape of OmpR highlights its expanded regulatory roles under osmotic stress in Escherichia coli K-12 MG1655

Sang Woo Seo et al., Scientific Reports (Nature)

High-Definition Electronic Genome Maps From Single Molecule Data

John S. Oliver et al., BioRxiv

Local genes for local bacteria: evidence of allopatry in the genomes of transatlantic Campylobacter populations

Ben Pascoe et al., PeerJ (not peer reviewed)

Feature: Mining microbes: Creating genomic tools to fight disease

Amber Dance, Science

Microbiology – Other

Variation in soil microbial community structure associated with different legume species is greater than that associated with different grass species

Yang Zhou et al., Frontiers in Microbiology

Microbial Community Dynamics in Soil Depth Profiles Over 120,000 Years of Ecosystem Development

Stephanie Turner et al., Frontiers in Microbiology

Autotrophic and heterotrophic acquisition of carbon and nitrogen by a mixotrophic chrysophyte established through stable isotope analysis

Ramon Terrado et al., The ISME Journal

Hypothesis & Theory: The hyperarid core of the Atacama Desert, an extremely dry and carbon deprived habitat of potential interest for the field of carbon science

Armando Azua-Bustos et al., Frontiers in Microbiology

non-Microbiology picks

Divergent prebiotic synthesis of pyrimidine and 8-oxo-purine ribonucleotides

Shaun Stairs et al., Nature Communications

Virus origin could relate to the act of prey among primitive life forms

Eslam Abbas, PeerJ (not peer reviewed)

Beyond the protein-only hypothesis: A novel mineral-lipid hypothesis in prion and protein-misfolding disease

Kavitha Reddy, PeerJ (not peer reviewed)

Feature: Introducing ORCID

John Bohannon and Kirk Doran, Science

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Microbiome Digest – Bik's Picks

A daily digest of scientific microbiome papers, by the MD team. Founded by Elisabeth Bik, microbiome and science integrity consultant. Twitter: @microbiomdigest

Author Archives: JP Cardenas

August 23, 2017

August 22, 2017

August 19, 2017

August 18, 2017

July 28, 2017

July 25, 2017

July 7, 2017

June 23, 2017

May 24, 2017

Human Microbiome

Animal Microbiome

Probiotics – Prebiotics

Food Microbiology

Pathogen Research

Environmental Microbiology

Bioinformatics

Other

May 19, 2017

Microbiome research

Pathogen microbiology

Probiotics – Prebiotics

Antimicrobials

Genomics

Microbiology – Other

non-Microbiology picks