July 26, 2017

A study of chemical interactions between fungi and ants by imaging mass spectrometry, characterization of forty-six Arthrobacter phages, influence of fruit fungal infestation on vertebrate fruit preferences.

Human gut microbiome

The essential genomic landscape of the commensal Bifidobacterium breve UCC2003 – Lorena Ruiz – Scientific Reports

Animal experiments

Fat binding capacity and modulation of the gut microbiota both determine the effect of wheat bran fractions on adiposity – Francesco Suriano – Scientific Reports

Effects of dietary supplementation with two alternatives to antibiotics on intestinal microbiota of preweaned calves challenged with Escherichia coli K99 – Yanliang Bi – Scientific Reports

Animal microbiome

Imaging mass spectrometry and MS/MS molecular networking reveals chemical interactions among cuticular bacteria and pathogenic fungi associated with fungus-growing ants – Cristopher A Boya P – Scientific Reports

Plant, root, and soil microbiome

Population structure of an orchid mycorrhizal fungus with genus-wide specificity – M P Ruibal – Scientific Reports

Water and extremophile microbiome

Review: Cultivation of microbes from the deep-sea environments – Zenghu Zhang – Deep Sea Research Part II: Topical Studies in Oceanography

Food microbiology

Fungal infestation boosts fruit aroma and fruit removal by mammals and birds – Josep E Peris – Scientific Reports

Pre-print: Resilience mechanisms of small intestinal lactobacilli to the toxicity of soybean oil fatty acids – Sara C Di Rienzi – bioRxiv

Probiotics/prebiotics

Dietary lipid content reorganizes gut microbiota and probiotic L. rhamnosus attenuates obesity and enhances catabolic hormonal milieu in zebrafish – Silvia Falcinelli – Scientific Reports

Phages and viruses

Tales of diversity: Genomic and morphological characteristics of forty-six Arthrobacter phages – Karen K Klyczek – PLOS ONE

Pre-print: Isolation and characterization of BpL1, a broad acting lytic bacteriophage against Brucella – Vimlesh Gupta – bioRxiv

Microbes in the news

Bac-for good: Bacteria passed between generations benefits you more than others – Phys.org

Microbes on the market

Verily Releases Bacteria-Infected Mosquitoes To Fight Zika And Dengue: Is Wolbachia Technique Safe For Humans? – Allan Adamson – Tech Times

Science, career, and publishing

Climate scientists flock to France’s call – Declan Butler – Nature

July 16, 2017

Posted on July 16, 2017 by Tiff

Events and jobs
Postdoctoral Fellow – Astrobiology – University of Florida

Microbiology Laboratory Manager – Cranleigh Scientific, Northamptonshire, England

Human respiratory microbiome
Review: Microbiome in chronic obstructive pulmonary disease – Eduard Monso – Annals of Translational Medicine

Monitoring clinical and microbiological evolution of a cystic fibrosis patient over 26 years: experience of a Brazilian CF Centre – Cassiana da Costa Ferreira Leite – BMC Pulmonary Medicine

Distal airway microbiome is associated with immunoregulatory myeloid cell responses in lung transplant recipients – Nirmal S. Sharma – The Journal of Heart and Lung Transplantation

Human oral microbiome
Diabetes Enhances IL-17 Expression and Alters the Oral Microbiome to Increase Its Pathogenicity – E. Xiao – Cell Host and Microbe

Microbiome of peri-implantitis affected and healthy dental sites in patients with a history of chronic periodontitis – Danae Apatzidou – Archives of Oral Biology

Human gut microbiome
Review: Gut–CNS-Axis as Possibility to Modulate Inflammatory Disease Activity—Implications for Multiple Sclerosis – Ann-Katrin Fleck – International Journal of Molecular Sciences

Determination of certain bacterial groups in gut microbiota and endotoxin levels in patients with nonalcoholic steatohepatitis – Ceren Özkul – The Turkish Journal of Gastroenterology

Animal experiments
Meat and bone meal as partial replacement of fishmeal in diets for gilthead sea bream (Sparus aurata) juveniles: Diets digestibility, digestive function, and microbiota modulation – Sara Moutinho – Aquaculture

Arachidonic acid sex-dependently affects obesity through linking gut microbiota-driven inflammation to hypothalamus-adipose-liver axis – Pan Zhuang – Biochimica et Biophysica Acta (BBA) – Molecular Basis of Disease

Disparity in the nasopharyngeal microbiota between healthy cattle on feed, at entry processing and with respiratory disease – Mohamed Zeineldin – Veterinary Microbiology

Animal microbiome
Effects of chromium(III) on enzyme activities and bacterial communities during swine manure composting – Yanan Yin – Bioresource Technology

Antimicrobial Activity of Actinobacteria Isolated From the Guts of Subterranean Termites – R. A. Arango – Environmental Entomology

Oral Disease and Microbiota in Free-roaming cats – Ana Whyte – Topics in Companion Animal Medicine

Plant, root, and soil microbiome
Investigating the durable effect of the hot water treatment used in nurseries on pathogenic fungi inhabiting grapevine wood and involved in Grapevine Trunk Diseases – Emilie Bruez – Crop Protection

Understanding the mycobiota of maize from the highlands of Guatemala, and implications for maize quality and safety – José Rodrigo Mendoza – Crop Protection

The uniqueness and biogeochemical cycling of plant root microbial communities in a floating treatment wetland – Hidetoshi Urakawa – Ecological Engineering

Water and extremophile microbiome
The Other Microeukaryotes of the Coral Reef Microbiome – T.D. Ainsworth – Trends in Microbiology

Taxonomic and functional diversity of a coastal planktonic bacterial community in a river-influenced marine area – Stefan Thiele – Marine Genomics

Built environment
Stimulation effect of electric current density (ECD) on microbial community of a three dimensional particle electrode coupled with biological aerated filter reactor (TDE-BAF) – Yan Feng – BioResource Technology

Food microbiology
Review: Bacteriocin-Antimicrobial Synergy: A Medical and Food Perspective – Harsh Mathur – Frontiers in Microbiology

Review: Low FODMAP Diet in the Treatment of Irritable Bowel Syndrome: A Systematic Review and Meta-Analysis – Dania Schumann – Nutrition

Macrophages treated with non-digestible polysaccharides reveal a transcriptionally unique phenotype – Yongfu Tang – Journal of Functional Foods

Microbial Ecology
Interplay between antibiotic efficacy and drug-induced lysis underlie enhanced biofilm formation at subinhibitory drug concentrations – Wen Yu – bioRxiv

A phylogenetic and evolutionary analysis of antimycin biosynthesis – Rebecca Joynt – bioRxiv

Probiotics / prebiotics
Review: Prenatal and postnatal administration of prebiotics and probiotics – Kristin Sohn – Seminars in Fetal and Neonatal Medicine

Techniques
Phototrophic microorganisms in the symbiotic communities of Baikal sponges: Diversity of psbA gene (encoding D1 protein of photosystem II) sequences – OV Kaluzhnaya – Mol Biol (Mosk)
Unfortunately, this article is in Russian and I cannot access the original. The abstract was interesting though, the goal of the study is to determine whether psbA sequences can be used as a marker for phototrophic organisms.

New sequences
Noncontiguous finished genome sequences and description of Bacillus massiliglaciei, Bacillus mediterraneensis, Bacillus massilinigeriensis, Bacillus phocaeensis and Bacillus tuaregi, five new species identified by culturomics – F. Cadoret – New Microbes and New Infections

Whole-Genome Sequences of Influenza A(H1N1)pdm09 Virus Isolates from Kerala, India – Sara Jones – Genome Announcements

Phoenicibacter massiliensis‘ gen. nov., sp. nov., a new bacterium isolated from the human gut of a pygmy woman – M. Bilen – New Microbes and New Infections

Phenotypic and genomic comparison of Mycobacterium aurum and surrogate model species to Mycobacterium tuberculosis: implications for drug discovery – Amine Namouchi – BMC Genomics

Microbes in the news
** Mini-Metagenomics Leads to Microbial Discovery – Abby Olena – The Scientist
Refers to Microfluidic-based mini-metagenomics enables discovery of novel microbial lineages from complex environmental samples – Feiqiao Brian Yu – ELife **

APC Microbiome Institute appoints Spinning Clock to Mind Your Microbes brief – Andy Black – The Drum
An app for kids to learn about the microbiome!

Microbial diversity: ‘key benchmark in the coming Third Wave cosmetic revolution’ – Lucy Whitehouse – Cosmetics Design

Novel bacterial physiology identified in the creation of biofilms – Science Daily

Physicists Just Found a Way to Spin Teeny Tiny Robot Motors With Bacteria – Gemma Conroy – Science Alert

New bacteria being developed for cheese may save industry $10m a year, researchers say – Melanie Vujkovic – ABC

Bacteria-infected mosquitoes are coming to Fresno – but it’s a good thing! – Bryant-Jon Anteola – Fresno Bee

BYU student overcomes flesh-eating bacteria to compete on ‘American Ninja Warrior’ – Braley Dodson – Daily Herald

Bacteria Actively Drive Development of Colorectal Cancer – Newswise
Looking at Streptococcus gallolyticus and its ability to promote colorectal cancer in cell culture, animal models, and human tissue.

Bacteria Hysteria
How surgeons can stop the spread of germs by operating NAKED instead of wearing surgical gowns – Colin Fernandez – Daily Mail

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

July 3, 2017

Posted on July 3, 2017 by TinaS

Pregnancy and early life
Maternal inheritance of bifidobacterial communities and bifidophages in infants through vertical transmission – Sabrina Duranti – Microbiome

Mini Review: The microbiome and disorders of the central nervous system – Valeria D. Felice – Pharmacology Biochemistry and Behavior

Human respiratory microbiome

Short Report: The metabolic footprint of the airway bacterial community in cystic fibrosis – Vaishnavi Narayanamurthy – Microbiome

Human gut microbiome

Gut microbial transformation of the dietary imidazoquinoxaline mutagen MeIQx reduces its cytotoxic and mutagenic potency – Jianbo Zhang – Toxicological Science

Review: Practical considerations for large-scale gut microbiome studies – Doris Vandeputte – FEMS Microbiology Reviews

Association of altered gut microbiota composition with chronic urticaria – Edris Nabizadeh – Annals of Allergy, Asthma & Immunology

Animal microbiome

A genomic investigation of ecological differentiation between free-living and Drosophila-associated bacteria – Nathan J. Winans – Molecular Ecology

The Gut Bacterial Community Composition of Wild Cervus albirostris (White-Lipped Deer) Detected by the 16S Ribosomal RNA Gene Sequencing – Jun-gang Li – Current Microbiology

Microbial influence on Drosophila biology – ME Martino – Current Opinion in Microbiology

Plant, root, and soil microbiome

Organic carbon and nitrogen availability determine bacterial community composition in paddy fields of the Indo-Gangetic plain – Arvind Kumar – Biotech

Water and extremophile microbiome

Spatiotemporal Dynamics of the Bacterial Microbiota on Lacustrine Cladophora glomerata (Chlorophyta) – Michael J. Braus – bioRxiv

Quantity and quality of particulate organic matter controls bacterial production in the Columbia River estuary – Byron C. Crump – Limnology and Oceanography

Relating genomic characteristics to environmental preferences and ubiquity in different microbial taxa – Marta Cobo-Simón – BMC Genomics

Comparison of four DNA extraction methods for comprehensive assessment of 16S rRNA bacterial diversity in marine biofilms using high-throughput sequencing – Natàlia Corcoll – FEMS Microbiology Letters

Food microbiology

Cleaning and disinfection of biofilms composed of Listeria monocytogenes and background microbiota from meat processing surfaces – Annette Fagerlund – Applied and Environmental Microbiology

Probiotics / prebiotics

A human gut commensal ferments cranberry carbohydrates to produce formate – Ezgi Özcan – Applied and Environmental Microbiology

Review: Lifestyles in transition: evolution and natural history of the genus Lactobacillus – Rebbeca M. Duar – FEMS Microbiology Reviews

Phages and viruses

Synergistic elimination of bacteria by phage and the innate immune system – Chung Yin (Joey) Leung – Journal of Theoretical Biology

Biotechnology

Effect of zinc oxide nanoparticles on nitrogen removal, microbial activity and microbial community of CANON process in a membrane bioreactor – Xiaojing Zhang – Bioresource Technology

Microbes in the news

A new approach to tackling drug-resistant bacteria

New technology to cool the body: make the clothes made of microorganisms

Microbes on the market (news about biotech companies)

New Belgian Biotech will use Microorganisms to Replace Pesticides and Fertilizers

June 15, 2017

Posted on June 15, 2017 by edwardmessick

Today’s digest is full of plant, animal, and soil microbiome studies as well as a nice serving of human gut science, specifically about FMT.

Events and jobs

Visiting Assistant Professor of Microbiology – Methodist University, North Carolina

GENEWIZ Week – many small events, contests, giveaways, and webinars (including mine on using Metagenomics for Biomarker Discovery posted here on Sunday’s blog post. Since my webinar was yesterday, it will be archived and can be downloaded from genewiz.com, starting next week – don’t forget to check it out!)

General microbiome

* Comprehensive analysis of microorganisms accompanying human archaeological remains – Anna Philips – Gigascience

Pregnancy and early life

Relationships Among Microbial Communities, Maternal Cells, Oligosaccharides, and Macronutrients in Human Milk – Williams JE – Journal of Human Lactation

Human oral microbiome

Targeted Antimicrobial Therapy in the Microbiome Era – Victoria N. Stone – Molecular Oral Microbiology

Human gut microbiome

* Identification of donor microbe species that colonize and persist long term in the recipient after fecal transplant for recurrent Clostridium difficile – Ranjit Kumar – npj Biofilms and Microbiomes

* Fecal microbiota transplantation in metabolic syndrome: History, present and future – P. F. de Groot – Gut microbes

Intestinal microbiota, fecal microbiota transplantation, and inflammatory bowel disease – Weingarden AR – Gut Microbes

Faecal microbiota study reveals specific dysbiosis in spondyloarthritis – Maxime Breban – Annals of Rheumatic Diseases

Metaproteomic analysis of human gut microbiota: where are we heading? – Pey Yee Lee – Journal of Biomedical Science

Animal experiments (mouse/rat experiments, chickens/pigs on different diets)

Variability, stability, and resilience of fecal microbiota in dairy cows fed whole crop corn silage – Minh Thuy Tang – Applied Microbiology and Biotechnology

Plantago ovata in broiler chicken nutrition: Performance, carcass criteria, intestinal morphology, immunity, and intestinal bacterial population – A. Divani – Animal Physiology and Animal Nutrition

Chronic treatment with prebiotics, probiotics and synbiotics attenuated cardiac dysfunction by improving cardiac mitochondrial dysfunction in male obese insulin-resistant rats – Tunapong W – European Journal of Nutrition

Amelioration of obesity-related characteristics by a probiotic formulation in a high-fat diet-induced obese rat model – Joo-Hyun Shin – European Journal of Nutrition

Early Gut Microbiota Intervention Suppresses DSS-Induced Inflammatory Responses by Deactivating TLR/NLR Signalling in Pigs – Yi Xiao – Scientific Reports

* Profound perturbation induced by triclosan exposure in mouse gut microbiome: a less resilient microbial community with elevated antibiotic and metal resistomes – Bei Gao – BMC Pharmacology and Toxicology

Animal microbiome (for animals in the wild)

[PrePrint] Ecophysiology of freshwater Verrucomicrobia inferred from genomes recovered through time-series metagenomics – Shaomei He – bioRxiv

Long-Term Survey Is Necessary to Reveal Various Shifts of Microbial Composition in Corals – Shan-Hua Yang – Aquatic Microbiology (Frontiers in Microbiology)

Preferential suppression of Anopheles gambiae host sequences allows detection of the mosquito eukaryotic microbiome – Eugeni Belda – Scientific Reports

Social odours covary with bacterial community in the anal secretions of wild meerkats – Sarah Leclaire – Scientific Reports

Plant, root, and soil microbiome

Imidacloprid application changes microbial dynamics and enzymes in rice soil – Bibhab Mahapatra – Ecotoxicology and Environmental Safety

Comparison of ammonia oxidation bacteria community structure in paddy soil with different utilized years – Zhao WeiYe – Southwest China Journal of Agricultural Sciences

[MS Thesis] Variation of Soil Microbial Communities within a Consociation Soil Map Unit and a Vegetative Transect through an Oak Motte – Sarah Elizabeth Shawver – Tarleton State University

Effects of different intercropping patterns on rhizosphere soil bacteria colony characteristics and flue-cured tobacco yield and quality – Wei Jun – Guangxi Academy of Agricultural Sciences

Rhizospheric bacteria diversity of Cypripedium macranthum estimated via high throughput sequencing – Zhang Jian -Southwest China Journal of Agricultural Sciences

Denitrifying bacterial communities display different temporal fluctuation patterns across Dutch agricultural soils – Lopez-Lozano NE – Antonie van Leeuwenhoek

Ecophylogeny of the endospheric root fungal microbiome of co-occurring Agrostis stolonifera – Amandine Le Van – PeerJ

Consistent effects of nitrogen fertilization on soil bacterial communities in black soils for two crop seasons in China – Jing Zhou – Scientific Reports

A next generation sequencing approach with a suitable bioinformatics workflow to study fungal diversity in bioaerosols released from two different types of composting plants – Hamza Mbareche – Science of The Total Environment

The Effects of Cropping Regimes on Fungal and Bacterial Communities of Wheat and Faba Bean in a Greenhouse Pot Experiment Differ between Plant Species and Compartment – Granzow S – Frontiers in Microbiology

Water and extremophile microbiome

Unraveling the environmental and anthropogenic drivers of bacterial community changes in the Estuary of Bilbao and its tributaries – Mikel Aguirre – PLOS ONE

Food microbiology

Metagenomics insights into food fermentations – Francesca De Filippis – Microbial Biotechnology

Probiotics / prebiotics

Effect of probiotic Lactobacillus on lipid profile: A systematic review and meta-analysis of randomized, controlled trials – Yuncheng Wu – PLOS ONE

Growing Literature but Limited Evidence: A Systematic Review regarding Prebiotic and Probiotic Interventions for those with Traumatic Brain Injury and/or Posttraumatic Stress Disorder – Lisa A. Brenner – Brain, Behavior, Immunity

Microbes on the market

$10 million gift boosts gut microbiome research at Wash U

Ed’s non-microbiology picks

Computational design of trimeric influenza-neutralizing proteins targeting the hemagglutinin receptor binding site – Eva-Maria Strauch – Nature Biotechnology

Aberrant telomere length and mitochondrial DNA copy number in suicide completers – Ikuo Otsuka – Scientific Reports

Impact of nutrition on social decision making – Sabrina Strang – PNAS

Oral vitamin D rapidly attenuates inflammation from sunburn: an interventional study – Jeffrey F. Scott – JID

Adaptive self-organization of Bali’s ancient rice terraces – J. Stephen Lansing – PNAS

Ravens remember the nature of a single reciprocal interaction sequence over 2 days and even after a month – J. J. A. Muller – Animal Behaviour

June 13, 2017

Posted on June 13, 2017 by Tiff

Excellent reviews across all sections, with many from the Nature Journals. Also, multiple articles on the tree of life and animal experiments.

General microbiome
1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life – Supratim Mukherjee – Nature Biotechnology

Lokiarchaea are close relatives of Euryarchaeota, not bridging the gap between prokaryotes and eukaryotes – Violette Da Cunha – PLoS Genetics

Review: Natural Products and the Gene Cluster Revolution – Paul R. Jensen – Trends in Microbiology

Pregnancy and early life
Review: How nutrition and the maternal microbiota shape the neonatal immune system – Andrew J. MacPherson – Nature Reviews Immunology

Multi-site human microbiome
Review: Role of oral and gut microbiome in nitric oxide mediated colon motility – Miriam Y. Walker – Nitric Oxide

Human skin microbiome
Review: Chemical signaling in mosquito–host interactions: the role of human skin microbiota – William Takken – Current Opinion in Insect Science

Human oral microbiome
Reduced Susceptibility to Antiseptics Is Conferred by Heterologous Housekeeping Genes – Supathep Tansirichaiya – Microbial Drug Resistance

Human gut microbiome
*Alcohol-associated intestinal dysbiosis impairs pulmonary host defense against Klebsiella pneumoniae – Derrick R. Samuelson – PLoS Pathogens

Review: Fungal dysbiosis: immunity and interactions at mucosal barriers – Ilian D. Iliev – Nature Reviews Immunology

Review: Transmission of the gut microbiota: spreading of health – Hilary P. Browne – Nature Reviews Microbiology

Editorial: Post-dieting weight gain: the role of persistent microbiome changes – Christoph A Thaiss – Future Microbiology

Animal experiments
*Thermoneutral housing exacerbates nonalcoholic fatty liver disease in mice and allows for sex-independent disease modeling – Daniel A. Giles – Nature Medicine

*Cold-induced conversion of cholesterol to bile acids in mice shapes the gut microbiome and promotes adaptive thermogenesis – A. Worthmann – Nature Medicine

Integrated Metagenomic Analyses of the Rumen Microbiome of Cattles Reveals Key Biological Mechanisms Associated with Methane Traits – Haiying Wang – Methods

Long-term multi-species Lactobacillus and Bifidobacterium dietary supplement enhances memory and changes regional brain metabolites in middle-aged rats – Caroline O’Hagan – Neurobiology of Learning and Memory

Soy compared with milk protein in a Western diet changes fecal microbiota and decreases hepatic steatosis in obese OLETF rats – Matthew R. Panasevich – Journal of Nutritional Biochemistry

Targeted metabolomics analysis of aromatic amino acids and their gut microbiota-host co-metabolites in rat serum and urine by liquid chromatography with tandem mass spectrometry – Yifeng Zeng – Journal of Separation Science

Effect of cocoa’s theobromine on intestinal microbiota of rats – Sandra Martin-Pelaez – Molecular Nutrition and Food Research

Water and extremophile microbiome
Review: Microbial Extracellular Polymeric Substances (EPSs) in Ocean Systems – Alan W. Decho – Frontiers in Microbiology

Review: Linking genes to microbial biogeochemical cycling: lessons from arsenic – Yong-Guan Zhu – Environmental Science and Technology

Food microbiology
Review: Extremozymes from metagenome: Potential applications in food processing – Mahejibin Khan – Critical Reviews in Food Science and Nutrition

Phages and viruses
Review: Interplay between viruses and bacterial microbiota in cancer development – Dariia Vyshenska – Seminars in Immunology

Bioinformatics
A novel method to determine the minimum number of sequences required for reliable microbial community analysis – Jiajia Ni – Journal of Microbiological Methods

Power and sample size calculations for high-throughput sequencing-based experiments – Chung-I Li – Briefings in Bioinformatics
Only a short section on microbiome.

Techniques
*A stabilized microbial ecosystem of self-limiting bacteria using synthetic quorum-regulated lysis – Spencer R. Scott – Nature Microbiology

Body fluid prediction from microbial patterns for forensic application – Eirik Nataas Hanssen – Forensic Science International: Genetics

Multi-locus and long amplicon sequencing approach to study microbial diversity at species level using the MinIONTM portable nanopore sequencer – Alfonso Benítez-Páez – GigaScience

Review: Phenotyping of gut microbiota: Focus on capillary electrophoresis – Manuel Ferrer – Electrophoresis

Review: Panacea in progress: CRISPR and the future of its biological research introduction – Michael Carroll – Microbiological Research

June 8, 2017

Posted on June 8, 2017 by anjacobson

Modeling colon physiology to predict microbiota growth, a review of plant-bacteria genome-wide association studies, sporeforming bacteria isolated from beer.

General microbiome

Review: Systematic Review: The Impact of Cancer Treatment on the Gut and Vaginal Microbiome in Women With a Gynecological Malignancy – Ann Muls – International Journal of Gynecological Cancer

Pregnancy and early life

Contributions of the maternal oral and gut microbiome to placental microbial colonization in overweight and obese pregnant women – Luisa F Gomez-Arango – Scientific Reports

Human gut microbiome

Bread Affects Clinical Parameters and Induces Gut Microbiome-Associated Personal Glycemic Responses – Tal Korem – Cell Metabolism

* Global metabolic interaction network of the human gut microbiota for context-specific community-scale analysis – Jaeyun Sung – Nature Communications

The gut metagenome changes in parallel to waist circumference, brain iron deposition and cognitive function – Gerard Blasco – Journal of Clinical Endocrinology and Metabolism

Gut microbiota composition in relation to the metabolic response to 12-week combined polyphenol supplementation in overweight men and women – J Most – European Journal of Clinical Nutrition

Complete genome sequence of Clostridium perfringens CBA7123 isolated from a faecal sample from Korea – Yeon Bee Kim – Gut Pathogens

Review: The Research Progress on Intestinal Stem Cells and Its Relationship with Intestinal Microbiota – Qihang Hou – Frontiers in Immunology

Review: Gut microbiota: Intestinal fungi fuel the inflammatory fire in alcoholic liver disease – Hugh Thomas – Nature Reviews Gastroenterology and Hepatology

* Effect of water flow and chemical environment on microbiota growth and composition in the human colon – Jonas Cremer – PNAS

Animal experiments

Gut-Associated Lymphoid Tissue: A Key Tissue Inside the Mucosal Immune System of Hens Immunized with Escherichia coli F4 – Maria F Peralta – Frontiers in Immunology

Gut Dysbiosis and Neurobehavioral Alterations in Rats Exposed to Silver Nanoparticles – Angela B Javurek – Scientific Reports

Improved detection of gene-microbe interactions in the mouse skin microbiota using high-resolution QTL mapping of 16S rRNA transcripts – Meriem Belheouane – Microbiome

In Vitro Study of the Metabolic Characteristics of Eight Isoquinoline Alkaloids from Natural Plants in Rat Gut Microbiota – Chi-Yu He – Molecules

Animal microbiome

Symbionts in waiting: the dynamics of incipient endosymbiont complementation and replacement in minimal bacterial communities of psyllids – Jennifer L Morrow – Microbiome

Plant, root, and soil microbiome

Applying community ecological theory to maximize productivity of cultivated biocrusts – Matthew A Bowker – Ecological Applications

Is soil microbial diversity affected by soil and groundwater salinity? Evidences from a coastal system in central Italy – Loredana Canfora – Environmental Monitoring and Assessment

* Review: Genome-Wide Association Studies In Plant Pathosystems: Toward an Ecological Genomics Approach – Claudia Bartoli – Frontiers in Plant Science

Linking rhizosphere microbiome composition of wild and domesticated Phaseolus vulgaris to genotypic and root phenotypic traits – Juan E Pérez-Jaramillo – The ISME Journal

Water and extremophile microbiome

Changes in Microbial (Bacteria and Archaea) Plankton Community Structure after Artificial Dispersal in Grazer-Free Microcosms – Hera Karayanni – Microorganisms

Identifying the core seed bank of a complex boreal bacterial metacommunity – Clara Ruiz-González – The ISME Journal

Genomic insights into temperature-dependent transcriptional responses of Kosmotoga olearia, a deep-biosphere bacterium that can grow from 20oC to 79oC – Stephen M J Pollo – bioRxiv

Transient exposure to oxygen or nitrate reveals ecophysiology of fermentative and sulfate-reducing benthic microbial populations – Zainab Abdulrahman Beiruti – bioRxiv

Food microbiology

Evolution of class 1 integrons: Mobilization and dispersal via food-borne bacteria – Timothy M Ghaly – PLOS ONE

* Sporeforming bacteria in beer: Occurrence, diversity, presence of hop resistance genes and fate in alcohol-free and lager beers – Allan R G Munford – Food Control

Probiotics/prebiotics

Probiotic Bifidobacterium bifidum G9-1 attenuates 5-fluorouracil-induced intestinal mucositis in mice via suppression of dysbiosis-related secondary inflammatory responses – Shinichi Kato – Clinical and Experimental Pharmacology and Physiology

Review: The Role of the Microbiome and the use Of Probiotics in Gastrointestinal Disorders in Adults in the Asia-Pacific Region – Uday C Goshal – Journal of Gastroenterology and Hematology

Phages and viruses

Evolution of selective-sequencing approaches for virus discovery and virome analysis – Arvind Kumar – Virus Research

Techniques

Review: Novel approaches in function-driven single-cell genomics – Devin F R Doud – FEMS Microbiology Reviews

Fast Method for the determination of Short-chain-length Polyhydroxyalkanoates (scl-PHAs) in Bacterial Samples by In Vial-Thermolysis (IVT) – Federica Abbondanzi – New Biotechnology

Microbes in the news

Are Pets the New Probiotic? – Richard Schiffman – The New York Times

Gut bacteria could protect cancer patients and pregnant women from Listeria, study suggests – EurekAlert

Impact of protective bacteria linked to infection route, study finds – EurekAlert

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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

Category Archives: Food Microbiology

July 26, 2017

July 25, 2017

July 23, 2017

July 20, 2017

July 16, 2017

July 7, 2017

July 3, 2017

June 15, 2017

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June 8, 2017