Category Archives: Human gut

August 24, 2018

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Intra-individual microbiome biogeography, a review on IgA responses to the microbiota, seasonal fluctuations in the gut microbiota of white-faced capuchin monkeys, and the microbial composition of fog.

Pregnancy and early life

Sex-specific associations of infants’ gut microbiome with arsenic exposure in a US population – Anne G Hoen – Scientific Reports

Multi-site human microbiome

Assessing and Interpreting the Within-Body Biogeography of Human Microbiome Diversity – Zhanshan Ma – Frontiers in Microbiology

Human vaginal microbiome

Review: Investigating the effect of an abnormal cervico‐vaginal and endometrial microbiome on assisted reproductive technologies: A systematic review – Timothy Bracewell-Milnes – American Journal of Reproductive Immunology

Human gut microbiome

Review: IgA Responses to Microbiota – Jeffrey J Bunker – Immunity

Review: Comparing fecal microbiota transplantation to standard-of-care treatment for recurrent Clostridium difficile infection: a systematic review and meta-analysis – Muhammad Y Khan – European Journal of Gastroenterology & Hepatology

Animal experiments

Dietary L-Tryptophan Modulates the Structural and Functional Composition of the Intestinal Microbiome in Weaned Piglets – Haiwei Liang – Frontiers in Microbiology

Animal microbiome

Seasonality of the gut microbiota of free-ranging white-faced capuchins in a tropical dry forest – Joseph D Orkin – The ISME Journal

The microbiota in the intestinal and respiratory tracts of naked mole-rats revealed by high-throughput sequencing – Wei Cong – BMC Microbiology

Differential effects of selective and non-selective cyclooxygenase inhibitors on fecal microbiota in adult horses – Canaan M Whitfield-Cargile – PLOS ONE

Plant, root, and soil microbiome

Soil microbiomes with distinct assemblies through vertical soil profiles drive the cycling of multiple nutrients in reforested ecosystems – Shuo Jiao – Microbiome

Fungal Communities Along a Small-Scale Elevational Gradient in an Alpine Tundra Are Determined by Soil Carbon Nitrogen Ratios – Yingying Ni – Frontiers in Microbiology

Water and extremophile microbiome

The biology of fog: results from coastal Maine and Namib Desert reveal common drivers of fog microbial composition – Sarah E Evans – Science of the Total Environment

Growth promotion and inhibition induced by interactions of groundwater bacteria – Patricia Geesink – FEMS Microbiology Ecology

Microbial diversity along a gradient in peatlands treating mining-affected waters – Katharina Kujala – FEMS Microbiology Ecology

Food microbiology

Volatile Flavor Components, Microbiota and Their Correlations in Different Sufu, a Chinese Fermented Soybean Food – Chunzhi Xiv – Journal of Applied Microbiology

Biogenic amines analysis and microbial contribution in traditional fermented food of Douchi – Lu Li – Scientific Reports

Changes in the microbial communities in vacuum-packaged smoked bacon during storage – Xinfu Li – Food Microbiology

Phages and viruses

MARVEL, a Tool for Prediction of Bacteriophage Sequences in Metagenomic Bins – Deyvid Amgarten – Frontiers in Genetics

Techniques

Comparative evaluation of a new magnetic bead-based DNA extraction method from fecal samples for downstream next-generation 16S rRNA gene sequencing – Kara D McGaughey – PLOS ONE

August 22, 2018

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Today’s digest is a mix of exciting reviews and research articles. The research articles are about – association between (site-specific) microbiota changes and stunded chilhood growth, bronchopulmonary dysplasia and Ankylosing Spondylitis; new tools to analyze mother-infant phage transmission; and low cost platform to analyze gut microbiota and host biomarkers. Also includes statement from FDA on regulation of live microbiome-based products, and comparison of single versus multiple strain probiotics in intestinal dysbiosis.

General microbiome

Review: Microbiology of the built environment – Jack A Gilbert – Nature Reviews Microbiology

Considerations for Best Practices in Studies of Fiber or Other Dietary Components and the Intestinal Microbiome – David M Klurfeld – American Journal of Physiology Endocrinology and Metabolism

Review: Impact of the commensal microbiota in atherosclerosis and arterial thrombosis – Klytaimnistra Kiouptsi – British Journal of Pharmacology

Pregnancy and early life

Metagenomic analysis with strain-level resolution reveals fine-scale variation in the human pregnancy microbiome – Daniela SA Goltsman – bioRxiv

Human respiratory microbiome

Early Airway Microbial Metagenomic and Metabolomic Signatures are Associated with Development of Severe Bronchopulmonary Dysplasia – Charitharth V Lal – American Journal of Physiology

Human gut microbiome

Stunted childhood growth is associated with decompartmentalization of the gastrointestinal tract and overgrowth of oropharyngeal taxa – Pascale Vonaesch – PNAS

Tracing mother-infant transmission of bacteriophages by means of a novel analytical tool for shotgun metagenomic datasets: METAnnotatorX – Christian Milani – Microbiome

Altered Bacteria-Fungi Inter-Kingdom Network in Gut of Ankylosing Spondylitis Patients – Ming Li – bioRxiv

Animal experiments

Hyperactivated PI3Kd promotes self and commensal reactivity at the expense of optimal humoral immunity – Silvia Preite – Nature Immunology

The Potential Role of the Dipeptidyl Peptidase-4-Like Activity From the Gut Microbiota on the Host Health – Marta Olivares – Frontiers in Microbiology

Plant, root, and soil microbiome

Effects of compost containing oxytetracycline on enzyme activities and microbial communities in maize rhizosphere soil – Lisha Zhen – Environmental Science and Pollution Research

Impact of soil salinity on the microbial structure of halophyte rhizosphere microbiome – Salma Mukhtar – World Journal of Microbiology and Biotechnology

Water and extremophile microbiome

Inter-Kingdom beach warfare: Microbial chemical communication activates natural chemical defences – Zeinab G Khalil – The ISME Journal

Biogeography and taxonomic overview of terrestrial hot spring thermophilic phages – Olivier Zablocki – Extremophiles

Food microbiology

How Fine Structural Differences of Xylooligosaccharides and Arabinoxylooligosaccharides Regulate Differential Growth of Bacteroides Species – Mihiri Mendis – Journal of Agricultural and Food Chemistry

Probiotics / prebiotics

Influence of monostrain and multistrain probiotics on immunity, intestinal ultrastructure and microbiota in experimental dysbiosis – E Ermolenko – Beneficial Microbes

Effect of probiotic Bifidobacterium bifidum G9-1 on the relationship between gut microbiota profile and stress sensitivity in maternally separated rats – Hirokazu Fukui – Scientific Reports

Techniques

A low-cost paper-based synthetic biology platform for analyzing gut microbiota and host biomarkers – Melissa K Takahashi – Nature Communications

Microbes in the news

Statement from FDA Commissioner Scott Gottlieb, M.D., on advancing the science and regulation of live microbiome-based products used to prevent, treat, or cure diseases in humans – Food and Drug Administration

Non-microbiology picks

Mechanisms regulating intestinal barrier integrity and its pathological implications – Chaithanya Chelakkot – Experimental and Molecular Medicine

 

August 20, 2018

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Happy Monday! Today’s Microbiome Digest is chock-full. You’ll find: a review of approaches towards predictive microbial ecology, insights into function gleaned from rumen metatranscriptomics, diet studies in hunter-gatherers and mice, characterization of the mosquito and termite microbiota, the wild side of plant microbiomes, fermentation for traditional liquors, and much more!

General microbiome
Systems biology approaches towards predictive microbial ecology – Anne E. Otwell – Environmental Microbiology

One Health Relationships Between Human, Animal, and Environmental Microbiomes: A Mini-Review – Pauline Trinh – Frontiers in Public Health

Tuning of human MAIT cell activation by commensal bacteria species and MR1-dependent T-cell presentation – Cihan Tastan – Mucosal Immunology

Holistic Assessment of Rumen Microbiome Dynamics through Quantitative Metatranscriptomics Reveals Multifunctional Redundancy during Key Steps of Anaerobic Feed Degradation – Andrea Söllinger – mSystems

Multi-site human microbiome
A prospective study to examine the association of the urinary and fecal microbiota with prostate cancer diagnosis after transrectal biopsy of the prostate using 16sRNA gene analysis – Shaheen Alanee – Prostate

Streptococcus and Prevotella are associated with the prognosis of oesophageal squamous cell carcinoma – Yanfang Liu – Journal of Medical Microbiology

Urinary symptoms are associated with certain urinary microbes in urogynecologic surgical patients – Cynthia S. Fok – International Urogynecology Journal

Human gut microbiome
Links between environment, diet, and the hunter-gatherer microbiome – Gabriela K. Fragiadakis – Gut Microbes

Klebsiella oxytoca expands in cancer cachexia and acts as a gut pathobiont contributing to intestinal dysfunction – Sarah A. Pötgens – Scientific Reports

Co-Administration of Probiotics with Prescribed Antibiotics for Preventing Clostridium difficile Diarrhea – Ahmed S. I. Hamed – Academic Emergency Medicine

Animal experiments
Effect of industrial trans-fatty acids-enriched diet on gut microbiota of C57BL/6 mice – Yueting Ge – European Journal of Nutrition

AIEC infection triggers modification of gut microbiota composition in genetically predisposed mice, contributing to intestinal inflammation – Alexis Bretin – Scientific Reports

Effect of probiotic Bifidobacterium bifidum G9-1 on the relationship between gut microbiota profile and stress sensitivity in maternally separated rats – Hirokazu Fukui – Scientific Reports

Animal microbiome
Comparison of microbiomes of cold-water corals Primnoa pacifica and Primnoa resedaeformis, with possible link between microbiome composition and host genotype – Dawn B. Goldsmith – Scientific Reports

Neonatal gut and immune maturation is determined more by postnatal age than by post-conceptional age in moderately preterm pigs – Shuqiang Ren – American Journal of Physiology-Gastrointestinal and Liver Physiology

Functional metagenomics reveals abundant polysaccharide-degrading gene clusters and cellobiose utilization pathways within gut microbiota of a wood-feeding higher termite –  Ning Liu – ISME Journal

Mosquito microbiota cluster by host sampling location – Ephantus J. Muturi – Parasites and Vectors

Plant, root, and soil microbiome|
The wild side of plant microbiomes – Juan E. Pérez-Jaramillo – Microbiome

Unraveling the Composition of the Root-Associated Bacterial Microbiota of Phragmites australis and Typha latifolia – Laura Pietrangelo – Frontiers in Microbiology

Vermicompost addition influences symbiotic fungi communities associated with leek cultivated in metal-rich soils – Antoine Pierart – Environmental Science and Pollution Research

Plant drought resistance is mediated by soil microbial community structure and soil-plant feedbacks in a savanna tree species – Nianxun Xi – Environmental and Experimental Botany

Metabolic specialization of denitrifiers in permeable sediments controls N2 O emissions – Hannah K. Marchant – Environmental Microbiology

Bacterial Biomarkers of Marcellus Shale Activity in Pennsylvania – Jeremy R. Chen See – Frontiers in Microbiology

Eighteen-Year Farming Management Moderately Shapes the Soil Microbial Community Structure but Promotes Habitat-Specific Taxa – Huaihai Chen – Frontiers in Microbiology

Water and extremophile microbiome
Bacterial and archaeal profiling of hypersaline microbial mats and endoevaporites, under natural conditions and methanogenic microcosm experiments – José Q. García-Maldonado – Extremophiles

Subsurface landfill leachate contamination affects microbial metabolic potential and their expression in the Banisveld aquifer – Neslihan Taş – FEMS Microbiology Ecology

Food microbiology
Robust Domination of Lactobacillus sakei in Microbiota During Traditional Japanese Sake Starter Yamahai-Moto Fermentation and the Accompanying Changes in Metabolites – Atsushi Tsuji – Current Microbiology

DaQu fermentation selects for heat resistant Enterobacteriaceae and bacilli – Zhiying Wang – Applied and Environmental Microbiology

Exploitation of autochthonous Tuscan sourdough yeasts as potential starters – Michela Palla – International Journal of Food Microbiology

Techniques
Conventional culture methods with commercially available media unveil the presence of novel culturable bacteria – Tamaki Ito – Gut Microbes

August 19, 2018

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Featured today: culturing novel bacteria, microbiota of cystic fibrosis, marker in urine for determining gut microbial diversity, stress determinant of soil microbial communities, fescue enhances the PAH degradation by rhizospheric microbes, phages from healthy skin metavirome.

General microbiome

Dietary specialization in mutualistic acacia‐ants affects relative abundance but not identity of host‐associated bacteria – BER Rubin – Journal Molecular Ecology

Conventional culture methods with commercially available media unveil the presence of novel culturable bacteria – T Ito – Gut Microbes

Multi-site human microbiome

The urinary microbiome associated with bladder cancer – V Bučević Popović – Scientific Reports

Human respiratory microbiome

Review: Cystic fibrosis respiratory microbiota: unraveling complexity to inform clinical practice – LJ Caverly – Expert Review of Respiratory Medicine

Human vaginal microbiome

Vulvovestibular Syndrome and Vaginal Microbiome: A Simple Evaluation – M Vadala – Journal of Clinical Medicine Research

Human gut microbiome

Gut microbiota composition explains more variance in the host cardiometabolic risk than genetic ancestry – SJ Guzman-Castaneda – bioRxiv

Assessment of urinary 3-indoxyl sulfate as a marker for gut microbiota diversity and abundance of Clostridiales – F Farowski – Gut Microbes

Periodontal Therapy Favorably Modulates the Oral-Gut-Hepatic Axis in Cirrhosis – JS Bajaj – American Journal of Physiology-Gastrointestinal and Liver Physiology

Animal experiments

Neonatal gut and immune maturation is determined more by postnatal age than by post-conceptional age in moderately preterm pigs – S Rens – American Journal of Physiology-Gastrointestinal and Liver Physiology

Effects of Astragalus membranaceus fiber on growth performance, nutrient digestibility, microbial composition, VFA production, gut pH, and immunity of weaned pigs – D Che – Microbiology Open

Plant, root, and soil microbiome

Soil microbial communities alter conspecific and congeneric competition consistent with patterns of field coexistence in three Trifolium congeners – A Siefert – Journal of Ecology

Initial state of soil microbial communities determines their stress response – W Riah-Anglet – Journal of Environmental Chemical Engineering

Natural grassland as the optimal pattern of vegetation restoration in arid and semi-arid regions: Evidence from nutrient limitation of soil microbes – Y Cui – Science of The Total Environment

Characteristics of microbial community indicate anthropogenic impact on the sediments along the Yangtze Estuary and its coastal area, China – X-p Guo – Science of The Total Environment

Soil bacterial communities exhibit systematic spatial variation with landform across a commercial potato field – S Neupane – Geoderma

Plant host habitat and root exudates shape fungal diversity – M Hugoni – Mycorrhiza

Enhanced polycyclic aromatic hydrocarbons degradation in rhizosphere soil planted with tall fescue: Bacterial community and functional gene expression mechanisms – M Guo – Chemosphere

Microbial community of nitrogen cycle‐related genes in aquatic plant rhizospheres of Lake Liangzi in winter – X Yin – Journal of Basic Microbiology

Water and extremophile microbiome 

Surviving in hot and cold: psychrophiles and thermophiles from Deception Island volcano, Antarctica – AG. Bendia – Extremophiles

Probiotics / prebiotics

Probiotics and Evidence-based Medicine: To All Involved – M Koch – Journal of Clinical Gastroenterology

Co‐Administration of Probiotics with Prescribed Antibiotics for Preventing Clostridium difficile Diarrhea – SI Ahmed – Academic Emergency Medicine

Phages and viruses

Novel phages of healthy skin metaviromes from South Africa – LJ van Zyl – Scientific Reports

 

August 15, 2018

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A nice crop of plant/root/soil microbiome studies, some interesting analyses of early life/pregnancy and vaginal microbiota, a belly-load of gut microbiome science, a herd of animal studies, and a few really bad puns… Enjoy!

Events and jobs

A summary of the third annual HIV microbiome workshop – Dr. Brett Williams – AIDS Research and Human Retroviruses

Pregnancy and early life

Early childhood antibiotics use and autism spectrum disorders: a population-based cohort study – Amani F Hamad – International Journal of Epidemiology

The effects of gut microbiota on metabolic outcomes in pregnant women and their offspring – You Lv – Food & Function

Human vaginal microbiome

Cervicovaginal microbiota, women’s health, and reproductive outcomes – Samuel J. Kroon – Fertility and Sterility

Relevance of assessing the uterine microbiota in infertility – Inmaculada Moreno – Fertility and Sterility

Cervicovaginal microbiota, women’s health, and reproductive outcomes – Samuel J. Kroon – Fertility and Sterility

Human nearly-sterile sites

Ursodeoxycholic acid improves liver function via phenylalanine/tyrosine pathway and microbiome remodelling in patients with liver dysfunction – Da Jung Kim – Scientific Reports

Human gut microbiome

Assessing antibiotic resistance gene load in vegan, vegetarian and omnivore human gut microbiota – Losasso Carmen – International Journal of Antimicrobial Agents

Immunomodulatory tetracyclines ameliorate DNBS-colitis: Impact on microRNA expression and microbiota composition – J. Garrido-Mesa – Biochemical Pharmacology

Effects of anthocyanins from the fruit of Lycium ruthenicum Murray on intestinal microbiota – Yamei Yan – Journal of Functional Foods

Disparate Effects of Antibiotics on Hypertension – Sarah Galla – Physiological Genomics

Variability of core microbiota in newly diagnosed treatment-naïve paediatric inflammatory bowel disease patients – T. G. J. de Meij – PLOS One

Dietary soybean protein ameliorates high-fat diet-induced obesity by modifying the gut microbiota-dependent biotransformation of bile acids – Keita Watanabe – PLOS One

* Gut microbiota alterations in moderate to severe acne vulgaris patients – Hui‐Min Yan – The Journal of Dermatology

Implication of gut microbiota metabolites in cardiovascular and metabolic diseases – Francois Brial – Cellular and Molecular Life Sciences

Making Sense of… the Microbiome in Psychiatry – Thomaz F S Bastiaanssen – International Journal of Neuropsychopharmacology

The Microbiome in Cirrhosis and its Complications – Chathur Acharya – Clinical Gastroenterology and Hepatology

Lactobacillus rhamnosus GG induced protective effect on allergic airway inflammation is associated with gut microbiota – Juan Zhang – Cellular Immunology

The gut microbiome as a driver of individual variation in cognition and functional behaviour – Gabrielle L. Davidson – Philosophical Transactions of the Royal Society B

Animal experiments

The impact of Clostridium butyricum MIYAIRI 588 on the murine gut microbiome and colonic tissue – Mao Hagihara – Anaerobe

Monitoring and evaluation of the interaction between deoxynivalenol and gut microbiota in Wistar rats by mass spectrometry-based metabolomics and next-generation sequencing – Eugènia Miró-Abella – Food and Chemical Toxicology

Lentil (Lens culinaris Medikus) Diet Affects the Gut Microbiome and Obesity Markers in Rat – Niroshan Siva – Journal of Agricultural and Food Chemistry

Gut bacterial composition in a mouse model of Parkinson’s disease – P. Perez-Pardo – Beneficial Microbes

Gut Microbiome in BALB/c and C57BL/6J Mice Undergoing Experimental Thyroid Autoimmunity Associate with Differences in Immunological Responses and Thyroid Function – Sajad Moshkelgosha – Hormone and Metabolic Research

Ultraviolet Irradiation of Skin Alters the Faecal Microbiome Independently of Vitamin D in Mice – Simon Ghaly – Nutrients

Impact of lincosamides antibiotics on the composition of the rat gut microbiota and the metabolite profile of plasma and feces – C. Behr – Toxicology Letters

Animal microbiome

Understanding bacterial communities for informed biosecurity and improved larval survival in Pacific oysters – Olivier Laroche – Aquaculture

A meta-analysis reveals the environmental and host factors shaping the structure and function of the shrimp microbiota – Fernanda Cornejo-Granados​ – PeerJ

Do the microorganisms from laboratory culture spent growth medium affect house dust mite fitness and microbiome composition? – Vit Molva – Insect Science

Plant, root, and soil microbiome

Microbial diversity associated to the intestinal tract of soil invertebrates – Dayana da Silva Correia – Applied Soil Ecology

Yellow Canopy Syndrome in sugarcane is associated with shifts in the rhizosphere soil metagenome but not with overall soil microbial function – Kelly Hamonts – Soil Biology and Biochemistry

Anthropogenic influence shapes the distribution of antibiotic resistant bacteria (ARB) in the sediment of Sundarban estuary in India – Anish Bhattacharyya – Science of the Total Environment

Disentangling effects of temperature on microbial community and copper extraction in column bioleaching of low grade copper sulfide – Yuguang Wang – Bioresource Technology

Long-term Plastic Greenhouse Cultivation Changes Soil Microbial Community Structures: A Case Study – Yang Song – Journal of Agricultural and Food Chemistry

Flooding and prolonged drought have differential legacy impacts on soil nitrogen cycling, microbial communities and plant productivity – Linh T. T. Nguyen – Plant and Soil

[PhD Dissertation] Microbial Communities and Their Impact on Bioenergy Crops in Dynamic Environments – Brandon Monier, South Dakota State University – Open Prairie

[PDF] Characterization of osmotolerant rhizobacteria for plant growth promoting
activities in vitro and during plant-microbe association under osmotic stress – Bandeppa – Indian Journal of Experimental Biology

Isolation and Analysis of Microbial Communities in Soil, Rhizosphere, and Roots in Perennial Grass Experiments – Morgan R. McPherson – J. Vis. Exp

Water and extremophile microbiome 

[PDF download] Monitoring biofilm communities in operational drinking water distribution systems and the impact on water quality – I. Douterelo – 1st International WDSA

Molecular detection of microbial communities associated with Microcystis vs Synechococcus dominated waters in Tianjin, China – Da Huo – Journal of Oceanology and Limnology

Metagenomic assessment of the microbial community and methanogenic pathways in biosolids from a municipal wastewater treatment plant in Medellín, Colombia – Katherine Bedoya – Science of the Total Environment

Profiling microbial communities in a watershed undergoing intensive anthropogenic activities – Hehuan Liao – Science of the Total Environment

The gut microbiome and aquatic toxicology: An emerging concept for environmental health – Ondrej Adamovsky – PeerJ

Microbial community composition of a hydrocarbon reservoir 40 years after a CO2 enhanced oil recovery flood – Jenna L K Shelton – FEMS Microbiology Ecology

Temporal dynamics of activated sludge bacterial communities in two diversity variant full-scale sewage treatment plants – Xiao-Tao Jiang – Applied Microbiology and Biotechnology

The Nile River Microbiome Reveals a Remarkably Stable Community Between Wet and Dry Seasons, and Sampling Sites, in a Large Urban Metropolis (Cairo, Egypt) – Eraqi WA – OMICS

Probiotics / prebiotics

Influence of monostrain and multistrain probiotics on immunity, intestinal ultrastructure and microbiota in experimental dysbiosis – E. Ermolenko – Beneficial Microbes

Effects of Probiotics on Inflammation and Uremic Toxins Among Patients on Dialysis: A Systematic Review and Meta-Analysis – Charat Thongprayoon – Digestive Diseases and Sciences

Bioinformatics

Biomarker panels for characterizing microbial community biofilm formation as composite molecular process – Magnus Bosse – PLOS One

* Maximal viral information recovery from sequence data using VirMAP – Nadim J Ajami – Nature Communications

Techniques

Using Bioreactors to Study the Effects of Drugs on the Human Microbiota – Mabel Guzman-Rodriguez – Methods

Ed’s non-microbiology picks

Human activities might influence oncogenic processes in wild animal populations – Mathieu Giraudeau – Nature Ecology & Evolution

In apoptosis, cell death spreads through perpetuating waves – James Ferrell – Stanford Medicine

Study finds Tdap vaccination for pregnant women does not increase risk of autism

Boys should be given HPV vaccine, says joint committee

New Study: Omega-3s Can Help Keep Kids Out of Trouble

Mars (probably) has a lake of liquid water

August 13, 2018

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Today’s Digest is full of amazing research from focusing on causation in microbiome studies to increased efficacy of BLAST searches in the age of high throughput sequencing.

General Microbiome

Microbiome: Focus on Causation and Mechanism.Fischbach MA. Cell.

Effect of Antibiotic-Mediated Microbiome Modulation on Rotavirus Vaccine Immunogenicity: A Human, Randomized-Control Proof-of-Concept Trial.Harris VC. Cell Host and Microbe

Enhancing Rotavirus Vaccination: A Microbial Fix? Parker EPK. Cell Host and Microbe

Snapshot of an early Paleoproterozoic ecosystem: Two diverse microfossil communities from the Turee Creek Group, Western Australia. Barlow EV. Geobiology.

Background levels of microorganisms in the busy urban environment of transport hubs.Patel KV. Journal of Applied Microbiology.

Immunomodulation as Therapy for Fungal Infection: Are We Closer?Sam QH. Frontiers in Microbiology

Profiling of Bacterial and Fungal Microbial Communities in Cystic Fibrosis Sputum Using RNA.Grahl N. mSphere.

Oral Microbiome

Comparison of oral microbiota in orthodontic patients and healthy individuals.Sun F. Microbial Pathogenesis

Skin Microbiome

Mud therapy and skin microbiome: a review.Antonelli M. International Journal of Biometeorology

Gut Microbiome

Phylogeny-corrected identification of microbial gene families relevant to human gut colonization.Bradley PH. PLoS Computational Biology

Dynamic changes in human-gut microbiome in relation to a placebo-controlled anthelminthic trial in Indonesia.Martin I. PLoS Neglected Tropical Disease.

Faecal Microbiome

Effects of metal and metalloid pollutants on the microbiota composition of feces obtained from twelve commercial pig farms across China.Peng Z. Science Total Environment

Fecal Microbiota Alterations Associated With Diarrhea-Predominant Irritable Bowel Syndrome.Zhuang X. Frontiers in Microbiology.

Plant, Soils, and Air Microbiome

Environmental variables better explain changes in potential nitrification and denitrification activities than microbial properties in fertilized forest soils.Tang Y. Science of Total Environment

Metagenomic analysis of rhizosphere microflora of oil-contaminated soil planted with barley and alfalfa. Kumar V. PLoS One.

Trichoderma polysporum selectively inhibits white-nose syndrome fungal pathogen Pseudogymnoascus destructans amidst soil microbes.Singh A. Microbiome.

Tissue Microbiome of Norway Spruce Affected by Heterobasidion-Induced Wood Decay.Ren F. Microbial Ecology

Evidence for complete nitrification in enrichment culture of tidal sediments and diversity analysis of clade a comammox Nitrospira in natural environments. Yu C. Applied Microbiology and Biotechnology.

Traits-Based Integration of Multi-Species Inoculants Facilitates Shifts of Indigenous Soil Bacterial Community.Wang J. Frontier in Microbiology

Spatial Patterns and Drivers of Microbial Taxa in a Karst Broadleaf Forest.Song M. Frontiers in Microbiology

Water Microbiome

Response of Microbial Communities to Changing Climate Conditions During Summer Cyanobacterial Blooms in the Baltic Sea.Berner C. Frontiers in Microbiology

Coral Microbiome Database: Integration of sequences reveals high diversity and relatedness of coral-associated microbes.Huggett MJ. Environmental Microbiology Reports

Animal Experiments and Microbiome

Diet and other environmental factors shape the bacterial communities of fish gut in an eutrophic lake. Kashinskaya EN. Journal of Applied Microbiology

Yeast-like microorganisms in the scale insect Kermes quercus (Insecta, Hemiptera, Coccomorpha: Kermesidae). Newly acquired symbionts?Podsiadło E. Arthropod Structure and Development

Initial description of the core ocular surface microbiome in dogs: Bacterial community diversity and composition in a defined canine population.Leis ML. Veterinary Ophthalmology

High-Throughput Analysis Reveals Seasonal Variation of the Gut Microbiota Composition Within Forest Musk Deer (<i>Moschus berezovskii</i>).Hu X. Frontiers in Microbiology

A Comprehensive Research on Antibiotic Resistance Genes in Microbiota of Aquatic Animals.Hong B. Frontiers in Microbiology

Identification of spider-mite species and their endosymbionts using multiplex PCR.Zélé F. Experimental and Applied Acarology

Soil microarthropods alter the outcome of plant-soil feedback experiments.Kuťáková E. Scientific Reports

Techniques/Bioinformatics 

Metagenome complexity and template length are the main causes of bias in PCR-based bacteria community analysis.Peng W. Journal of Basic Microbiology

Single-cell RNA sequencing technologies and bioinformatics pipelines.Hwang B. Experimental and Molecular Medicine

Negative Binomial Mixed Models for Analyzing Longitudinal Microbiome Data.Zhang X. Frontiers in Microbiology

Stationary and portable sequencing-based approaches for tracing wastewater contamination in urban stormwater systems. Hu Y. Scientific Reports

CrocoBLAST: Running BLAST efficiently in the age of next-generation sequencing.Tristão Ramos RJ. Bioinformatics

August 10, 2018

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This Friday enjoy reading about the global topsoil microbiome, human pharyngeal microbiota profiles and microbial biomarkers associated with chronic kidney disease. There’s an interesting podcast [Mapping microbes on the metro]! Happy weekend!

Human gut microbiome

Neonatal selection by Toll-like receptor 5 influences long-term gut microbiota composition – Marcus Fulde – Nature

*Altered gut microbiota and microbial biomarkers associated with chronic kidney disease – Hengzhong Lun – Microbiologyopen.

Review: Rebuilding the Gut Microbiota Ecosystem – Antonella Gagliardi – Int. J. Environ. Res. Public Health

Human respiratory microbiome

*Human pharyngeal microbiota in age-related macular degeneration – Eliza Xin Pei Ho – PLoS One

Plant, root and soil microbiome

*Structure and function of the global topsoil microbiome – Mohammad Bahra – Nature

Mini review: Root colonization: imperative mechanism for efficient plant protection and growth – Swati Sachdev and Rana Pratap Singh – MOJ Ecology & Environmental Sciences

Review: From Microscopy to Genomic Approach in Soil Biodiversity Assessment – Lucia Popescu and Zhi-Ping Cao – Curr. Issues Mol. Biol.

Review: You Are What You Can Find to Eat: Bacterial Metabolism in the Rhizosphere – Nicola Holden – Curr. Issues Mol. Biol.

Podcast

*Gut bacteria vs the immune system; Mapping microbes on the metro – Adam Levy and Benjamin Thompson – Nature Podcast

Microbes in the news

Checkpoint for gut microbes after birth – Andrew J. Macpherson and Stephanie C. Ganal-Vonarburg – Nature News and Views

August 7, 2018

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Today’s Digest features a lot of soil and plant microbiome articles. Highlights include an opinion piece on hypothesis-driven microbiome research, a study on the spread of MCR-3 colistin resistance in China, and a consortium of bacteria to protect plants from pathogents.

General microbiology

** Are microbiome studies ready for hypothesis-driven research? – Anupriya Tripathi et al. – Current Opinion in Microbiology

Mitracarpus frigidus: A promising antifungal in the treatment of vulvovaginal candidiasis – Lara M. Campos et al. – Industrial Crops and Products

Isolation, growth, enzyme assay and identification via 16S rRNA full sequencing of cellulolytic microbes from Nepal for biofuel production – Binayak Raj Pandey et al. – Renewable Energy

Review (Uncorrected Proof): From hairballs to hypotheses – biological insights from microbial networks – Lisa Röttjers & Karoline Faust – FEMS Microbiology Reviews

Review: Barriers and opportunities in bio-based production of hydrocarbons – Yongjin J. Zhou, Eduard J. Kerkhoven & Jens Nielsen – Nature Energy

Antibiotic resistance

** Spread of MCR-3 Colistin Resistance in China: An Epidemiological, Genomic and Mechanistic Study – Yongchang Xu et al. – EBioMedicine

Long-term organic fertilization increased antibiotic resistome in phyllosphere of maize – Qing-Lin Chen et al. – Science of The Total Environment

Carbapenem resistance in bacteria isolated from soil and water environments in Algeria – Katia DJENADI et al. – Journal of Global Antimicrobial Resistance

Human respiratory microbiome

Prospective study of timing and pattern of bacteria and viruses in the nasopharyngeal microbiome in a birth cohort – J.L.Mathew et al. – International Journal of Infectious Diseases

Human gut microbiome

Population changes of colon lumen microbiota in patients with chronic hepatitis C – A. Sydorchuk et al. – International Journal of Infectious Diseases

Multi-site human microbiome

Metagenomics of pigmented and cholesterol gallstones: the putative role of bacteria – S. H. Kose et al. – Scientific Reports

Food microbiology

Amplicon and shotgun metagenomic sequencing indicates that microbial ecosystems present in cheese brines reflect environmental inoculation during the cheese production process – Louise Vermote et al. – International Dairy Journal

Exploring core functional microbiota responsible for the production of volatile flavour during the traditional brewing of Wuyi Hong Qu glutinous rice wine – Zi-Rui Huang et al. – Food Microbiology

Review: Spoilage yeasts: What are the sources of contamination of foods and beverages? – A. Hernández et al. – International Journal of Food Microbiology

Animal experiments

Consumption of virgin coconut oil in Wistar rats increases saturated fatty acids in the liver and adipose tissue, as well as adipose tissue inflammation – Marianade Moura e Dias et al. – Journal of Functional Foods

Experimental microbial dysbiosis does not promote disease progression in SIV-infected macaques – Alexandra M. Ortiz et al. – Nature Medicine

Animal microbiome

Whole genome sequences to assess the link between antibiotic and metal resistance in three coastal marine bacteria isolated from the mummichog gastrointestinal tract – Nicole A. Lloyd, Sylvie Nazaret & TamarBarkay – Marine Pollution Bulletin

Inferences of gut bacterial diversity from next-generation sequencing of 16S rDNA in deep sea blind ray – Benthobatis moresbyi – Tina Kollannoor Johny et al. – Ecological Genetics and Genomics

Characterization of the fecal microbiota of healthy horses – Holly L. Stewart et al. – American Journal of Veterinary Research

Plant, root and soil microbiome

Comparative mangrove metagenome reveals global prevalence of heavy metals and antibiotic resistome across different ecosystems – Madangchanok Imchen et al. – Scientific Reports

Structural development and assembly patterns of the root-associated microbiomes during phytoremediation – Yanmei Chen et al. – Science of The Total Environment

A Method for Collecting Atmospheric Microbial Samples From Set Altitudes for Use With Next-Generation Sequencing Techniques to Characterize Communities – Allison M Spring et al. – Air, Soil and Water Research

Plant-microbe interactions drive denitrification rates, dissolved nitrogen removal, and the abundance of denitrification genes in stormwater control measures – Natalie R Morse et al. – Environmental Science & Technology

Short- and long-term warming alters soil microbial community and relates to soil traits – Hongying Yu et al. – Applied Soil Ecology

Environmental variables better explain changes in potential nitrification and denitrification activities than microbial properties in fertilized forest soils – Yuqian Tang et al. – Science of The Total Environment

Wheat rhizosphere harbors a less complex and more stable microbial co-occurrence pattern than bulk soil – Kunkun Fan et al. – Soil Biology and Biochemistry

Influence of biochars on the accessibility of organochlorine pesticides and microbial community in contaminated soils – Neelum Ali et al. – Science of The Total Environment

Structure and activity of soil microbial communities in three Mediterranean forests – Felicia Grosso et al. – Applied Soil Ecology

Species-associated differences in the below-ground microbiomes of wild and domesticated Setaria – Srinivasa R. Chaluvadi & Jeff Bennetzen – Frontiers in Plant Science

Review: Processes that determine the interplay of root exudation, methane emission and yield in rice agriculture – D. Maurer et al. – Plant Biology

** Nutrient-and Dose-Dependent Microbiome-Mediated Protection against a Plant Pathogen – Maureen Berg & Britt Koskella – Current Biology

Network Analyses Can Advance Above-Belowground Ecology – Kelly S.Ramirez et al. – Trends in Plant Science

Minireview: Microbial anaerobic Fe(II) oxidation – ecology, mechanisms and environmental implications – C Bryce et al. – Environmental Microbiology

Phages and viruses

No detectable effect of Wolbachia wMel on the prevalence and abundance of the RNA virome of Drosophila melanogaster – Mang Shi et al. – Proceedings B

Co-Infection Patterns in Individual Ixodes scapularis Ticks Reveal Associations between Viral, Eukaryotic and Bacterial Microorganisms – Shaun T. Cross et al. – Viruses

Investigation of recombination-intense viral groups and their genes in the Earth’s virome – Jan P. Meier-Kolthoff et al. – Scientific Reports

Microbes in the news

Endophytes: Study Shows GMO Corn Has No Impact On Good Bacteria – Science 2.0

August 5, 2018

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Have a good sunday! Today, in Microbiome Digest: several reviews focused in clinical aspects of the microbiome, associations between malnutrition and dysbiosis, a study observing the effect of prebiotics on autism spectrum disorders, influence of the microbiome on mouse brain, the impact of storage and DNA extraction on microbiota analysis, and much more!

 

Human and General Microbiome

Review: The Interaction of the Gut Microbiota with the Mucus Barrier in Health and Disease in Human – Anthony P. Corfield – Microorganisms

Review: Next generation microbiology and cystic fibrosis diagnostics: are we there yet? – Claus Moser – Current Opinion in Pulmonary Medicine

Review: Proton Pump Inhibitors: Risks and Rewards and Emerging Consequences to the Gut Microbiome –  Amandeep Singh – Nutrition in Clinical Practice

Review: The Gut Microbiome in Patients with Intestinal Failure: Current Evidence and Implications for Clinical Practice – Esther Neelis – Journal of Parenteral and Enteral Nutrition

Review: The Esophageal Microbiome in Health and Disease – Brooke Corning – Current Gastroenterology Reports

Review: Microbiota issue in CKD: how promising are gut-targeted approaches? – Carmela Cosola – Journal of Nephrology

Review: Neuroimmunophysiology of the gut: advances and emerging concepts focusing on the epithelium – Keith A. Sharkey – Nature Reviews Gastroenterology & Hepatology

Commentary: The Perturbance of Microbiome and Gut-Brain Axis in Autism Spectrum Disorders – Greta Fowlie – International Journal of Molecular Sciences

Comment: Causality in dietary interventions-building a case for gut microbiota – Yan Y. Lam – Genome Medicine

Emergent simplicity in microbial community assembly – Joshua E. Goldford – Science

Contraception: Influence on Vaginal Microbiota and Identification of Vaginal Lactobacilli Using MALDI-TOF MS and 16S rDNA Sequencing – Sonia E. Fosch – The Open Microbiology Journal

Gut Microbiota Dysbiosis is Associated with Malnutrition and Reduced Plasma Amino Acid Levels: Lessons from Genome-Scale Metabolic Modeling – Manish Kumar – Metabolic Engineering

Photobiomodulation of the microbiome: implications for metabolic and inflammatory diseases – Brian Bicknell – Lasers in Medical Science

Roxithromycin regulates intestinal microbiota and alters colonic epithelial gene expression – Cheng Zhang – Applied Microbiology and Biotechnology

Whole Cell Cross-Linking to Discover Host-Microbe Protein Cognate Receptor/Ligand Pairs – Bart C. Weimer – Frontiers in Microbiology

 

Animal Microbiome

The gut microbiota drives the impact of bile acids and fat source in diet on mouse metabolism – Sarah Just – Microbiome

Changes in feeding habits promoted the differentiation of the composition and function of gut microbiotas between domestic dogs (Canis lupus familiaris) and gray wolves (Canis lupus) – Tianshu Lyu – AMB Express

The effect of dietary lipid on gut microbiota in a senescence-accelerated prone mouse model (SAMP8) – Kazushi Yamamoto – Biogerontology

Moderate Dietary Protein Restriction Optimized Gut Microbiota and Mucosal Barrier in Growing Pig Model – Xiyue Chen – Frontiers in Cellular and Infection Microbiology

Effects of Sub-Chronic MPTP Exposure on Behavioral and Cognitive Performance and the Microbiome of Wild-Type and mGlu8 Knockout Female and Male Mice – Eileen Ruth S. Torres – Frontiers in Behavioral Neuroscience

Microbiota influence the development of the brain and behaviors in C57BL/6J mice – Jing Lu – PLoS ONE

Intestinal Microbiota Lipid Metabolism Varies across Rainbow Trout (Oncorhynchus mykiss) Phylogeographic Divide – Christina C. Yildirimer – Journal of Applied Microbiology

Chronic refined low-fat diet consumption reduces cholecystokinin satiation in rats – Mathilde Guerville – European Journal of Nutrition

The dynamics of the piglet gut microbiome during the weaning transition in association with health and nutrition – Robin B. Guevarra – Journal of Animal Science and Biotechnology

 

Methodologies

Combined bacterial and fungal intestinal microbiota analyses: Impact of storage conditions and DNA extraction protocols – Cécile Angebault – PLoS ONE

 

Beneficial Microbes and Compounds

A prebiotic intervention study in children with autism spectrum disorders (ASDs) – Roberta Grimaldi – Microbiome

Chemical Compositions of Cold-pressed Broccoli, Carrot and Cucumber Seed Flours, and Their in Vitro Gut Microbiota Modulatory, Anti-inflammatory and Free Radical Scavenging Properties – Uyory Choe – Journal of Agricultural and Food Chemistry

 

Pathogen Research

Review: Nontuberculous Mycobacteria in Cystic Fibrosis – Brian S. Furukawa – Seminars in Respiratory and Critical Care Medicine

August 3, 2018

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Happy Friday! Today’s digest includes the axolotl microbiome, carbon processing in thawing permafrost, and esterases discovered in hot spring microbial mats. In addition, there’s a Nature career column discussing why it’s not a ‘failure’ to leave academia. Enjoy!

Multi-site human microbiome

Optimizing body fluid recognition from microbial taxonomic profiles – Eirik Nataas Hanssen – Forensic Science International

Human oral microbiome

Dysbiosis of the buccal mucosa microbiome in primary Sjögren’s syndrome patients – Taco A van der Meulen – Rheumatology

Human respiratory microbiome

Comparison of the upper and lower airway microbiota in children with chronic lung diseases – Bushra Ahmed – PLoS One

Human vaginal microbiome

Review: Case for a role of the microbiome in gynecologic cancers: Clinician’s perspective – Ismail Mert – Journal of Obstetrics and Gynecology Research

Human gut microbiome

Enhanced preservation of the human intestinal microbiota by ridinilazole, a novel Clostridium difficile-targeting antibacterial, compared to vancomycin – Cheleste M. Thorpe – PLoS One

Animal experiments

Euphorbia kansui fry-baked with vinegar modulates gut microbiota and reduces intestinal toxicity in rats – DongjingJiang – Journal of Ethnopharmacology

Animal microbiome

Experimentally induced metamorphosis in highly regenerative axolotl (ambystoma mexicanum) under constant diet restructures microbiota – Turan Demircan – Scientific Reports

Response of host–bacterial colonization in shrimp to developmental stage, environment and disease – Jinbo Xiong – Molecular Ecology

Wild Bee Pollen Usage and Microbial Communities Co-vary Across Landscapes – Quinn S. McFrederick – Microbial Ecology

Microbiomes of gall-inducing copepod crustaceans from the corals Stylophora pistillata (Scleractinia) and Gorgonia ventalina (Alcyonacea) – Pavel V. Shelyakin – Scientific Reports

Effect of dietary fat to starch content on fecal microbiota composition and activity in dogs – Sofia Schauf – Journal of Animal Science

Primer: The importance of being persistent: The first true resident gut symbiont in Drosophila – Dali Ma – PLoS Biology

Plant, root, and soil microbiome

Genome-centric view of carbon processing in thawing permafrost – Ben J. Woodcroft – Nature

Review: Uptake of bacteria into living plant cells, the unifying and distinct feature of the nitrogen-fixing root nodule symbiosis – Martin Parniske – Current Opinion in Plant Biology

Pre-print: Unlocking a high bacterial diversity in the coralloid root microbiome from the cycad genus Dioon – Pablo de Jesus Suarez-Moo – bioRxiv

Water and extremophile microbiome

Discovery of a diverse set of esterases from hot spring microbial mat and sea sediment metagenomes – RaviRanjan – International Journal of Biological Macromolecules

Built environment

Microbial communities and functional genes of nitrogen cycling in an electrolysis augmented constructed wetland treating wastewater treatment plant effluent – Pengfei Zhang – Chemosphere

Science, publishing, and career

Why it is not a ‘failure’ to leave academia – Philipp Kruger – Nature