Category Archives: Human gut

August 10, 2017

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Human urinary microbiome

The microbiome in urogenital schistosomiasis and induced bladder pathologies – Adewale S. Adebayo – PLoS Negl Trop Dis

Human gut microbiome

A 3-dimensional mathematical model of microbial proliferation that generates the characteristic cumulative relative abundance distributions in gut microbiomes – Lena Takayasu – PLoS ONE

Plant, root, and soil microbiome

Evolutionary conservation of a core root microbiome across plant phyla along a tropical soil chronosequence – Yun Kit Yeoh – Nature Communications

Spatiotemporal Variation and Networks in the Mycobiome of the Wheat Canopy – Rumakanta Sapkota – Frontiers in Plant Science

Water and extremophile microbiome

Active microorganisms thrive among extremely diverse communities in cloud water – Pierre Amato – PLoS ONE

Seasonal Analysis of Microbial Communities in Precipitation in the Greater Tokyo Area, Japan – Satoshi Hiraoka – Frontiers in Microbiology

Built environment

The US National Mall Microbiome: A Census of Rhizosphere Bacteria Inhabiting Landscape Turf – Jo Anne Crouch – Crop Science

Microbes in the news

For Healthy Skin, Just Add…Bacteria? – Adam Hurly – GQ

Microbes on the market

Reality vs. hype: A macro look at the microbiome market – Juliet Preston – MedCityNews

Science, publishing, and career

Prof claims victory over ‘#manel’ at microbiome conference – Dan Jackson – Campus Reform

August 7, 2017

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General microbiome

Viruses in the 21st Century: From the Curiosity-Driven Discovery of Giant Viruses to New Concepts and Definition of Life – Patrick Forterre, Clinical Infectious Diseases

Spatial Organization Plasticity as an Adaptive Driver of Surface Microbial Communities – Arnaud Bridier, Frontiers in Microbiology

Functions and emerging applications of bacteriocins – Michael L Chikindas, Current Opinion in Biotechnology

Pregnancy and early life

Ontogenesis of the Gut Microbiota Composition in Healthy, Full-Term, Vaginally Born and Breast-Fed Infants over the First 3 Years of Life: A Quantitative Bird’s-Eye View – Ravinder Nagpal, Frontiers in Microbiology

Multi-site human microbiome

Profiling of faecal water and urine metabolites among Papua New Guinea highlanders believed to be adapted to low protein intake – Eriko Tomitsuka, Metabolomics

Evidence based selection of probiotic strains to promote astronaut health or alleviate symptoms of illness on long duration spaceflight missions – G.L. Douglas, Beneficial Microbes

Human oral microbiome

Salivary microbiome in non-oral disease: A summary of evidence and commentary – Aneesha Acharya, Archives of Oral Biology

Human gut microbiome

Dysbiotic Proteobacteria expansion: a microbial signature of epithelial dysfunction – Yael Litvak, Current Opinion in Microbiology

Role of gut microbiota in idiopathic nephrotic syndrome in children – Kazunari Kaneko, Medical Hypotheses

A preliminary examination of gut microbiota, sleep, and cognitive flexibility in healthy older adults – Jason R. Anderson, Sleep Medicine

Diarrhea after bariatric procedures: Diagnosis and therapy – Yves M Borbély, World Journal of Gastroenterology

The Intestinal Microbiome and Childhood Obesity – Jessica McCann, Current Pediatrics Reports

Cross-modulation of pathogen-specific pathways enhances malnutrition during enteric co-infection with Giardia lamblia and enteroaggregative Escherichia coli – Luther A. Bartelt, PLoS Pathogens

Animal experiments

Streptococcus pneumoniae colonization is required to alter the nasal microbiota in cigarette smoke-exposed mice – Pamela Shen, Infection and Immunity

Fenugreek galactomannan and citrus pectin improve several parameters associated with glucose metabolism, and modulate gut microbiota in mice  – Miriam G. Shtriker, Nutrition

Animal microbiome

The B Vitamin Nutrition of Insects: The contributions of diet, microbiome and horizontally-acquired genes – Angela E. Douglas, Current Opinion in Insect Science

Effects of Disodium Fumarate on In Vitro Rumen Fermentation, The Production of Lipopolysaccharide and Biogenic Amines, and The Rumen Bacterial Community – Wei Jin, Current Microbiology

Cutaneous Microbial Community Variation across Populations of Eastern Hellbenders (Cryptobranchus alleganiensis alleganiensis) – Obed Hernández-Gómez, Frontiers in Microbiology

Microorganisms associated with microscopic insects Megaphragma amalphitanum and Scydosella musawasensis – A. V. Nedoluzhko, Microbiology

Plant, root, and soil microbiome

Polyphasic characterization of bacteria obtained from upland rice cultivated in Cerrado soil – Lívia Fabiana Braga, Brazilian Journal of Microbiology

Taxonomic and functional patterns across soil microbial communities of global biomes – Melline Fontes Noronha, Science of The Total Environment

Phylloplane bacteria of Jatropha curcas : diversity, metabolic characteristics and growth promoting attributes towards vigor of maize seedling – Garima Dubey, Canadian Journal of Microbiology

Bioorganic fertilizer maintains a more stable soil microbiome than chemical fertilizer for monocropping – Feng Cai, Biology and Fertility of Soils

Root exudates of potato onion are involved in the suppression of clubroot in a Chinese cabbage-potato onion-Chinese cabbage crop rotation – Shaocan Chen, European Journal of Plant Pathology

Isolation, characterization and inter-relationship of Phosphate Solubilizing Bacteria from the Rhizosphere of Sugarcane and Rice – Muhammad Awais, Biocatalysis and Agricultural Biotechnology

Distribution of Rhizosphere and Endosphere Fungi on the First-Class Endangered Plant Cypripedium japonicum – Geun-Hye Gang, Mycobiology

Effects of different nitrogen additions on soil microbial communities in different seasons in a boreal forest – Guoyong Yan, Ecosphere

Temporal assessment of microbial communities in soils of two contrasting mangroves – Janaina Rigonato, Brazilian Journal of Microbiology

Bio-fertilizer application induces soil suppressiveness against Fusarium wilt disease by reshaping the soil microbiome – Wu Xiong, Soil Biology and Biochemistry

Bioorganic fertilizer maintains a more stable soil microbiome than chemical fertilizer for monocropping – Feng Cai, Biology and Fertility of Soils

Comparative metagenomics reveals alterations in the soil bacterial community driven by N-fertilizer and Amino 16® application in lettuce – Apostolos Kalivas, Genomics Data

Genetic Diversity of Nitrogen-Fixing and Plant Growth Promoting PseudomonasSpecies Isolated from Sugarcane Rhizosphere – Hai-Bi Li, Frontiers in Microbiology

A Review of Conventional PCR Assays for the Detection of Selected Phytopathogens of Wheat – Adam Kuzdraliński, Journal of Molecular Microbiology and Biotechnology

Effect of mixed edible bacterial inoculants on the early development of improved cultivars of cocoa (Theobroma cacao L.) in a traditional agroforestry system in northern Oaxaca, Mexico – E. Hipólito-Romero, Argentina Journal of Microbiology

Draft Genome Sequence of Cronobacter sakazakiiGP1999, Sequence Type 145, an Epiphytic Isolate Obtained from the Tomato’s Rhizoplane/Rhizosphere Continuum – Hannah R. Chase, Genome Anouncements

Plant-mediated restriction of Salmonella enterica on tomato and spinach leaves colonized with Pseudomonas plant growth-promoting rhizobacteria – Chiun-Kang Hsu, International Journal of Food Microbiology

Water and extremophile microbiome

Assessment upon heterotrophic microalgae screened from wastewater microbiota for concurrent pollutants removal and biofuel production – Liang Shen, Bioresource Technology

Compositions of the Microbial Consortia Present in Biological Sulphate Reduction Processes During Mine Effluent Treatment – Marja Salo, Mine Water and Circular Economy

An underappreciated hotspot of antibiotic resistance: The groundwater near the municipal solid waste landfill – Qing-Lin Chen, Science of The Total Environment

Methane-Fueled Syntrophy through Extracellular Electron Transfer: Uncovering the Genomic Traits Conserved within Diverse Bacterial Partners of Anaerobic Methanotrophic Archaea – Connor T. Skennerton, mBio

A multi-omics based ecological analysis of coastal marine sediments from Gladstone, in Australia’s Central Queensland, and Heron Island, a nearby fringing platform reef – D.J. Beale, Science of The Total Environment

Glaciers and Ice Sheets As Analog Environments of Potentially Habitable Icy Worlds –  Eva Garcia-Lopez, Frontiers in Microbiology

Changes in microbial community structure in response to changing oxygen stress in column tests of denitrification and selenium reduction – Chiachi Hwang, Mine Water and Circular Economy

Next-generation sequencing for investigating the diversity of microorganisms and pathogenic bacteria in a water source – Yingliang Ge, Tropical Journal of Pharmaceutical Research

Microbial community dynamics in aerated biological fluidized bed (ABFB) with continuously increased p-nitrophenol loads – Fangzhou Ji, Process Biochemistry

Food microbiology

RNA-Based Amplicon Sequencing Reveals Microbiota Development during Ripening of Artisanal versus Industrial Lard d’Arnad – Ilario Ferrocino, Applied and Environmental Microbiology

The individual contribution of starter and non-starter lactic acid bacteria to the volatile organic compound composition of Caciocavallo Palermitano cheese – Valeria Guarrasi, International Journal of Food Microbiology

Antimicrobial resistance of Lactobacillus spp. from fermented foods and human gut – Qinqin Ma, LWT – Food Science and Technology

Probiotics / prebiotics

Applications of prebiotics in food industry: A review – Vinti Singla,
Food Science and Technology International

Human milk oligosaccharide consumption by probiotic and human-associated bifidobacteria and lactobacilli – Taksawan Thongaram, Journal of Dairy Science

Probiotic properties of Weissella cibaria and Leuconostoc citreum isolated from tejuino – A typical Mexican beverage – Monique Suela Silva, LWT – Food Science and Technology

A Consumer’s Guide for Probiotics: 10 Golden Rules for a Correct Use – Marco Toscano, Digestive and Liver Disease

Bioinformatics

PATRIC as a unique resource for studying antimicrobial resistance – Dionysios A. Antonopoulos, Briefings in Bioinformatics

Techniques

Optimized experimental workflow for tandem mass spectrometry molecular networking in metabolomics – Florent Olivon, Analytical and Bioanalytical Chemistry

Microbes in the news

Taking too many antibiotics to treat eczema may worsen your condition – DR. LESLIE BAUMANN, Miami Herald

August 5, 2017

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General microbiome

Stay connected: Electrical conductivity of microbial aggregates – C Li – Biotechnology Advances

Preprint: Anti-infective potential of a quorum modulatory polyherbal extract (Panchvalkal) against certain pathogenic bacteria – P Patel – bioRxiv

 

Human respiratory microbiome

Fungal and Bacterial Diversity of Airway Microbiota in Adults with Cystic Fibrosis: Concordance Between Conventional Methods and Ultra-Deep Sequencing, and Their Practical use in the Clinical Laboratory. – F Botterel – Mycopathologia

 

Human skin microbiome

The skin microbiome and immune system: Potential target for chemoprevention? – MA Sherwani – Photodermatol. Photoimmunol. Photomed.

 

Human gut microbiome

Assessing gut microbiota perturbations during the early phase of infectious diarrhea in Vietnamese children – HC The – Gut Microbes

Heritable components of the human fecal microbiome are associated with visceral fat – CI Le Roy – Gut Microbes

Gut-Liver Axis Derangement in Non-Alcoholic Fatty Liver Disease – M Poeta – Children (Basel)

Review:Antigen-specific regulatory T-cell responses to intestinal microbiota – EV Russler-Germain – Mucosal Immunol.

Review:Sulfur Cycling and the Intestinal Microbiome – LL Barton – Dig. Dis. Sci.

Mucosal microbiome dysbiosis in gastric carcinogenesis – OO Coker – Gut

 

Animal microbiome 

Recent developments in understanding the role of the gut microbiota in brain health and disease – E Sherwin – Ann. N. York Acad. Sc

Review:The Gut Microbiome and Mental Health: Implications for Anxiety- and Trauma-Related Disorders – S Malan-Muller – Omics

Phylogenetic diversity and functional characterization of the Manila clam microbiota: a culture-based approach. – L Leite – Environ Sci Pollut Res Int.

 

Plant, root, and soil microbiome

Environment and geographic distance differ in relative importance for determining fungal community of rhizosphere and bulk soil – Kaoping Zhang – Environmental Microbiology

Below- and above-ground effects of deadwood and termites in plantation forests – MD Ulyshen – Ecosphere

Effects of biosolids from a wastewater treatment plant receiving manufactured nanomaterials on Medicago truncatula and associated soil microbial communities at low nanomaterial concentrations – C Chen – Sci Total Environ.

Compartmentalized metabolic network reconstruction of microbial communities to determine the effect of agricultural intervention on soils – MC Alvarez-Silva – PLoS One

The Aboveground Vegetation Type and Underground Soil Property Mediate the Divergence of Soil Microbiomes and the Biological Interactions – SH Wu – Microbial Ecology

 

Water microbiome and extremophiles

Preprint: A dynamic microbial community with high functional redundancy inhabits the cold, oxic subseafloor aquifer – B Tully – bioRxiv

 

Built environment 

Salt-tolerance aerobic granular sludge: formation and microbial community characteristics – O Doung – Bioresource Technology

Airborne bacterial assemblage in a zero carbon building: a case study – MHY Leung – Indoor Air

 

Microbes in space

Anaerobic microorganisms in astrobiological analogue environments: from field site to culture collection – CS Cockell – International Journal of Astrobiology

 

 

Phages and viruses

Bacteriophages as potential new mammalian pathogens. – GV Tetz – Scientific Reports

 

Techniques

Preprint: An Efficient Moments-Based Inference Method for Within-Host Bacterial Infection Dynamics – D Price – bioRxiv

Novel co-culture plate enables growth dynamic-based assessment of contact-independent microbial interactions – Jr TJ Moutinho – PloS One

PCR cycles above routine numbers do not compromise high-throughput DNA barcoding results – J. Vierna – Genome

Assessment of Bacteria and Archaea in Metalworking Fluids Using Massive Parallel 16S rRNA Gene Tag Sequencing – N. Di Maiuta – Letters in Applied Microbiology

Exploring the microbiome of healthy and diseased peri-implant sites using Illumina Sequencing – I Sanz-Martin – J. Clin. Periodontol.

Isolation and Laboratory Domestication of Natural Yeast Strains – G Liti – Cold Spring Harb Protoc.

 

Microbes in the news

How Metagenomics Are Advancing Infectious Disease Diagnostics – Medscape

Human Microbiome Market Trend to 2022 Profiling Merck, DuPont, MicroBiome Therapeutics, Osel, Vedanta BioSciences & More – MedGadget

New Mexico Tech scientist finds cure for plant disease – El Defensor Chieftain

Permitting pain – Nature Reviews Neuroscience

When He’s Not Charting a Course for the Moon, This Entrepreneur Is Planning Big Things for Your Gut – Inc.

What you eat will protect you from flu — but only if you have the right gut bacteria – Coach

How a tick gut gene serves as a gateway for Lyme disease – YaleNews

Methane-Eating Bacteria Discovered Under The Antarctic Shelf – Iflscience

Blueberries and black tea can help your gut bacteria fight the flu – Cosmos

Microbiology Professor Wanted for Murder – The Scientist

Judge halts Margate sand dune project due to bacteria-filled ponds – NJ

August 2, 2017

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Enjoy your new  Microbiome Digest with some hot news on this very hot day. Methane- eating microbes found in lake deep beneath Antarctic ice sheet, while some some unexpected life was also found at the bottom of high Arctic Lakes.

 

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

 
The oral microbiota in patients with pancreatic cancer, patients with IPMNs, and controls: a pilot study – Sara H. Olson – Cancer Causes & Control

 
Metabolic Fingerprints from the Human Oral Microbiome Reveal a Vast Knowledge Gap of Secreted Small Peptidic Molecules – Anna Edlund –  mSystems
Prevalence of periodontal pathogens among italian patients with chronic periodontitis: a retrospective study on 2992 patients – L. Tettamanti- Oral & Implantology

 

 

Human gut microbiome

 
Metabolites and microbial composition of stool of women with fecal incontinence: Study design and methods – Lily A. Arya – Neurology Urodynamics

 
Microscopic Colitis After Fecal Microbiota Transplant – Matthew J. Fasullo – ACG Case Reports Journal
Alteration in the gastric microbiota and its restoration by probiotics in patients with functional dyspepsia – Muneki Igarashi  – BMJ Open Gastroenterology

 
Aggravation of collagen-induced arthritis by orally administered Porphyromonas gingivalis through modulation of the gut microbiota and gut immune system – Keisuke Sato – Scientific Reports

 
The gut microbiota, a new cardiovascular risk factor? – Caroline Chong-Nguyen – La Presse Médicale

 
The Association between Cardiorespiratory Fitness and Gut Microbiota Composition in Premenopausal Women – Yifan Yang – Nutrients

 
Gut microbiota metabolites for sweetening type I diabetes – Thamer Aljtaily – Cellular & Molecular Immunology

 
Vasopressin deletion is associated with sex-specific shifts in the gut microbiome – Christopher T. Fields – Gut Microbes

 
Stable engraftment of human microbiota into mice with a single oral gavage following antibiotic conditioning –  Christopher Staley – Microbiome

 
Animal microbiome 

 
Temporal dynamics of in-situ fiber-adherent bacterial community under ruminal acidotic conditions determined by 16S rRNA gene profiling – Renee M. Petri – PLOS One

 
Plant, root, and soil microbiome

 
Activity, biomass and composition of microbial communities and their degradation pathways in exposed propazine soil – C. Jiang  – Ecotoxicology and Environmental Safety

 
Response of microbial community and catabolic genes to simulated petroleum hydrocarbon spills in soils/sediments from different geographic locations– Qinglong Liu – Journal of Applied Microbiology

 
Primary productivity as a control over soil microbial diversity along environmental gradients in a polar desert ecosystem – Kevin M. Geyer – PeerJ

 
Steering Soil Microbiomes to Suppress Aboveground Insect Pests – Ana Pineda –  Trends in Plant Science

 
Importance of exposure dynamics of metal-based nano-ZnO, -Cu and -Pb governing the metabolic potential of soil bacterial communities  – Yujia Zhai – Ecotoxicology and Environmental Safety

 
Water and extremophile microbiome 

 
Production and degradation of fluorescent dissolved organic matter derived from bacteria –  Ken Arai – Journal of Oceanography

 
Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition – Adriana Alberti – Scientific Data
Watershed Urbanization Linked to Differences in Stream Bacterial Community Composition – Jacob D. Hosen – Frontiers in Microbiology

 
Influence of Igneous Basement on Deep Sediment Microbial Diversity on the Eastern Juan de Fuca Ridge Flank – Jessica M. Labonté – Frontiers in Microbiology

 
Coordinated regulation of growth, activity and transcription in natural populations of the unicellular nitrogen-fixing cyanobacterium Crocosphaera – Samuel T. Wilson – Nature Microbiology

 
The global biogeography of amino acid variants within a single SAR11 population is governed by natural selection – Tom O. Delmont – bioRxiv

 

Food microbiology

 
Microorganisms in Fermented Apple Beverages: Current Knowledge and Future Directions – Fabien J. Cousin – Microorganisms

 
Probiotics / prebiotics

 
Next-generation probiotics targeting Clostridium difficile through precursor-directed antimicrobial biosynthesis – Jennifer K. Spinler – Infection and Immunity

 
Biotechnology
Forum: Genetically Engineered Bacteria for Treating Human Disease – Buyun Ma – Trends in Pharmacological Sciences

 

Microbes in news

 

Methane-eating microbes found beneath Antarctica’s melting ice sheets

Unexpected Life Found at the Bottom of High Arctic Lakes

Tracking microbial succession in petroleum wells

August 1, 2017

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Today’s digest is relatively short, but there is an amazing commentary on rhizosheath and advantages of using phylogenetic distances to examine the microbial communities

Human gut microbiome

Maternal modifiers of the infant gut microbiota: metabolic consequences

Mulligan CM. Journal of Endocrinology

Association between gut microbiota and bone health: potential mechanisms and prospective

Chen YC. The Journal of Clinical Endocrinology & Metabolism

Plant, soil, and air microbiome

Amynthas agrestis invasion increases microbial biomass in Mid-Atlantic deciduous forests

Chang CH. Soil Biology and Biochemistry

Effect of nanoparticles on crops and soil microbial communities

Rajput VD. Journal of Soils and Sediments

Bottom-up effects on herbivore-induced plant defences: a case study based on compositional patterns of rhizosphere microbial communities.

Benítez E. Scientific reports

Unwrapping the rhizosheath

Pang J. Plant and Soil

Marine and inland waters

Marine archaea and archaeal viruses under global change

Danovaro R-F1000 Research

Bacterial community structure in the intertidal biofilm along the Yangtze Estuary, China

Guo X .Marine Pollution Bulletin

Fronts at the surface ocean can shape distinct regions of microbial activity and community assemblages down to the bathypelagic zone: The Azores Front as a case study

Baltar F. Frontiers in Marine Science

Microbiome Approaches/Techniques

A deep metaproteomics approach for the study of human microbiomes

Zhang X Analytical Chemistry, 2017

Advantages of phylogenetic distance based constrained ordination analyses for the examination of microbial communities.

Shankar V. Scientific reports

Oral/Nasal Microbiome 

The periodontal war: microbes and immunity

Ebersole JL. PERIODONTOLOGY 2000

Design and validation of a DNA-microarray for phylogenetic analysis of bacterial communities in different oral samples and dental implants

Parolin C. Scientific Reports

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

Mika M. Microbiome

Food Microbiology 

Comparison study of the volatile profiles and microbial communities of Wuyi Qu and Gutian Qu, two major types of traditional fermentation starters of Hong Qu glutinous rice wine

Liu Z.Food Microbiology

Plant-mediated restriction of Salmonella enterica on tomato and spinach leaves colonized with Pseudomonas plant growth-promoting rhizobacteria

Hsu CK.International Journal of Food Microbiology, 2017

July 31, 2017

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Short digest today, with many articles from Applied and Environmental Microbiology (AEM)!

General microbiome
Review: Bacterial infection increases risk of carcinogenesis by targeting mitochondria – Jesper A.B. Strickertsson – Seminars in Cancer Biology

Pregnancy and early life
Iron in Micronutrient Powder Promotes an Unfavorable Gut Microbiota in Kenyan Infants – Minghua Tang – Nutrients

Multi-site human microbiome
Review: Role of uremic toxin indoxyl sulfate in the progression of cardiovascular disease – Huichang Gao – Life Sciences

Human gut microbiome
The sortase-dependent fimbriome of the genus Bifidobacterium: extracellular structures with potential to modulate microbe-host dialogue – Christian Milani – Applied and Environmental Microbiology

Repression of Salmonella host cell invasion by aromatic small molecules from the human fecal metabolome – Rafael J.M. Peixoto – Applied and Environmental Microbiology

Animal experiments
Antibiotic-Induced Microbiota Dysbiosis Impairs Neuromuscular Function in Juvenile Mice – Valentina Caputi – British Journal of Pharmacology

10-oxo-12(Z)-octadecenoic acid, a linoleic acid metabolite produced by gut lactic acid bacteria, enhances energy metabolism by activation of TRPV1 – Minji Kim – FASEB

Water and extremophile microbiome
Dissimilatory Nitrate Reduction to Ammonium in the Yellow River Estuary: Rates, Abundance, and Community Diversity – Cuina Bu – Scientific Reports

Built environment
Phage-host associations in a full-scale activated sludge plant during sludge bulking – Ruyin Liu – Applied Microbiology and Biotechnology

Phages and viruses
Metagenomic Analysis of Dairy Bacteriophages: Extraction Method and Pilot Study on Whey Samples Derived from Using Undefined and Defined Mesophilic Starter Cultures – Veronica Barragan – Applied and Environmental Microbiology

Microbes in the news
Flesh-Eating Vibrio Can Come From Cleaning Fish…As Well As Swimming – Judy Stone – Forbes

Burp! Singapore scientists hope for probiotic beer hit – Reuters – Deccan Chronicle

Bacteria Hysteria
Blowing out birthday candles increases bacteria on cake’s icing – study –
Daily Mail

Deadly mix: Brewing faecal bacteria in your coffee cup? – Jagruti Verma – Deccan Chronicle

July 29, 2017

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Enjoy perusing this beefy Microbiome Digest, which is heavy on information about plant/root/soil microbes, water/extremophile microbes, and new microbial techniques.

Events and jobs

Microbiome Symposium 2017 – September 11, Quadras Conference Center

General microbiome

Temperature, inocula and substrate: Contrasting electroactive consortia, diversity and performance in microbial fuel cells – E.S. Heidrich, Bioelectrochemistry

Effect of glucose on nitrogen removal and microbial community in anammox-denitrification system – Yujie Qin, Bioresource Technology

Horizontal Gene Transfer and Ecosystem Function Dynamics – Maarten van de Guchte, Trends in Microbiology

Pregnancy and early life

Patterns of Early-Life Gut Microbial Colonization during Human Immune Development: An Ecological Perspective – Isabelle Laforest-Lapointe, Frontiers in Microbiology

Maternal Gut Microbiome Biodiversity in Pregnancy – Marcela C. Smid, American Journal of Perinatology

Sphingolipid metabolism potential in fecal microbiome and bronchiolitis in infants: a case–control study – Kohei Hasegawa, BMC Research Notes

Adverse events in women and children who have received intrapartum antibiotic prophylaxis treatment: a systematic review – Farah Seedat, BMC Pregnancy and Childbirth

Human skin microbiome

Bacterial diversity in Buruli ulcer skin lesions: Challenges in the clinical microbiome analysis of a skin disease – Chloé Van Leuvenhaege, PLoS ONE

Human oral microbiome

16S rDNA analysis of periodontal plaque in chronic obstructive pulmonary disease and periodontitis patients – Wu X., Journal of Oral Microbiology

Porphyromonas gingivalis disturbs host-commensal homeostasis by changing complement function – Olsen I., Journal of Oral Microbiology

Human gut microbiome

The Present Status of Fecal Microbiota Transplantation and Its Value in the Elderly – Yao-Wen Cheng, Current Treatment Options in Gastroenterology

Fecal total iron concentration is inversely associated with fecal Lactobacillus in preschool children – Sasank Kalipatnapu, Gastroenterology

Long-term irritable bowel syndrome symptom control with reintroduction of selected FODMAPs – Ruth M. Harvie, World Journal of Gastroenterology

Distinct gut microbiota profiles in patients with primary sclerosing cholangitis and ulcerative colitis – Lukas Bajer, World Journal of Gastroenterology

Eubiotic properties of rifaximin: Disruption of the traditional concepts in gut microbiota modulation – Francesca Romana Ponziani, World Journal of Gastroenterology

Helicobacter pylori and gut microbiota in multiple sclerosis versus Alzheimer’s disease: 10 pitfalls of microbiome studies – Ah-Mee Park, Clinical and Experimental Neuroimmunology

Partners of patients with ulcerative colitis exhibit a biologically relevant dysbiosis in fecal microbial metacommunities – Guang-Lan Chen, World Journal of Gastroenterology

Animal Experiments

Oral administration of live- or heat-killed Candida albicansworsened cecal ligation and puncture sepsis in a murine model possibly due to an increased serum (1→3)-β-D-glucan – Wimonrat Panpetch, PLoS ONE

Cross-modulation of pathogen-specific pathways enhances malnutrition during enteric co-infection with Giardia lambliaand enteroaggregative Escherichia coli – Luther A. Bartelt, PLoS Pathogens

Animal microbiome

Changes in the Intestinal Microbiota of Gibel Carp (Carassius gibelio) Associated with Cyprinid herpesvirus2 (CyHV-2) Infection – Rong She, Current Microbiology

Diversity and stability of coral endolithic microbial communities at a naturally high pCO2 reef – Vanessa R. Marcelino, Molecular Ecology

Characterization of feather-degrading bacterial populations from birds’ nests – Potential strains for biomass production for animal feed – Maria Saarela, International Biodeterioration & Biodegradation

The impact of the bovine fecal microbiome on Escherichia coli O157:H7 prevalence and enumeration in naturally infected cattle – Minseok Kim, Journal of Applied Microbiology

Burying beetles regulate the microbiome of carcasses and use it to transmit a core microbiota to their offspring – Shantanu P. Shukla, Molecular Ecology

Plant, root, and soil microbiome

Elevated CO2 and nitrogen addition have minimal influence on the rhizospheric effects of Bothriochloa ischaemum – Lie Xiao, Scientific Reports

Soil nutritional status and biogeography influence rhizosphere microbial communities associated with the invasive tree Acacia dealbata – Casper N. Kamutando, Scientific Reports

Biotoxic impact of heavy metals on growth, oxidative stress and morphological changes in root structure of wheat (Triticum aestivum L.) and stress alleviation by Pseudomonas aeruginosa strain CPSB1 – Asfa Rizvi, Chemosphere

Use of microbial indicators combined with environmental factors coupled to metrology tools for discrimination and classification of Luzhou-flavored pit muds – Q.Y. Zhang, Journal of Applied Microbiology

Fertilization decreases compositional variation of paddy bacterial community across geographical gradient – Ruirui Chen, Soil Biology and Biochemistry

Effects of snow cover plus straw mulching on microorganisms in paddy soil during winter – Hao Zhang, Applied Soil Ecology

The Contribution of Pyrene Degrading Bacteria and Chemical Reagents to Scirpus triqueterPhytoremediation of Pyrene and Ni Co-contaminated Soil – Xiaoxin Hu, Water, Air, & Soil Pollution

Investigating whether light intensity can modify decomposition rates in peatlands through control of the ‘enzymic latch’ – Christian Dunn, Ecological Engineering

Analysis of microbiota in rhizosphere, water and gut of grass carp (Ctenopharyngodon idella) in ponds treated with artificial floating beds – Jian Li, Water and Environment Journal

Scaling from the growth chamber to the greenhouse to the field: Demonstration of diminishing effects of mitigation of salinity in peppers inoculated with plant growth-promoting bacterium and humic acids – Macario Bacilio, Applied Soil Ecology

Disease management of tomato through PGPB: current trends and future perspective – Vipin Kumar Singh, 3 Biotech

Soil bacteria and archaea change rapidly in the first century of Fennoscandian boreal forest development – Stephanie A. Yarwood, Soil Biology and Biochemistry

Leaf litterfall decomposition of pedunculate (Quercus robur L.) and sessile (Q. petraea [Matt.] Liebl.) oaks and their hybrids and its impact on soil microbiota – Girmantė Jurkšienė, Dendrobiology

On the controls of abundance for soil-dwelling organisms on the Tibetan Plateau – Ke Zhao, Ecosphere

Water and extremophile microbiome

Microbial planktonic communities in the Red Sea: high levels of spatial and temporal variability shaped by nutrient availability and turbulence – John K. Pearman, Scientific Reports

Characterization of a highly efficient antibiotic-degrading metallo-β-lactamase obtained from an uncultured member of a permafrost community – Marcelo Monteiro Pedroso, Metallomics

Polycyclic aromatic hydrocarbons (PAHs) enrich their degrading genera and genes in human-impacted aquatic environments – Ke Yuan, Environmental Pollution

Spatial autocorrelation of microbial communities atop a debris-covered glacier is evidence of a supraglacial chronosequence – Jack L. Darcy, FEMS Microbiology Ecology

Eco-friendly and efficient in situ restoration of the constructed sea stream by bioaugmentation of a microbial consortium – Jangyeon Yoo, Korean Journal of Microbiology

Identification of two organohalide-respiring Dehalococcoidiaassociated to different dechlorination activities in PCB-impacted marine sediments – Andrea Nuzzo, Microbial Cell Factories

Draft genome sequence of the halophilic Halobacillus mangroviKTB 131 isolated from Topan salt of the Jeon-nam in Korea – Mingyeong Woo, Genomics Data

First draft genome sequence of a strain from the genus Fusibacter isolated from Salar de Ascotán in Northern Chile – Antonio E. Serrano, Extended Genome Report

Draft Genome Sequence of the Deep-Sea Bacterium Moritella sp. JT01 and Identification of Biotechnologically Relevant Genes – Robert Cardoso de Freitas, Marine Biotechnology

Bacterial and Archaeal Diversity in Hypersaline Cyanobacterial Mats Along a Transect in the Intertidal Flats of the Sultanate of Oman – Janina C. Vogt, Microbial Ecology

Bacterial and fungal communities and contribution of physicochemical factors during cattle farm waste composting – Huhe, Microbiology Open

Built environment

Bioprotection of the built environment and cultural heritage – Geoffrey Michael Gadd, Microbial Biotechnology

Food microbiology

Food waste conversion to microbial polyhydroxyalkanoates – Chad Nielsen, Microbial Biotechnology

Insect frass in stored cereal products as a potential source of Lactobacillus sanfranciscensis for sourdough ecosystem – Federica Boiocchi, Journal of Applied Microbiology

Probiotics

Evaluation of Probiotic Diversity from Soybean (Glycine max) Seeds and Sprouts Using Illumina-Based Sequencing Method – Yali Huang, Probiotics and Antimicrobial Proteins

Bioinformatics

Visibiome: an efficient microbiome search engine based on a scalable, distributed architecture – Syafiq Kamarul Azman, BMC Bioinformatics

Techniques

Inferring Past Environments from Ancient Epigenomes – David Gokhman, Microbial Ecology and Evolution

Comparison of DNA extraction methods used to detect bacterial and yeast DNA from spiked whole blood by real-time PCR – Libera M. Dalla-Costa, Journal of Microbiological Methods

Understanding the fundamental mechanisms of biofilms development and dispersal: BIAM (Biofilm Intensity and Architecture Measurement), a new tool for studying biofilms as a function of their architecture and fluorescence intensity – Marine Baudin, Journal of Microbiological Methods

Comparison of sequencing the D2 region of the large subunit ribosomal RNA gene (MicroSEQ®) versus the internal transcribed spacer (ITS) regions using two public databases for identification of common and uncommon clinically relevant fungal species – S. Arbefeville, Journal of Microbiological Methods

The feasibility of improved live-dead distinction in qPCR-based microbial source tracking – Laura Seidel, Journal of Microbiological Methods

Comparison of two bioinformatics tools used to characterize the microbial diversity and predictive functional attributes of microbial mats from Lake Obersee, Antarctica – Hyunmin Koo, Journal of Microbiological Methods

Multiplex polymerase chain reaction for identification of Escherichia coli, Escherichia albertii and Escherichia fergusonii – Rebecca L. Lindsey, Journal of Microbiological Methods

Nontargeted virus sequence discovery pipeline and virus clustering for metagenomic data – David Paez-Espino, Nature Protocols

SigTree: A Microbial Community Analysis Tool to Identify and Visualize Significantly Responsive Branches in a Phylogenetic Tree – John R. Stevens, Computational and Structural Biotechnology Journal

July 28, 2017

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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 27, 2017

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General microbiome

Microbiota-host Transgenomic Metabolism, Bioactive Molecules from the Inside –  S Turroni – J. Med. Chem.

Cyanophages exhibit rhythmic infection patterns under light-dark cycles – R Liu – bioRxiv

The effect of aspartate supplementation on the microbial composition and innate immunity on mice – P Bin – Amino Acids

Clinical impact of pre-transplant gut microbial diversity on outcomes of allogeneic hematopoietic stem cell transplantation – N Doki – Annals of Hematology

Differentiating botulinum-neurotoxin-producing clostridia with a simple, multiplex PCR assay – CHD Williamson – Appl. Environ. Microbiol.

Review: Antimicrobial resistance in the next 30 years, humankind, bugs and drugs: a visionary approach – M Bassetti – Intensive Care Med.

Lactobacillus fermentum CECT 5716 and a reduction of the Staphylococcus load in breast milk which reduces the risk of infectious mastitis: evaluation of a health claim pursuant to Article 14 of Regulation (EC) No 1924/2006 – EFSA Panel – EFSA Journal

 

Human gut microbiome

Specific signatures of the gut microbiota and increased levels of butyrate in children treated with fermented cow’s milk containing heat-killed Lactobacillus paracasei CBA L74 – R Canani Berni – Appl. Environ. Microbiol.

Examining the gut bacteriome, virome, and mycobiome in glucose metabolism disorders: Are we on the right track? –  C Stefenaki – Metab.Clin.Exp.

 

Animal microbiome

Assessment of Cultivable Oral Bacterial Flora from Important Venomous Snakes of India and Their Antibiotic Susceptibilities – IK Shaikh – Current Microbiology

 

Plant, root and soil microbiome

Rhizosphere Sampling Protocols for Microbiome (16S/18S/ITS rRNA) Library Preparation and Enrichment for the Isolation of Drought Tolerance-Promoting Microbes – V Lakshmanan – Methods in Molecular Biology

Toward a Resilient, Functional Microbiome: Drought Tolerance-Alleviating Microbes for Sustainable Agriculture – V Lakshmanan – Methods in Molecular Biology

Review: Biochar-rhizosphere interactions – A review – S Głuszek – Pol J Microbiol.

Interactions between Pteris vittata L. genotypes and a polycyclic aromatic hydrocarbon (PAH)-degrading bacterium (Alcaligenes sp.) in arsenic uptake and PAH-dissipation – L Sun -Environmental Pollution

 

Built environment

The performance and microbial communities of biodegradation-electron transfer with sulfur metabolism integrated process for flue gas desulfurization wastewater treatment – C Wei – Bioprocess Biosyst Eng.

 

Techniques

Dual RNA-Seq of Lysobacter capsici AZ78 – Phytophthora infestans interaction shows the implementation of attack strategies by the bacterium and unsuccessful oomycete defense responses –  S Tomada – Environmental Microbiology

 

Microbes in news

Infant Gut Microbiome May Influence Cognitive Development – Whole Foods Magazine

HEALTHY BITES: The importance of a healthy gut – My Web Times

Why apartment dwellers need indoor plants – Phys.org

Algae cultivation technique could advance biofuels – Science Daily

Bacteria may explain why uncircumcised face higher HIV risk – UPI

Cafe shut down at LA Fitness that had Legionnaires’ bacteria – Orlando Sentinel

Link between Saharan Dust and Vibrio bacteria – Kiiitv.com

Life evolves adaptions to microgravity – Phys.org

Algal solution- Could Spirulina modify the microbiome to protect against age related damage – Nutra Ingredients

Penis Microbiome Could Enhance Risk of Infection with HIV – Invisiverse

Building Codes for Bacterial Cities – Quanta Magazine

Researchers offer new and novel paradigm for advancing research on beneficial microbes – Phys.org

15 facts about fecal transplants – The straight poop – Genetic Literacy Project

He thought he just had blisters from a hike. He had flesh-eating bacteria and nearly died – The Washington Post

$1.8 million NIH grant to Wayne State to aid in developing improved cholera treatments – EurekAlert

Investigator | High levels of E.Coli bacteria found at local shopping malls – WKYC

Beautiful and bizarre things to buy: From wall art to a probiotic deodorant – Livemint

July 26, 2017

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General microbiome

Microbiome analysis and confocal microscopy of used kitchen sponges reveal massive colonization by Acinetobacter, Moraxella and Chryseobacterium species – Massimiliano Cardinale – Scientific Reports

Review: The mother–offspring dyad: microbial transmission, immune interactions and allergy development – Maria C. Jenmalm – Journal of Internal Medicine

Human skin microbiome

The Skin Microbiome of Cohabiting Couples – Ashley A. Ross – mSystems

Animal microbiome

Influence of Host Plant on Thaumetopoea pityocampa Gut Bacterial Community – Cinzia P. Strano – Microbial Ecology

The time-course of broiler intestinal microbiota development after administration of cecal contents to incubating eggs – Erin E. Donaldson – PeerJ

Plant, root, and soil microbiome

Review: Sphingomonads in Microbe-Assisted Phytoremediation: Tackling Soil Pollution – Michael Gatheru Waigi – Trends in Biotechnology

Response of soil microbial community composition and function to a bottomland forest restoration intensity gradient – Michael S. Strickland – Applied Soil Ecology

Changes of soil microbial communities during decomposition of straw residues under different land uses – Hong Zhang – Journal of Arid Land

Water and extremophile microbiome

Metagenomics of urban sewage identifies an extensively shared antibiotic resistome in China – Jian-Qiang Su – Microbiome

An anaerobic ~3400 Ma shallow-water microbial consortium: presumptive evidence of Earth’s Paleoarchean anoxic atmosphere – J. William Schopf – Precambrian Research

Iron oxides alter methanogenic pathways of acetate in production water of high-temperature petroleum reservoir – Pan Pan – Applied Microbiology and Biotechnology

Food Microbiology

Editorial: Microbiology of Ethnic Fermented Foods and Alcoholic Beverages of the World – Jyoti P. Tamang – Frontiers in Microbiology

Probiotics / prebiotics

Specific signatures of the gut microbiota and increased levels of butyrate in children treated with fermented cow’s milk containing heat-killed Lactobacillus paracasei CBA L74 – Roberto Berni Canani – Applied and Environmental Microbiology

Phages and viruses

Review : The Human Virome – Implications for Clinical Practice in Transplantation Medicine – Susanna K. Tan – Journal of Clinical Microbiology

Anitha’s non-microbiology picks

Quantum tunneling takes time, new study shows

Perovskites power up the solar industry

Scientists develop fast chemistry that unlocks a new class of polymers

Medicine’s Movable Feast: What Jumping Genes Can Teach Us about Treating Disease