Category Archives: Human oral

September 7, 2018

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Happy Friday everyone! Today’s digest covers microbiota dysbiosis in bowel obstruction, the soil microbial communities in apple orchards, and the bacterial and diatom composition of killer whale skin. Enjoy!

Human oral microbiome

Human defects in STAT3 promote oral mucosal fungal and bacterial dysbiosis – Abusleme – JCI Insight

High-resolution ISR amplicon sequencing reveals personalized oral microbiome – Mukherjee – Microbiome

Human gut microbiome

Review: Inflammasomes in the gastrointestinal tract: infection, cancer and gut microbiota homeostasis – Man – Nature Reviews Gastroenterology and Hepatology

Review: Norovirus interactions with the commensal microbiota – Sullender – PLoS Pathogens

Microbiota dysbiosis and its pathophysiological significance in bowel obstruction – Hegde – Scientific Reports

Microbiota-derived short-chain fatty acids promote Th1 cell IL-10 production to maintain intestinal homeostasis – Sun – Nature Communications

Animal experiments

Irreversible effects of trichloroethylene on the gut microbial community and gut-associated immune responses in autoimmune-prone mice – Khare – Journal of Applied Toxicology

Animal microbiome

Preprint: Efficacy of fecal sampling as a gut proxy in the study of chicken gut microbiota – Yan – BioRxiv

Preprint: Diet influences early microbiota development in dairy calves without long-term impacts on milk production – Dill-McFarland – BioRxiv

Host-derived population genomics data provides insights into bacterial and diatom composition of the killer whale skin – Hooper – Molecular Ecology

Plant, root, and soil microbiome

Diverse Bacteria Utilize Alginate Within the Microbiome of the Giant Kelp Macrocystis pyrifera – Lin – Frontiers in Microbiology

Spatial structuring of soil microbial communities in commercial apple orchards – Deakin – Applied Soil Ecology

Isolation and characterization of antagonistic bacteria with the potential for biocontrol of soil-borne wheat diseases – Wang – Journal of Applied Microbiology

Science, publishing, and career

Experimental technique isn’t my strong suit, but I can still be a scientist – Anderson – Science Careers

September 1, 2018

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Have a nice weekend! Today, several reviews about different aspects of human genome (from Vitamin D to the Impact of Colonialism in the changes of health in Indigenous people). Today, we have also several studies about poultry microbiome and changes in food microbiota, in addition with interesting studies about microbiota drug metabolism.

 

General and Human Microbiome

Review: The hygiene hypothesis at a glance: early exposures, immune mechanism and novel therapies – Gabriel M.Alexandre-Silva – Acta Tropica

Review: Dietary vitamin D, vitamin D receptor, and microbiome – Jun Sun – Current Opinion in Clinical Nutrition and Metabolic Care

Theory and Synthesis: Consequences of colonialism: A microbial perspective to contemporary Indigenous health – Emily Skelly – American Journal of Physical Anthropology

Review: Early-Life Exposures and Risk of Diabetes Mellitus and Obesity – Véronique Gingras – Current Diabetes Reports

Review: Aspects of Gut Microbiota and Immune System Interactions in Infectious Diseases, Immunopathology, and Cancer – Veronica Lazar – Frontiers in Immunology

Review: Early Disruption of the Microbiome Leading to Decreased Antioxidant Capacity and Epigenetic Changes: Implications for the Rise in Autism – Rebecca S. Eshraghi – Frontiers in Cellular Neuroscience

Review: Energy balance and gastrointestinal cancer: risk, interventions, outcomes and mechanisms – Cornelia M. Ulrich – Nature Reviews Gastroenterology & Hepatology

Review: Microbial Production of Conjugated Linoleic Acid and Conjugated Linolenic Acid Relies on a Multienzymatic System – Ana S. Salsinha – Microbiology and Molecular Biology Reviews

News & Views: Gut microbiome, microbial metabolites and the development of NAFLD – Cyrielle Caussy – Nature Reviews Gastroenterology & Hepatology

Does Severity of Alzheimer’s Disease Contribute to Its Responsiveness to Modifying Gut Microbiota? A Double Blind Clinical Trial – Azadeh Agahi – Frontiers in Neurology

Evaluation of relationship between dental caries, diabetes mellitus and oral microbiota in diabetics – Bhagyashri Ramachandra Latti – Journal of Oral and Maxillofacial Pathology

Effects of Japanese diet in combination with exercise on visceral fat accumulation – Masaki Asano – Nutrition

Enteric Virome and Bacterial Microbiota in Children with Ulcerative Colitis and Crohn’s Disease – Melissa A. Fernandes – Journal of Pediatric Gastroenterology and Nutrition

Temporal instability of the post-surgical maxillary sinus microbiota – Ioannis Koutsourelakis – BMC Infectious Diseases

Influence of cigarette smoking on the human duodenal mucosa-associated microbiota – Erin R. Shanahan – Microbiome

 

Animal Microbiome

Review: A Review of Prebiotics Against Salmonella in Poultry: Current and Future Potential for Microbiome Research Applications – Andrew C. Micciche – Frontiers in Veterinary Science

Gut Microbiota and Relevant Metabolites Analysis in Alcohol Dependent Mice – Guanhao Wang – Frontiers in Microbiology

Gut microbiota mediates the anti-obesity effect of calorie restriction in mice – Shuo Wang – Scientific Reports

Effect of humic substances on rumen fermentation, nutrient digestibility, methane emissions, and rumen microbiota in beef heifers – Stephanie A Terry – Journal of Animal Science

Effects of glucose oxidase on growth performance, gut function, and cecal microbiota of broiler chickens – Shengru Wu – Poultry Science

16S ribosomal RNA sequencing reveals a modulation of intestinal microbiome and immune response by dietary L-theanine supplementation in broiler chickens – Muhammad Saeed – Poultry Science

Microbial effects of livestock manure fertilization on freshwater aquaculture ponds rearing tilapia (Oreochromis shiranus) and North African catfish (Clarias gariepinus) – Jeremiah J. Minich – Microbiology Open

Effect of oat hulls as a free choice feeding on broiler performance, short chain fatty acids and microflora under a mild necrotic enteritis challenge – Sarbast K.Kheravii – Animal Nutrition

Application of Illumina-MiSeq high throughput sequencing and culture-dependent techniques for the identification of microbiota of silver carp (Hypophthalmichthys molitrix) treated by tea polyphenols – Shiliang Jia – Food Microbiology

 

Beneficial Microbes and Compounds

Rhubarb Peony Decoction Ameliorates Ulcerative Colitis in Mice by Regulating Gut Microbiota to Restoring Th17/Treg Balance – Shuang Luo – Journal of Ethnopharmacology

Bifidobacterium bifidum PRL2010 alleviates intestinal ischemia/reperfusion injury – Sabrina Duranti – PLoS One

Beneficial Effect of Virgin Coconut Oil on Alloxan-Induced Diabetes and Microbiota Composition in Rats – Sinisa Djurasevic – Plant Foods for Human Nutrition

 

Food Microbiome

Microbiota dynamics and volatilome profile during stink bean fermentation (Sataw-Dong) with Lactobacillus plantarum KJ03 as a starter culture – Krittanon Jampaphaeng – Food Microbiology

Microbial spoilage investigation of thawed common cuttlefish (Sepia officinalis) stored at 2 °C using next generation sequencing and volatilome analysis – F. F. Parlapani – Food Microbiology

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 – Food Microbiology

Revealing the influence of microbiota on the quality of Pu-erh tea during fermentation process by shotgun metagenomic and metabolomic analysis – Zhongyuan Li – Food Microbiology

Influence of lactate and acetate removal on the microbiota of French fresh pork sausages – Agnès Bouju-Albert – Food Microbiology

 

Plant Microbiome

The future has roots in the past: the ideas and scientists that shaped mycorrhizal research – Paola Bonfante – New Phytology Trust

 

Experiments

Chemoselective Probe Harboring a Unique Bioorthogonal Cleavage Site for Investigation of Gut Microbiota Metabolism – Neeraj Garg – Angewandte Chemie  

An ex vivo fermentation screening platform to study drug metabolism by human gut microbiota – Evita van de Steeg – Drug Metabolism and Disposition

 

August 27, 2018

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Highlights: how microbes influence the system they inhabit, maternal microbial metabolism, gut microbiota in pancreatic disease and other metabolic disorders, core and staphylococcal microbiota in skin & nose of pigs, wheat head microbiome bacteria,  abundant & rare biospheres of hot springs, antibiotic degradation by microbes, virome.

General microbiome

Review: Understanding how microbiomes influence the systems they inhabit – Ed K. Hall – Nature Microbiology

Male Bladder Microbiome Relates to Lower Urinary Tract Symptoms – Petar Bajic – European Urology Focus

Pregnancy and early life

Is maternal microbial metabolism an early-life determinant of health? – Kymberleigh A. Romano – LabAnimal

Human oral microbiome

The oral microbiome in oral lichen planus during a one‐year randomized clinical trial – Camilla Kragelund – Oral Diseases

Human respiratory microbiome

Interaction between the microbiome and TP53 in human lung cancer – K. Leigh Greathouse – Genome Biology

Human gut microbiome

The Gut Microbiome in Pancreatic Disease – Venkata S. Akshintala – Clinical Gastroenterology and Hepatology

FXR-Dependent Modulation of the Human Small Intestinal Microbiome by the Bile Acid Derivative Obeticholic Acid – Elliot S. Friedman – Gastroenterology

Review: Role of gut microbiota in chronic low‐grade inflammation as potential driver for atherosclerotic cardiovascular disease: a systematic review of human studies – I. C. L. van den Munckhof – Obesity Reviews

Bile acid homeostasis and intestinal dysbiosis in alcoholic hepatitis – Dragos Ciocan – Alimentary Pharmacology & Therapeutics

Characterization and induction of prophages in human gut-associated Bifidobacterium hosts – Travis N. Mavrich – Scientific Reports

In Vitro Ecological Response of the Human Gut Microbiome to Bioactive Extracts from Edible Wild Mushrooms – Emanuel Vamanu – Molecules

Review: The journey of gut microbiome – An introduction and its influence on metabolic disorders – Ankita Chattopadhyay -Frontiers in Biology

Animal experiments 

Sulfated polysaccharide from sea cucumber modulates the gut microbiota and its metabolites in normal mice – Zhenjun Zhu – International Journal of Biological Macromolecules

Chitin-based barrier immunity and its loss predated mucus-colonization by indigenous gut microbiota – Keisuke Nakashima – Nature Communications

Reduced particle size wheat bran is efficiently colonized by lactic acid producing community and reduces Enterobacteriaceae levels in the cecal microbiota of broilers – Karen Vermeulen – Applied and Environmental Microbiology

A High Salt Diet Modulates the Gut Microbiota and Short Chain Fatty Acids Production in a Salt-Sensitive Hypertension Rat Model – Ariel Bier – Nutrients

Animal microbiome 

A detailed investigation of the porcine skin and nose microbiome using universal and Staphylococcus specific primers – Mikael Lenz Strube – Scientific Reports

Characterization of bacterial microbiota compositions along the intestinal tract in pigs and their interactions and functions – Daniel Crespo-Piazuelo – Scientific Reports

Cnidarian Interaction with Microbial Communities: From Aid to Animal’s Health to Rejection Responses – Loredana Stabili – Marine Drugs

Plant, root, and soil microbiome

Wheat microbiome bacteria can reduce virulence of a plant pathogenic fungus by altering histone acetylation – Yun Chen – Nature Communications

Biodegradation of oxytetracycline and enrofloxacin by autochthonous microbial communities from estuarine sediments – Malek Harrabi – Science of The Total Environment

Soil micro-food web interactions and rhizosphere priming effectSoil micro-food web interactions and rhizosphere priming effect – Xinchang Kou – Plant and Soil

Burkholderia pseudomallei-absent soil bacterial community results in secondary metabolites that kill this pathogen – Chotima Potisap – AMB Express

Variation in the leaf and root microbiome of sugar maple (Acer saccharum) at an elevational range limit – Jessica Wallace – PeerJ

Contrasting responses of the bacterial communities in ectomycorrhizal roots and rhizosphere soils to defoliation or winter hardening – Hironari Izumi – Rhizosphere

Water and extremophile microbiome 

Abundant and rare microbial biospheres respond differently to environmental and spatial factors in Tibetan hot springs – Yanmin Zhang – Frontiers in Microbiology

Built environment 

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

Application of hybrid anaerobic reactor: Treatment of increasing cyanide containing effluents and microbial composition identification – Pragya Gupta – Journal of Environmental Management

A little breath of fresh air into an anaerobic system: How microaeration facilitates anaerobic digestion process – Duc Nguyen – Biotechnology Advances

Managing microbial communities in membrane biofilm reactors – A. Ontiveros-Valencia – Applied Microbiology and Biotechnology

Phages and viruses

Preprint: May the phage be with you? Prophage-like elements in the genomes of Soft Rot Pectobacteriaceae (Pectobacterium spp. and Dickeya spp.) – Robert Czajkowski – bioRxiv

Occurrence, integrity and functionality of AcaML1–like viruses infecting extreme acidophiles of the Acidithiobacillus species complex – Paulo C. Covarrubias – Research in Microbiology

Chapter: Robust Analysis of Time Series in Virome Metagenomics – Jose Manuel Martí – The Human Virome

Chapter: A Method for Isolation of the Virome from Plasma Samples – Pilar Domingo-Calap – The Human Virome

Chapter: Virome Sequencing of Stool Samples – Lenka Kramná – The Human Virome

Chapter: Protocol for Generating Infectious RNA Viromes from Complex Biological Samples – Sonia Monteil-Bouchard – The Human Virome

Techniques

Review: Transcriptome Sequencing Approaches to Elucidate Host–Microbe Interactions in Opportunistic Human Fungal Pathogens – Hrant Hovhannisyan – Current Topics in Microbiology and Immunology 

Chapter: Flow Cytometry and Direct Sequencing of Viruses – Mária Džunková – The Human Virome

 

 

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 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 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 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

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

 

July 31, 2018

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Today’s Digest features a report that different types of tobacco products can cause oral microbial dysbiosis, an update on fecal microbiome transplant, and exploration into Westernization and evolution of gut microbiota. Enjoy reading!

General microbiology

Alterations of Salmonella Typhimurium Antibiotic Resistance under Environmental Pressure – Mengfei Peng et al. – Applied and Environmental Microbiology

Preprint: Experimental demonstration that screening can enable the environmental recruitment of a defensive microbiome – Tabitha Innocent et al. – bioRxiv

Human oral microbiome

Chicken or the Egg: Microbial Alterations in Biopsy Samples of Patients with Oral Potentially Malignant Disorders – Gabor Decsi et al. – Pathology & Oncology Research

** Types of tobacco consumption and the oral microbiome in the United Arab Emirates Healthy Future (UAEHFS) Pilot Study – Yvonne Vallès et al. – Scientific Reports

Human respiratory microbiome

Decreased microbiome diversity in the HIV small airway epithelium – Stella Xu et al. – Respiratory Research

Human gut microbiome

Antibiotic Exposure and Reduced Short Chain Fatty Acid Production after Hematopoietic Stem Cell Transplant – Lindsey ERomick-Rosendale et al. – Biology of Blood and Marrow Transplantation

** Review: Fecal Microbiota Transplantation: Current Status in Treatment of GI and Liver Disease – Byron P.Vaughn et al. – Clinical Gastroenterology and Hepatology

The association between the incidence of intestinal graft-versus-host disease and antibiotic use after allogeneic hematopoietic stem cell transplantation – Daisuke Hidaka et al. – Clinical Transplantation

Ecological effects of cefepime use during antibiotic cycling on the Gram-negative enteric flora of ICU patients – Carola Venturini et al. – Intensive Care Medicine Experimental

** Gut microbiota is associated with obesity and cardiometabolic disease in a population in the midst of Westernization – Jacobo de la Cuesta-Zuluaga et al. – Scientific Reports

A diverse range of human gut bacteria have the potential to metabolise the dietary component gallic acid – María Esteban-Torres et al. – Applied and Environmental Microbiology

Metagenomic analysis of gut microbial communities from a Central Asian population – Almagul Kushugulova et al. – BMJ Open

Animal experiments

Early cellular responses of germ-free and specific-pathogen-free mice to Francisella tularensis infection – ZuzanaKrocova et al. – Microbial Pathogenesis

Rat: Gut microbiota modulation accounts for the neuroprotective properties of anthocyanins – Cláudia Marques et al. – Scientific Reports

Mouse: Complementary intestinal mucosa and microbiota responses to caloric restriction – Kalina Duszka et al. – Scientific Reports

Greater Microbial Translocation and Vulnerability to Metabolic Disease in Healthy Aged Female Monkeys – Quentin N. Wilson et al. – Scientific Reports

Medicinal Mushrooms Supplements Alter Chicken Intestinal Microbiome – Janelle Robinson et al. – International Journal of Medicinal Mushrooms

Review: Standardization in host-microbiota interaction studies: challenges, gnotobiology as a tool, and perspective – Catherine Mooser et al. – Current Opinion in Microbiology

Animal microbiome

Review: Where in the serotonergic system does it go wrong? Unravelling the route by which the serotonergic system affects feather pecking in chickens – Elske N.de Haas & Jerine A.J.van der Eijk – Neuroscience & Biobehavioral Reviews

Exploring the pathology of an epidermal disease affecting a circum-Antarctic sea star – Laura Núñez-Pons et al. – Scientific Reports

Assessment of rumen microbiota from a large cattle cohort reveals the pan and core bacteriome contributing to varied phenotypes – Mingyuan Xue et al. – Applied and Environmental Microbiology

Preprint: Whole genome screen reveals a novel relationship between Wolbachia and Drosophila host translation – Yolande Grobler et al. – bioRxiv

Food microbiology

Dynamics and biodiversity of bacterial and yeast communities during the fermentation of cocoa beans – Jatziri Mota-Gutierrez et al. – Applied and Environmental Microbiology

Plant, root and soil microbiome

Alternate life history phases of a common seaweed have distinct microbial surface communities – Matthew A Lemay et al. – Molecular Ecology

Diversity of bacterial microbiota of coastal halophyte Limonium sinense and amelioration of salinity stress damage by symbiotic plant growth-promoting actinobacterium Glutamicibacter halophytocola KLBMP 5180 – Sheng Qin et al. – Applied and Environmental Microbiology

Bacterial microbiota protect an invasive bark beetle from a pine defensive compound – Chihang Cheng et al. – Microbiome

Structural inflexibility of the rhizosphere microbiome in mangrove plant Kandelia obovata under elevated CO2 – Panqing Yin et al. – Marine Environmental Research

Mutualistic fungus Phomopsis liquidambari increases root aerenchyma formation through auxin-mediated ethylene accumulation in rice (Oryza sativa L.) – Li-Yan Hu et al. – Plant Physiology and Biochemistry

Characteristics of archaea and bacteria in rice rhizosphere along a mercury gradient – Ming Ma et al. – Science of The Total Environment

Isolation and diversity of culturable rhizobacteria associated with economically important crops and uncultivated plants in Québec, Canada – Di Fan et al. – Systematic and Applied Microbiology

Phages and viruses

Hordes of Phages in the Gut of the Tilapia Sarotherodon melanotheron – Yvan Bettarel et al. – Scientific Reports

Bioinformatics

Joint Analysis of Long and Short Reads Enables Accurate Estimates of Microbiome Complexity – Anton Bankevich & Pavel A.Pevzner – Cell Systems

Microbes in the news

Gut bacteria can protect against Salmonella infections – Press Trust of India – Business Standard

July 28, 2018

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Have a good weekend! For this Saturday, we have more than 60 articles! 

Including: A set of reviews about mother, delivery and neonate microbiome; relationship between microbiome and cancer and Alzheimer; microbiome in primate models, reviews about pathogens and more…

 

Human and General Microbiome

Review: Gut Mycobiota and Fungal Metabolites in Human Homeostasis – Izabella Mogilnicka – Current Drug Targets

Review: Dietary Protein and Muscle in Aging People: The Potential Role of the Gut Microbiome – Mary Ni Lochlainn – Nutrients

Review: The interplay between neutrophils and microbiota in cancer – Carolyne K. Smith – Journal of Leukocyte Biology

Review: Flux, Impact, and Fate of Halogenated Xenobiotic Compounds in the Gut – Siavash Atashgahi – Frontiers in Physiology

Review: Akkermansia muciniphila in the Human Gastrointestinal Tract: When, Where, and How? – Sharon Y. Geerlings – Microorganisms

Review: Considering gut microbiota disturbance in the management of Helicobacter pylori infection – Loris R. Lopetuso – Expert Review of Gastroenterology & Hepatology

Microbiome Analyses for Toxicological Studies – Jacquelynn Benjamino – Current Protocols in Toxicology

Editorial: Caesarean-Section and Neonatal Gut Microbiome: Short and Long Term Effects and New Targets for Early Prevention – Giannattasio A. – Annals of Nutrition and Metabolism

Review: C-section and the Neonatal Gut Microbiome Acquisition: Consequences for Future Health – Arboleya S. – Annals of Nutrition and Metabolism

Review: Birth Mode-Related Differences in Gut Microbiota Colonization and Immune System Development – Francino M.P.  – Annals of Nutrition and Metabolism

Review: Intervention for Dysbiosis in Children Born by C-Section – Francavilla R. – Annals of Nutrition and Metabolism

Review: Gut Microbiota Composition in Healthy Japanese Infants and Young Adults Born by C-Section – Nagpal R. – Annals of Nutrition and Metabolism

Review: Dysbiosis in Children Born by Caesarean Section – Salas Garcia M.C. – Annals of Nutrition and Metabolism

 

Human Gut

Association between Alzheimer’s Disease and Oral and Gut Microbiota: Are Pore Forming Proteins the Missing Link? – Aguayo, Sebastian –  Journal of Alzheimer’s Disease

Gut microbiome analysis as a tool towards targeted non-invasive biomarkers for early hepatocellular carcinoma – Zhigang Ren – Gut

A Multi-omic Association Study of Trimethylamine N-Oxide – Ohad Manor – Cell Reports

Gut Bacterial Microbiota and its Resistome Rapidly Recover to Basal State Levels after Short-term Amoxicillin-Clavulanic Acid Treatment in Healthy Adults – Chad W. MacPherson – Scientific Reports

Cost-effectiveness analysis of ribotype-guided fecal microbiota transplantation in Chinese patients with severe Clostridium difficile infection – Minghuan Jiang – PLoS ONE

Microbiota Quality and Mitochondrial Activity Link with Occurrence of Muscle Cramps in Hemodialysis Patients using Citrate Dialysate: A Pilot Study – Durand P.-Y. – Blood Purification

Gut microbiota, dietary intakes and intestinal permeability reflected by serum zonulin in women – S. Mörkl – European Journal of Nutrition

Analysis of the Enteric Microbiome: First Tentative Steps Towards a Comprehensive Work-up of Prostate Cancer? – Ilaria Cavarretta – European Urology

 

Human Respiratory Tract

Respiratory Microbiome Profiling for Etiologic Diagnosis of Pneumonia in Mechanically Ventilated Patients – Georgios D. Kitsios – Frontiers in Microbiology

Oropharyngeal microbiome evaluation highlights Neisseria abundance in active celiac patients – Laura Iaffaldano – Scientific Reports

 

Newborn and Mother Microbiome

Maternal antimicrobial use at delivery has a stronger impact than mode of delivery on bifidobacterial colonization in infants: a pilot study – Naruaki Imoto – Journal of Perinatology

 

Human Urinary/Reproductive Tract

Endocervical and vaginal microbiota in South African adolescents with asymptomatic Chlamydia trachomatis infection – Christina Balle – Scientific Reports

Introduction: Microbes in the female reproductive function, do they matter? – Carlos Simon – Fertility and Sterility

 

Human Skin

Relations between epidermal barrier dysregulation and staphylococci-dominated microbiome dysbiosis in atopic dermatitis – Can Altunbulakli – Atopic Dermatitis Research

 

Animal Microbiome / Animal Experiments

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

Diarrhea-Associated Intestinal Microbiota in Captive Sichuan Golden Snub-Nosed Monkeys (Rhinopithecus roxellana) – Hui Zhu – Microbes and Environments

An orally administered oral pathobiont and commensal have comparable and innocuous systemic effects in germ-free mice – Keisuke Sato – Journal of Periodontal Disease

Effects of dietary tryptophan supplementation in the acetic acid-induced colitis mouse model – Shuai Chen – Food and Nutrition

Early-life stress leads to sex-dependent changes in pubertal timing in rats that are reversed by a probiotic formulation – Caitlin S. M. Cowan – Developmental Psychobiology

A Comparative Study on the Faecal Bacterial Community and Potential Zoonotic Bacteria of Muskoxen (Ovibos moschatus) in Northeast Greenland, Northwest Greenland and Norway – Emilie U. Andersen-Ranberg – Microorganisms

Gut microbiota influences Alzheimer’s disease pathogenesis by regulating acetate in Drosophila model – Yan Kong – Future Microbiology

Elevated Seawater Temperatures Decrease Microbial Diversity in the Gut of Mytilus coruscus – Yi-Feng Li – Frontiers in Physiology

Microbiome-metabolomics Analysis of the Impacts of Long-term Dietary Advanced Glycation End Products Consumption on the C57BL/6 Mouse Fecal Microbiota and Metabolite Perturbation – Wanting Qu – Journal of Agricultural and Food Chemistry

Papio spp. Colon microbiome and its link to obesity in pregnancy – XuanJi Li – Journal of Medical Primatology

Combination of Aronia, Red Ginseng, Shiitake Mushroom and Nattokinase Potentiated Insulin Secretion and Reduced Insulin Resistance with Improving Gut Microbiome Dysbiosis in Insulin Deficient Type 2 Diabetic Rats – Hye Jeong Yang – Nutrients

Short and long-term effects of a synbiotic on clinical signs, the fecal microbiome, and metabolomic profiles in healthy research cats receiving clindamycin: a randomized, controlled trial – Jacqueline C. Whittemore​ – PeerJ

Lactobacillus plantarum ZDY04 exhibits a strain-specific property of lowering TMAO via the modulation of gut microbiota in mice – Liang Qiu – Food and Function

Diet induced maternal obesity affects offspring gut microbiota and persists into young adulthood – Yanjie Guo – Food and Function

Antibiotic-induced acceleration of type 1 diabetes alters maturation of innate intestinal immunity – Xue-Song Zhang – eLife

Clostridium butyricum Attenuates Chronic Unpredictable Mild Stress-Induced Depressive-Like Behavior in Mice via the Gut-Brain Axis – Jing Sun – Journal of Agricultural and Food Chemistry

 

Food Microbiome

Analysis of Fish Commonly Sold in Local Supermarkets Reveals the Presence of Pathogenic and Multidrug-Resistant Bacterial Communities – Ama Okyere – Microbiology Insights

Short communication: Profiling white wine seed vinegar bacterial diversity through viable counting, metagenomic sequencing and PCR-DGGE – Vesna Milanović – International Journal of Food Microbiology

Acyl-homoserine-lactones receptor LuxR of Shewanella baltica involved in the development of microbiota and spoilage of refrigerated shrimp – Jinxin Jie – Journal of Food Science and Technology

 

Beneficial Microbes and Compounds

Review: Probiotics against airway allergy: host factors to consider – Irina Spacova – Disease Model and Mechanisms

Abundance of gut Prevotella at baseline and metabolic response to barley prebiotics – Jonna Sandberg – European Journal of Nutrition

Letter: Effect of Metformin or Chinese Herbal Formula in Patients with Type 2 Diabetes Mellitus and Hyperlipidemia: A Reassessment – Venu Gopal Jonnalagadda – mBio

Coreopsis Tinctoria Modulates Lipid Metabolism by Decreasing Low-Density Lipoprotein and Improving Gut Microbiota – Ren Z. – Cellular Physiology and Biochemistry

 

Pathogen Research

Review: Recent insights into Shigella – Stephen Baker – Current Opinion in Infectious Diseases

Review: Cholera: recent updates – Ana A. Weil – Current Opinion in Infectious Diseases

 

Soil and Plant Microbiome

Microbial community assembly differs across minerals in a rhizosphere microcosm – Thea Whitman – Environmental Microbiology

Bipartite interactions, antibiotic production and biosynthetic potential of the Arabidopsis leaf microbiome – Eric J. N. Helfrich – Nature Microbiology

Vineyard under-vine floor management alters soil microbial composition, while the fruit microbiome shows no corresponding shifts – Ming-Yi Chou – Scientific Reports

 

Methods

Methodology: A two-stage microbial association mapping framework with advanced FDR control – Jiyuan Hu – Microbiome

A Comprehensive Study on Predicting Functional Role of Metagenomes Using Machine Learning Methods – Jyotsna Talreja Wassan – IEEE/ACM Transactions on Computational Biology and Bioinformatics

Generalized Linear Models with Linear Constraints for Microbiome Compositional Data – Jiarui Lu – Biometrics

Analyzing differences between microbiome communities using mixture distributions – Konstantin Shestopaloff – Statistics in Medicine

Pathomimetic modeling of human intestinal diseases and underlying host-gut microbiome interactions in a gut-on-a-chip – Woojung Shin – Methods in Cell Biology

 

Other

A year of monitoring 20 mesophilic full-scale bioreactors reveals the existence of stable but different core microbiomes in bio-waste and wastewater anaerobic digestion systems – Magdalena Calusinska – Biotechnology for Biofuels