Category Archives: Metagenomics & Bioinformatics

August 30, 2018

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Today’s digest covers population based studies on regional specificity of the gut microbiome, guidelines on use of fecal microbiota transplant, and review articles on role of the gut microbiome in colorectal cancer, liver tumors and functional gastrointestinal disorders. Also includes articles on how xenobiotics and psychotropic drugs affect the gut microbiota, and link to wonderful bacterial art!

General microbiome

Regional variation limits applications of healthy gut microbiome reference ranges and disease models – Yan He – Nature Medicine

Depicting the composition of gut microbiota in a population with varied ethnic origins but shared geography – Melanie Deschasaux – Nature Medicine

The use of faecal microbiota transplant as treatment for recurrent or refractory Clostridium difficile infection and other potential indications: joint British Society of Gastroenterology (BSG) and Healthcare Infection Society (HIS) guidelines – Benjamin H Mullish – Gut

Bile Acids, the Microbiome, Immunity, and Liver Tumors – Christoph Schramm – The New England Journal of Medicine

Review: The gut microbiome and colorectal cancer: a review of bacterial pathogenesis – Jessica D. Dahmus – Journal of Gastrointestinal Oncology

Human gut microbiome

Review: The Gut Microbiome in Adult and Pediatric Functional Gastrointestinal Disorders – Andrea Shin – Clinical Gastroenterology and Hepatology

Changes in microbiota composition, bile and fatty acid metabolism, in successful faecal microbiota transplantation for Clostridioides difficile infection – Jillian RM Brown – BMC Gastroenterology

“Cocktail” of Xenobiotics at Human Relevant Levels Reshapes the Gut Bacterial Metabolome in a Species-Specific Manner – Yingdan Zhang – Environmental Science and Technology

Animal experiments

Microbial Sensing by Intestinal Myeloid Cells Controls Carcinogenesis and Epithelial Differentiation – Naoteru Miyata – Cell Reports

Transplacental immune modulation with a bacterial-derived agent protects against allergic airway inflammation – Kyle T Mincham – Journal of Clinical Investigation

Differential effects of psychotropic drugs on microbiome composition and gastrointestinal function – Sofia Cussotto – Pschycopharmocology

Butyrate and Dietary Soluble Fiber Improve Neuroinflammation Associated With Aging in Mice – Stephanie M Matt – Frontiers in Immunonology

Correlations between intestinal innate immune genes and cecal microbiota highlight potential for probiotic development for immune modulation in poultry – Nicky-Lee Willson – Applied Microbiology and Biotechnology

Plant, root, and soil microbiome

Convergence between the microcosms of Southeast Asian and North American pitcher plants – Leonora S Bittleston – Elife

Water and extremophile microbiome 

In situ development of a methanotrophic microbiome in deep-sea sediments – S E Ruff – ISME Journal

Probiotics/Prebiotics

Probiotics for management of infantile colic: a systematic review of randomized controlled trials – Radoslaw Dryl – Archives of Medical Science

Bioinformatics

A multi-source domain annotation pipeline for quantitative metagenomic and metatranscriptomic functional profiling – Ari Ugarte – Microbiome

Microbes in the news

The world’s smallest masterpieces? Microscopic version of Leonardo da Vinci’s Mona Lisa and portraits of Albert Einstein and Charles Darwin are recreated using MILLIONS of bacteria – Daily Mail

Non-microbiology picks 

Evaluating the replicability of social science experiments in Nature and Science between 2010 and 2015 – Colin F Camerer – Nature Human Behaviour

 

August 28, 2018

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A brief Digest today featuring a review on how the microbiota affects drug disposition, a study adopting fungal growth measurement in the soil to that in the medium and in the plants, and a genetic approach to specifically depleting microbiome-derived metabolites in the host tissue.

General microbiology

* Minireview: How to determine the role of the microbiome in drug disposition – Jordan E Bisanz et al. – Drug Metabolism and Disposition

Loss of genomic diversity in a Neisseria meningitidis clone through a colonization bottleneck – Araceli Lamelas et al. – Genome Biology and Evolution

Human gut microbiome

Gut microbiota, short chain fatty acids, and obesity across the epidemiologic transition: the METS-Microbiome study protocol – Lara R. Dugas et al. – BMC Public Health

Multi-omics analyses to deliver the most effective treatment to every patient with inflammatory bowel disease – Rinse K. Weersma et al. – Gastroenterology

Plant, root and soil microbiome

Preprint: Antimicrobial, Antioxidant and Anti-Inflammatory Activities of Proteins of Phaseoulus lunatus (Fabaceae) Baby Lima Beans Produced in Ecuador – Javier Tamayo et al. – bioRxiv

* Preprint: Fungal growth is affected by and affects pH and redox potential (Eh) of the growth medium – Lydia Bousset et al. – bioRxiv

Water and extremophile microbiome

Preprint: The role of land use types and water chemical properties in structuring the microbiome of a connected lakes system – Sophi Marmen et al. – bioRxiv

Phages and viruses

Preprint: Repurposing of drugs as novel influenza inhibitors from clinical gene expression infection signatures – Mario Andres Pizzorno et al. – bioRxiv

Technology

Preprint: Differential amplicons for the evaluation of RNA integrity extracted from complex environmental samples – Fabien Cholet et al. – bioRxiv

** Preprint: Depletion of microbiome-derived molecules in the host using Clostridium genetics – Chun-Jun Guo et al. – bioRxiv

Bioinformatics

Identifying mixed Mycobacterium tuberculosis infections from whole genome sequence data – Benjamin Sobkowiak et al. – BMC Genomics

August 25 2018

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Todays Microbiome Digest covers the topics on microbiome of animalia kingdom ranging from humans ⇒mammals ⇒ amphibians ⇒ insects , cyanobacteria, AMR versus AMS, host microbe interactions, how & which microbes create homeostatis in the human body sites.  Happy Reading!

GUT or INTESTINAL MICROBIOME:

Gut microbiome: Microflora association with obesity and obesity-related comorbidities – Lone JB – Microb Pathog

Relevance of gut microbiota in cognition, behaviour and Alzheimer’s disease – de J R De-Paula V – Pharmacol Res.

Small intestinal microbiota: the neglected stepchild needed for fat digestion and absorption – Chang EB – Gut Microbes.

Prospects for Primary Prevention of Type 1 Diabetes by Restoring a Disappearing Microbe – Insel R – Pediatr Diabetes

ANIMAL MICROBIOME:

Synergetic action between the rumen microbiota and bovine health – Zeineldin M – Microb Pathog

Establishment of a Macaca fascicularis gut microbiome gene catalog and comparison with the human, pig and mouse gut microbiomes – Li X – Gigascience

Analyses of Aerosol Concentrations and Bacterial Community Structures for Closed Cage Broiler Houses at Different Broiler Growth Stages in Winter – Jiang L – J Food
Prot.

Characterization of the bacterial community of braised chicken, a specialty poultry product in China – Liu DY – Poult Sci.

Metagenomics analysis reveals significant modulation of cecal microbiota of broilers fed palm kernel expeller diets – Chen WL- Poult Sci.

Microbial diversity in the rumen, reticulum, omasum, and abomasum of yak on a rapid fattening regime in an agro-pastoral transition zone – Xue D – J Microbiol.

INSECT MICROBIOME:

Field-collected Triatoma sordida from central Brazil display high microbiota diversity that varies with regard to developmental stage and intestinal segmentation –
Oliveira JL – PLoS Negl Trop Dis.

FISH MICROBIOME:

Dietary salt levels affect digestibility, intestinal gene expression, and the microbiome, in Nile tilapia (Oreochromis niloticus) – Hallali E – PLoS One

WATER MICROBIAL ECOLOGY:

Bacterial bioclusters relate to hydrochemistry in New Zealand groundwater – Sirisena KA – FEMS Microbiol Ecol

 

PLANT MICROBIOME:

Technique : Metagenomic assembly of new (sub)polar Cyanobacteria and their associated microbiome from non-axenic cultures – Cornet L – Microb Genom

High PAH degradation and activity of degrading bacteria during alfalfa growth where a contrasted active community developed in comparison to unplanted soil – Bourceret
A – Environ Sci Pollut Res Int.

 

INFANT MICROBIOME:

Investigating the effects of cesarean delivery and antibiotic use in early childhood on risk of later attention deficit hyperactivity disorder – Axelsson PB – J Child
Psychol Psychiatry

 

PROBIOTICS or PREBIOTICS:

The effect of a multispecies probiotic on microbiota composition in a clinical trial of patients with diarrhea-predominant irritable bowel syndrome – Hod K –
Neurogastroenterol Motil.

ANTI- MICROBIAL RESISTANCE and SUSCEPTANCE:

Un-segregated waste disposal: an alarming threat of antimicrobials in surface and ground water sources in Delhi – Velpandian T – Environ Sci Pollut Res Int.

Novel bioactive peptides from PD-L1/2, a type 1 ribosome inactivating protein from Phytolacca dioica L. Evaluation of their antimicrobial properties and anti-biofilm
activities – Pizzo E – Biochim Biophys Acta

 

RESPIRATORY MICROBIOME:

Lower airway microbiota for ‘biomarker’ measurements of cystic fibrosis disease progression – Sherrard LJ – Thorax

Sputum microbiota is predictive of long-term clinical outcomes in young adults with cystic fibrosis – Acosta N- Thorax

 

HOST MICROBE INTERACTIONS:

Preventive effects of bovine colostrum supplementation in TNBS-induced colitis in mice – Filipescu IE – PLoS One

Role of wnt5a in metabolic inflammation in humans – Relling I – J Clin Endocrinol Metab.

 

TECHNIQUES:

Review: Evidence-Based Strategies for the Prehabilitation of the Abdominal Wall Reconstruction Patient – Joslyn NA – Plast Reconstr Surg.

QMEC: a tool for high-throughput quantitative assessment of microbial functional potential in C, N, P, and S biogeochemical cycling – Zheng B – Sci China Life Sci.

Review: Advances in Imaging Specific Mediators of Inflammatory Bowel Disease – Dmochowska N – Int J Mol Sci.

 

NUTRITION or DIET and TREATMENT:

Glucomannan hydrolysate promotes gut proliferative homeostasis and extends lifespan in Drosophila melanogaster – Si Y – J Gerontol A Biol Sci Med Sci.

Cultivable butyrate-producing bacteria of elderly Japanese diagnosed with Alzheimer’s disease – Nguyen TTT – J Microbiol.

Efficacy of Proanthocyanidins from Pelargonium sidoides Root Extract in Reducing P. gingivalis Viability While Preserving Oral Commensal S. salivarius – Savickiene N –
Materials (Basel).

Effects of Tempeh Fermentation with Lactobacillus plantarum and Rhizopus oligosporus on Streptozotocin-Induced Type II Diabetes Mellitus in Rats – Huang YC – Nutrients

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 18, 2018

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The virome of California mosquitoes, effects of climate warming on grassland microbial communities, and a few “bacteria and art” entries including a 92-foot inflatable E. coli sculpture.

General microbiome

Communities of Niche-Optimized Strains: Small-Genome Organism Consortia in Bioproduction – Stephan Noack – Trends in Biotechnology

Growth tradeoffs produce complex microbial communities on a single limiting resource – Michael Manhart – Nature Communications

Human oral microbiome

Oral microbiome development during childhood: an ecological succession influenced by postnatal factors and associated with tooth decay – Majda Dzidic – The ISME Journal

Animal experiments

Loss of HDAC6 alters gut microbiota and worsens obesity – Arnon D Lieber – The FASEB Journal

Animal microbiome

Pre-print: CRISPR/Cas9-mediated gene deletion of the ompA gene in an Enterobacter gut symbiont impairs biofilm formation and reduces gut colonization of Aedes aegypti mosquitoes – Shivanand Hegde – bioRxiv

Plant, root, and soil microbiome

Climate warming leads to divergent succession of grassland microbial communities – Xue Guo – Nature Climate Change

Water and extremophile microbiome

Bacterial Diversity in Replicated Hydrogen Sulfide-Rich Streams – Scott Hotaling – Microbial Ecology

Long-term in situ permafrost thaw effects on bacterial communities and potential aerobic respiration – Sylvain Monteux – The ISME Journal

Phages and viruses

Virome of > 12 thousand Culex mosquitoes from throughout California – Mohammadreza Sadeghi – Virology

Comprehensive comparative analysis of methods and software for identifying viral integrations – Xun Chen – Briefings in Bioinformatics

Phage-inducible chromosomal islands are ubiquitous within the bacterial universe – Alfred Fillol-Salom – The ISME Journal

Metabolomics

Metabotypes Related to Meat and Vegetable Intake Reflect Microbial, Lipid and Amino Acid Metabolism in Healthy People – Runmin Wei – Molecular Nutrition & Food Research

More microbes

Comparative Genomics of Nitrogen Cycling Pathways in Bacteria and Archaea – Michaeline B N Albright – Microbial Ecology

Bacteria art

Linen and Bacteria: The Hidden History of Microbiology – Clara Rodríguez Fernández – Labiotech.eu

Pomona Arts: Sara Parent Ramos: Jumble, Bunch, Grow – Inland Empire

Oxford Natural History exhibition explores benefits of bacteria – BBC News

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 9, 2018

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Horizontal gene transfer in microbiomes, metabolic study of the microbiota isolated from the camel rumen, a review on the bacteriophage virome in IBD.

General microbiome

Review: Monitoring plasmid-mediated horizontal gene transfer in microbiomes: recent advances and future perspectives – Rafael Pinilla-Redondo – Plasmid

Review: Learning from bacterial competition in the host to develop antimicrobials – Manuela Raffatellu – Nature Medicine

Pregnancy and early life

Early life colonization of the human gut: microbes matter everywhere – Katri Korpela – Current Opinion in Microbiology

Human respiratory microbiome

Determinants of the Nasal Microbiome: Pilot Study of Effects of Intranasal Medication Use – Vijay R Ramakrishnan – Allergy & Rhinology

Human skin microbiome

Sensitive scalp is associated with excessive sebum and perturbed microbiome – Li Ma – Journal of Cosmetic Dermatology

Animal experiments

Effects of host genetics and environmental conditions on fecal microbiota composition of pigs – Tereza Kubasova – PLOS ONE

Animal microbiome

A metagenomic analysis of the camel rumen’s microbiome identifies the major microbes responsible for lignocellulose degradation and fermentation – Javad Gharechahi – Biotechnology for Biofuels

Plant, root, and soil microbiome

Nitrogen fixation in a landrace of maize is supported by a mucilage-associated diazotrophic microbiota – Allen Van Deynze – PLOS Biology

Brazilian Ironstone Plant Communities as Reservoirs of Culturable Bacteria With Diverse Biotechnological Potential – Washington L Caneschi – Frontiers in Microbiology

Water and extremophile microbiome

Coupling biogeochemical process rates and metagenomic blueprints of coastal bacterial assemblages in the context of environmental change – Trine Markussen – Environmental Microbiology

Pre-print: Resource diversity structures aquatic bacterial communities – Mario E Muscarella – bioRxiv

Pre-print: Modular assembly of polysaccharide-degrading microbial communities in the ocean – Tim N Enke – bioRxiv

Food microbiology

Review: Bakery yeasts, a new model for studies in ecology and evolution – Belen Carbonetto – Yeast

Inferences from inventories of microbes in ecological vineyard settings – Hans-Josef Schroers – International Journal of Environmental Quality

Phages and viruses

Review: Bacteriophage virome in IBD – Clemens Thoma – Nature Reviews Gastroenterology and Hepatology

Bioinformatics

Synthetic microbe communities provide internal reference standards for metagenome sequencing and analysis – Simon A Hardwick – Nature Communications

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 2, 2018

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In today’s Microbiome Digest you can read about: the connection of mother’s microbiota and development of psychiatric disorders by M.G. Codagnone; pulmonary microbiome by A.N. Costa; microbiome and allergic diseases by M.Pascal; olfactory communication via microbiota in birds by O. Maraci; global topsoil microbiome by M. Bahram and many more. Enjoy your hot summer read!

Pregnancy and early life

Review: Programming Bugs: Microbiota and the Developmental Origins of Brain Health and Disease – Martin G.Codagnone – Biological Psychiatry

Human respiratory microbiome

The pulmonary microbiome: challenges of a new paradigm – André Nathan Costa – Jornal Brasileiro de Pneumologia

Oral microbiology

Are the mutans streptococci still considered relevant to understanding the microbial etiology of dental caries? – Jeffrey A. Banas – BMC Oral Health

Predicting oral malodour based on the microbiota in saliva samples using a deep learning approach – Yoshio Nakano – BMC Oral Health

Human skin microbiome

The Environmental Exposures and Inner- and Intercity Traffic Flows of the Metro System May Contribute to the Skin Microbiome and Resistome – Kang Kang – Cell Reports

Human gut microbiome

Alterations in the Gut Microbiota of Rats Chronically Exposed to Volatilized Cocaine and Its Active Adulterants Caffeine and Phenacetin – Cecilia Scorza – Neurotoxicity Research

Origination, change, and modulation of geriatric disease-related gut microbiota during life – Muhammad Shahid Riaz Rajoka – Applied Microbiology and Biotechnology

Rapid gastrointestinal loss of Clostridial Clusters IV and XIVa in the ICU associates with an expansion of gut pathogens – Alexandra E. Livanos – PLOS One

Minireview: Microbiome and Allergic Diseases – Mariona Pascal – Frontiers in Immunology / Mucosal Immunity

Comparison of Microbiota in Patients Treated by Surgery or Chemotherapy by 16S rRNA Sequencing Reveals Potential Biomarkers for Colorectal Cancer Therapy – Xingming Deng – Frontiers in Microbiology / Antimicrobials, Resistance and Chemotherapy

Moxibustion treatment modulates the gut microbiota and immune function in a dextran sulphate sodium-induced colitis rat model – Qin Qi – World Journal of Gastroenterology

Helicobacter pylori in human health and disease: Mechanisms for local gastric and systemic effects – Denisse Bravo – World Journal of Gastroenterology

Acquisition of MACPF domain-encoding genes is the main contributor to LPS glycan diversity in gut Bacteroides species – Valentina Laclare McEneany – The ISME Journal

Drivers of Microbiome Biodiversity: A Review of General Rules, Feces, and Ignorance – Aspen T. Reese – mBio

Effects of prebiotic inulin-type fructans on blood metabolite and hormone concentrations and faecal microbiota and metabolites in overweight dogs – Celeste Alexander – British Journal of Nutrition

Standardization of gut microbiota analysis: Variability in samples taken at different times from single case and the effect of the freezing the sample – F. Saglam – International Journal of Infectious Diseases

Culture- and metagenomics-enabled analyses of the Methanosphaera genus reveals their monophyletic origin and differentiation according to genome size – Emily C. Hoedt – The ISME journal

Animal experiments 

A Polysaccharide Isolated from Dictyophora indusiata Promotes Recovery from Antibiotic-Driven Intestinal Dysbiosis and Improves Gut Epithelial Barrier Function in a Mouse Model – Sadia Kanwal – Nutrients

High Dose Vitamin D supplementation alters faecal microbiome and predisposes mice to more severe colitis – Simon Ghaly – Scientific Reports

Treatment with camu camu (Myrciaria dubia) prevents obesity by altering the gut microbiota and increasing energy expenditure in diet-induced obese mice – Fernando F Anhê – Gut Microbiota

Whole genome sequencing and function prediction of 133 gut anaerobes isolated from chicken caecum in pure cultures – Matej Medvecky – BMC Genomics

Addition of arabinoxylan and mixed linkage glucans in porcine diets affects the large intestinal bacterial populations – John B. Gorham – European Journal of Nutrition

Animal microbiome 

A prokaryotic-eukaryotic relation in the fat body of Bombus terrestris – Anneleen Parmentier – Environmental Microbiology Reports

Olfactory Communication via Microbiota: What Is Known in Birds? – Öncü Maraci – Genes

Unprecedented Diversity of ssDNA Phages from the Family Microviridae Detected within the Gut of a Protochordate Model Organism (Ciona robusta) – Alexandria Creasy – Viruses

Plant, root, and soil microbiome

Description of ‘Candidatus Methylocucumis oryzae’, a novel Type I methanotroph with large cells and pale pink colour, isolated from an Indian rice field – Pranitha S. Pandit – Antonie van Leeuwenhoek

Long-term effects of untreated wastewater on soil bacterial communities – Tianlin Shen – Science of The Total Environment

Minireview: Rhizoremediation of petroleum hydrocarbons: a model system for plant microbiome manipulation – Sara Correa-García – Microbial Biotechnology

Soil pre-fumigation could effectively improve the disease suppressiveness of biofertilizer to banana Fusarium wilt disease by reshaping the soil microbiome – Zongzhuan Shen – Biology and Fertility of Soils

Structure and function of the global topsoil microbiome – Mohammad Bahram – Nature

Globally rising soil heterotrophic respiration over recent decades – Ben Bond-Lamberty – Nature

Water and extremophile microbiome

Distinct Oceanic Microbiomes From Viruses to Protists Located Near the Antarctic Circumpolar Current – Flavia Flaviani – Frontiers in Microbiology / Aquatic Microbiology

Evaluation of biomethane potential of waste algal biomass collected from eutrophied lake: effect of source of inocula, co-substrate, and VS loading – Pushpendar Kumar – Journal of Applied Phycology

Distinct molecular signatures in dissolved organic matter produced by viral lysis of marine cyanobacteria – Xiufeng Ma – Environmental Microbiology

Increased biofilm formation due to high-temperature adaptation in marine Roseobacter – Alyssa G. Kent – Nature Microbiology

Adaptive mechanisms that provide competitive advantages to marine bacteroidetes during microalgal blooms – Frank Unfried – The ISME Journal

The anchoring effect—long-term dormancy and genetic population structure – Lisa Sundqvist – The ISME Journal

Genome biology of a novel lineage of planctomycetes widespread in anoxic aquatic environments – Stefan Spring – Environmental Microbiology

The distribution of active iron‐cycling bacteria in marine and freshwater sediments is decoupled from geochemical gradients – Julia M. Otte – Environmental Microbiology

Temporal and spatial dynamics in microbial community composition within a temperate stream network – Norman Hassell – Environmental Microbiology

Diel dynamics and coupling of heterotrophic prokaryotes and dissolved organic matter in epipelagic and mesopelagic waters of the central Red Sea – Francisca C. García – Environmental Microbiology

Probiotics / prebiotics

The effects of a multispecies probiotic on migraine and markers of intestinal permeability–results of a randomized placebo-controlled study – N M de Roos – European Journal of Clinical Nutrition

Phages and viruses

Eicosanoid biosynthesis influences the virulence of Candida parapsilosis – Tanmoy Chakraborty – Virulence

Competition between mobile genetic elements drives optimization of a phage-encoded CRISPR-Cas system: Insights from a natural arms-race – Amelia McKitterick – bioRxiv

Bioinformatics

BARM and BalticMicrobeDB, a reference metagenome and interface to meta-omic data for the Baltic Sea – Johannes Alneberg – Scientific Data

Bacteria & Art

The Beautiful World of Bacteria