June 12, 2018

Gut and General Microbiome

Screening for Nonalcoholic Fatty Liver Disease in Inflammatory Bowel Diseases: A Cohort Study Using Transient Elastography – Chiara Saroli Palumbo – Inflammatory Bowel Diseases

Review: A critical appraisal of advances in the diagnosis of diverticular disease – Antonio Tursi – Expert Review of Gastroenterology & Hepatology  

Antimicrobial-Induced Cytopenia and Bone Marrow Hypocellularity in Patients with Cirrhosis – Anupama Patil – Bone Marrow Research

Colonic Mucosal Microbiota in Colorectal Cancer: A Single-Center Metagenomic Study in Saudi Arabia – Ahmed O. Alomair – Gastroenterology Research and Practice

Connecting homocysteine and obesity through pyroptosis, gut microbiome, epigenetics, peroxisome proliferator-activator receptor γ (PPARγ) and zinc finger protein 407 (Zfp407) – Anwesha Laha – Canadian Journal of Physiology and Pharmacology

Review: Sexual dimorphism of cardiometabolic dysfunction: Gut microbiome in the play? – Tzu-Wen L. Cross – Molecular Metabolism

Individuality and convergence of the infant gut microbiota during the first year of life – Eric J. de Muinck – Nature Communications

Reconstruction of the bifidobacterial pan-secretome reveals the network of extracellular interactions between bifidobacteria and the infant gutGabriele Andrea Lugli – Applied and Environmental Microbiology

Commentary: Beyond Oxalobacter: the gut microbiota and kidney stone formation – Gwen Falony – Gut

Nutritional modulation of the intestinal microbiota: future opportunities for the prevention and treatment of neuroimmune and neuroinflammatory disease – Vincent C.Lombardi – The Journal of Nutritional Biochemistry


Reproductive and Urinary Tract Microbiome

Review: Implantation failure of endometrial origin: what is new? –  Jose Bellver – Current Opinion in Obstetrics and Gynecology

Detecting viral genomes in the female urinary microbiome – Andrea Garretto – Journal of General Virology

Commentary: Regional Caesarean Delivery Practices, the Maternal-Infant Microbiome, and Risk for Asthma – Rebecca Entz – Journal of Obstetrics and Gynaecology Canada


Skin Microbiome

Insights into the skin microbiome dynamics of leprosy patients during multi-drug therapy and in healthy individuals from Brazil – Paulo E. S. Silva – Scientific Reports

Skin Microbiota in Obese Women at Risk for Surgical Site Infection After Cesarean Delivery – Kara M. Rood – Scientific Reports


Oral and Respiratory Microbiome

Analysis of the oral microbiome on the surface of modified dental polymers – Denise Tornavoide Castro – Archives of Oral Biology

Bacterial biogeography of adult airways in atopic asthma – Juliana Durack – Microbiome

Review: Adenotonsillar microbiome: an update – James Jordan Johnston – Postgraduate Medical Journal


Animal Microbiome

The canine gut microbiome is associated with higher risk of gastric dilatation-volvulus and high risk genetic variants of the immune system – Meredith A. J. Hullar – PLOS ONE

Propolis from Different Geographic Origins Suppress Intestinal Inflammation in a Model of DSS‐Induced Colitis is Associated with Decreased Bacteroides spp. in the Gut – Kai Wang – Molecular Nutrition & Food Research

Deficiency of BrpA in Streptococcus mutans Reduces Virulence in Rat Caries Model – Zezhang T. Wen – Molecular Oral Microbiology

Huddling remodels gut microbiota to reduce energy requirements in a small mammal species during cold exposure – Xue-Ying Zhang – Microbiome

Abnormal gut microbiota composition contributes to cognitive dysfunction in SAMP8 mice – Gaofeng Zhan – Aging

The role of regulator FucP in Edwardsiella tarda pathogenesis and the inflammatory cytokine response in tilapia – Jiayan Wu – Fish & Shellfish Immunology

Malassezia pachydermatis from animals: Planktonic and biofilm antifungal susceptibility and its virulence arsenal – Raimunda Sâmia Nogueira Brilhante – Veterinary Microbiology


Beneficial Microbes

Oral administration of Bifidobacterium bifidum TMC3115 to neonatal mice may alleviate IgE-mediated allergic risk in adulthood – R.Y. Cheng – Beneficial Microbes

Three-Month Feeding Integration With Bifidobacterium Strains Prevents Gastrointestinal Symptoms in Healthy Newborns – Irene Aloisio – Frontiers in Nutrition


Bioinformatics and Genomics

Review: Interrogating the microbiome: experimental and computational considerations in support of study reproducibility – Carine Poussin – Drug Discovery Today

CowPI: A Rumen Microbiome Focussed Version of the PICRUSt Functional Inference Software – Toby J. Wilkinson – Frontiers in Microbiology

Benchmark Evaluation of True Single Molecular Sequencing to Determine Cystic Fibrosis Airway Microbiome Diversity – Andrea Hahn – Frontiers in Microbiology

Next-Generation Machine Learning for Biological Networks – Diogo M. Camacho – Cell



May 16, 2018

Today we have a interesting set of reviews. In addtion: research about virome in infants, microbiome changes in Alzheimer’s disease and changes in neonate and maternal microbiome under gestational diabetes. We have also the report of the Oral Microbiome Bank of China and some papers about invertebrate microbiome.  


Human/General Microbiome

Review: Microbiome-Immune Interactions and Liver Disease – James H. Tabibian –  Clinical Liver Disease

Review: Microbial Metabolism in the Mammalian Gut: Molecular Mechanisms and Clinical Implications – Anne Hall – Journal of Pediatric Gastroenterology and Nutrition

Review: Starch Tolerance and the Short Bowel – Jan de Laffolie – Journal of Pediatric Gastroenterology and Nutrition

Review: Microbial Fermentation of Starch: Its Impact on the Range of Acceptable Carbohydrate Intake – Satish C. Kalhan – Journal of Pediatric Gastroenterology and Nutrition

Review: Pathways and mechanisms linking dietary components to cardiometabolic disease: thinking beyond calories – K. L. Stanhope – Obesity Reviews

Review: On the potential role of intestinal microbial community in hepatocarcinogenesis in chronic hepatitis B – Ashraf Mohamadkhani – Cancer Medicine

Review: The gut microbiota and the brain-gut-kidney axis in hypertension and chronic kidney disease – Tao Yang – Nature Reviews Nephrology

Review: Epithelial Barrier Dysfunctions in Atopic Dermatitis: A Skin-Gut-Lung Model Linking Microbiome Alteration and Immune Dysregulation – T.H. Zhu – British Journal of Dermatology

Review: Association between Fusobacterium nucleatum and colorectal cancer: Progress and future directions – Sheng Zhang – Journal of Cancer

Viromes of one year old infants reveal the impact of birth mode on microbiome diversity – Angela McCann​ – PeerJ

Dysbiosis of maternal and neonatal microbiota associated with gestational diabetes mellitus – Jinfeng Wang – Gut

Analysis of Gut Microbiome and Diet Modification in Patients with Crohn’s Disease – Sumathi Sankaran Walters – SOJ Microbiology & Infectious Diseases

Gut Microbiome is Altered in Patients with Alzheimer’s Disease – Zhuang, Zhen-Qian – Journal of Alzheimer’s Disease

The Oral Microbiome Bank of China – Peng Xian – International Journal of Oral Science


Animal Microbiome

Microbiota modification by probiotic supplementation reduces colitis associated colon cancer in mice – Maria Carolina S Mendes – World Journal of Gastroenterology

A cytokine network involving IL-36γ, IL-23, and IL-22 promotes antimicrobial defense and recovery from intestinal barrier damage – Vu L. Ngo – PNAS

Biodegradation of polyethylene and plastic mixtures in mealworms (larvae of Tenebrio molitor) and effects on the gut microbiome – Anja Malawi Brandon – Environmental Science and Technology

Supplementation with organic acids showing different effects on growth performance, gut morphology and microbiota of weaned pigs fed with highly or less digestible diets – S. Li – Journal of Animal Science

Metagenomics Analysis of Gut Microbiota in a High Fat Diet-Induced Obesity Mouse Model Fed with (-)-Epigallocatechin 3-O-(3-O-Methyl) Gallate (EGCG3”Me) – Xin Zhang – Molecular Nutrition and Food Research

Low bacterial community diversity in two introduced aphid pests revealed with 16S rRNA amplicon sequencing – Francisca Zepeda-Paulo​ – PeerJ

Uncovering the hidden players in Lepidoptera biology: the heritable microbial endosymbionts – Anne Duplouy – PeerJ

The influence of diet and environment on the gut microbial community of field crickets – Soon Hwee Ng – Ecology and Evolution

Changes in intestinal microbiota across an altitudinal gradient in the lizard Phrynocephalus vlangalii – Wenya Zhang – Ecology and Evolution


Food Microbiome

The changes of dominant lactic acid bacteria and their metabolites during corn stover ensiling – Zhenshang Xu – Journal of Applied Microbiology

Characterization of the Microbiota in Air- or Vacuum-Packed Crisp Grass Carp ( Ctenopharyngodon idella C. et V.) Fillets by 16S rRNA PCR-Denaturing Gradient Gel Electrophoresis and High-Throughput Sequencing – Ziqiang Pan – Journal of Food Protection

Succession of bacterial microbiota in tilapia fillets at 4 °C and in situ investigation of spoilers – Shan Duan – World Journal of Microbiology and Biotechnology



Preprint: Measures of reproducibility in sampling and laboratory processing methods in high-throughput microbiome analysisPatricia Vera-Wolf (and featuring our Microbiome Digest founder, Elisabeth Bik)BioRxiv

Benchmarking taxonomic assignments based on 16S rRNA gene profiling of the microbiota from commonly sampled environments – Alexandre Almeida – GigaScience

Uncovering the drivers of host-associated microbiota with joint species distribution modeling – Johannes R. Björk – Molecular Ecology


Beneficial Microbes and Compounds

Review: Vitamin D in inflammatory bowel disease: more than just a supplement – John Gubatan – Current Opinion in Gastroenterology

Review: Bleach for Atopic Dermatitis – Melody Maarouf – Dermatitis

Simultaneous Amelioratation of Colitis and Liver Injury in Mice by Bifidobacterium longum LC67 and Lactobacillus plantarum LC27 – Se-Eun Jang – Scientific Reports



Cross-specificity of protective human antibodies against Klebsiella pneumoniae LPS O-antigen – Tim Rollenske – Nature Immunology


Environmental Microbiome (including Built environments)

Responses of stream microbes to multiple anthropogenic stressors in a mesocosm study – Julia K.Nuy – Science of The Total Environment

Fine grained compositional analysis of Port Everglades Inlet microbiome using high throughput DNA sequencing – Lauren O’Connell​​ – PeerJ


Antimicrobial Resistance

Emerging Infectious Diseases, Antimicrobial Resistance and Millennium Development Goals: Resolving the Challenges through One Health – G. V. Asokan – Central Asian Journal of Global Health



Discovery and characterization of a prevalent human gut bacterial enzyme sufficient for the inactivation of a family of plant toxins – Nitzan Koppel – eLife

The Interaction of Anti-diabetic α-Glucosidase Inhibitors and Gut Bacteria α-Glucosidase – Kemin Tan – Protein Science


May 9, 2018

Have a good Wednesday! Today, we have an interesting set of papers about the effect of different compounds on microbiota, as well the effect of some probiotics. We have also a paper about the use binding of  immunoglobulin A by gut microbiota commensals as a potential mechanism for stabilization; we have also papers about virome from urinary and female reproductive tracts, a study a multi-site study of maternal microbiota.

Gut and General Microbiome

Introduction: The host-associated microbiome: Pattern, process and function – Laura Wegener Parfrey – Molecular Ecology (Special Issue: The host-associated microbiome: Pattern, process and function)

Gut microbiota utilize immunoglobulin A for mucosal colonization – G. P. Donaldson – Science

Low Maternal Microbiota Sharing across Gut, Breast Milk and Vagina, as Revealed by 16S rRNA Gene and Reduced Metagenomic Sequencing – Ekaterina Avershina – Genes

Editorial: Bacteria in the ageing gut: Did the taming of fire promote a long human lifespan?Antoine Danchin – Environmental Microbiology

Commentary: Insights into the role of gut microbiota in obesity: pathogenesis, mechanisms, and therapeutic perspectives – Lijuan Sun – Protein & Cell

Review: Gut microbiota derived metabolites in cardiovascular health and disease – Zeneng Wang – Protein & Cell

Treating Clostridium difficile infections: Should fecal microbiota transplantation be reclassified from investigational drug to human tissue?Mark StuntzContemporary Clinical Trials Communications

Effects of intestinal colonization by Clostridium difficile and Staphylococcus aureus on microbiota diversity in healthy individuals in China – Danfeng Dong – BMC Infectious Diseases

BaiCD gene cluster abundance is negatively correlated with Clostridium difficile infection – Philipp Solbach – PLoS ONE

Microbiome Responses to an Uncontrolled Short-Term Diet Intervention in the Frame of the Citizen Science ProjectNatalia S. Klimenko – Nutrients

Respiratory Tract Microbiome

Relation between lower respiratory tract microbiota and type of immune response against tuberculosis – Maede Nakhaee – Microbial Pathogenesis

Microbiome characteristics of induced sputum compared to bronchial fluid and upper airway samples – Shi‐qi An – Pediatric Pulmonology

The association between inflammation, the microbiome and urethane-induced pulmonary adenocarcinoma – Zenghua Deng – Oncology Letters

Urinary/Reproductive Tract Microbiome

Urinary Virome Perturbations in Kidney Transplantation – Tara K. Sigdel – Frontiers in Medicine

The Vaginal Eukaryotic DNA Virome and Preterm Birth – Kristine M. Wylie – American Journal of Obstetrics and Gynecology

Beneficial Microbes and Compounds

Walnut Consumption Alters the Gastrointestinal Microbiota, Microbially Derived Secondary Bile Acids, and Health Markers in Healthy Adults: A Randomized Controlled TrialHannah D Holscher – The Journal of Nutrition

The effect of vitamin D on intestinal inflammation and faecal microbiota in patients with ulcerative colitis – Mayur Garg – Journal of Crohn’s and Colitis

Exopolysaccharide from Bifidobacterium longum subsp. longum 35624™ modulates murine allergic airway responses – E. Schiavi – Beneficial Microbes

Modulatory effect of three probiotic strains on infants’ gut microbial composition and immunological parameters on a placebo-controlled, double-blind, randomised study – J. De Andrés – Beneficial Microbes

Review: Role of Lactobacillus reuteri in Human Health and Diseases – Qinghui Mu – Frontiers in Microbiology

Intake of phytic acid and myo-inositol lowers hepatic lipogenic gene expression and modulates gut microbiota in rats fed a high-sucrose diet – Yukako Okazaki – Biomedical Reports

Animal Microbiome

Feminizing Wolbachia influence microbiota composition in the terrestrial isopod Armadillidium vulgare – Jessica Dittmer – Scientific Reports

Gut microbiomes of wild great apes fluctuate seasonally in response to diet – Allison L. Hicks – Nature Communications

Endophytic Fungi in Species of Artemisia – Andreea Cosoveanu – Journal of Fungi

Tributyltin exposure induces gut microbiome dysbiosis with increased body weight gain and dyslipidemia in mice – Hao Guo – Environmental Toxicology and Pharmacology

Food Microbiome

Unravelling the contribution of lactic acid bacteria and acetic acid bacteria to cocoa fermentation using inoculated organisms – Van Thi Thuy Ho – International Journal of Food Microbiology

Validation of standard method EN ISO 22964:2017 – Microbiology of the food chain – Horizontal method for the detection of Cronobacter sppAmparo de Benito – International Journal of Food Microbiology

Plant and Soil Microbiome

Mycobiome analysis of asymptomatic and symptomatic Norway spruce trees naturally infected by the conifer pathogens Heterobasidion spp. – Andriy Kovalchuk – Environmental Microbiology Reports

Perspective: Core microbiomes for sustainable agroecosystems – Hirokazu Toju – Nature Plants

Meetings: Holobiont: a conceptual framework to explore the eco-evolutionary and functional implications of host-microbiota interactions in all ecosystemsDenis Faure – New Phytologist


Marker microbiome clusters are determined by operational parameters and specific key taxa combinations in anaerobic digestion – Susanne Theuerl – Bioresource Technology


May 3, 2018

Have a good Thursday! Today, in Microbiome Digest: studies about Bacterial Vaginosis, dysbiosis associated with Hepatitis C infection, oral microbiome and oral cancer, microbiome reestablishment after cleaning, detection of microbes in culture-negative intra-amniotic infections and more…

Human Microbiome and General

A Prospective Metagenomic and Metabolomic Analysis of the Impact of Exercise and/or Whey Protein Supplementation on the Gut Microbiome of Sedentary Adults – Owen Cronin – mSystems

Review: Relationship between diet, the gut microbiota, and brain function – Anouk C Tengeler – Nutrition Reviews

Identification of Key Bacteria Involved in the Induction of Incident Bacterial Vaginosis: A Prospective Study – Christina A Muzny – The Journal of Infectious Diseases

Gut Dysbiosis Associated With Hepatitis C Virus InfectionTakako Inoue – Clinical Infectious Diseases

Research Highlight: Fibre aids fight against nasty gut infectionNature

Review: The Intestinal Epithelium: Central Coordinator of Mucosal Immunity – Joannie M. Allaire – Trends in Immunology

Humans as holobionts: implications for prevention and therapy -Maarten van de Guchte – Microbiome

Obese Subjects With Specific Gustatory Papillae Microbiota and Salivary Cues Display an Impairment to Sense Lipids – Philippe Besnard – Scientific Reports

Bacterial culture-negative subclinical intra-amniotic infection can be detected by bacterial 16S ribosomal DNA-amplifying polymerase chain reaction – Sachi Morimoto – Japanese Journal of Infectious Diseases

Impact of HIV and Type 2 diabetes on Gut Microbiota Diversity, Tryptophan Catabolism and Endothelial Dysfunction – Hedda Hoel – Scientific Reports

New Horizons in Obstructive Lung Disease. Microbiome Dynamics, Pulmonary Artery Enlargement, and Endobronchial Valves – Pujan H. Patel – American Journal of Respiratory and Critical Care Medicine

Oral Microbiota Community Dynamics Associated With Oral Squamous Cell Carcinoma Staging – Chia-Yu Yang – Frontiers in Microbiology

Bifidobacterium longum subsp infantis CECT7210-supplemented formula reduces diarrhea in healthy infants: a randomized controlled trial – Joaquin Escribano – Pediatric Research


Animal Microbiome

Transplantation of human microbiota into conventional mice durably reshapes the gut microbiota – Laura Wrzosek – Scientific Reports

Restructuring of the Gut Microbiome by Intermittent Fasting Prevents Retinopathy and Prolongs Survival in db/db Mice – Eleni Beli – Diabetes

Effects of shenling baizhu powder herbal formula on intestinal microbiota in high-fat diet-induced NAFLD rats – Yupei Zhang – Biomedicine & Pharmacotherapy

The effects of sewage treatment plant effluents on hepatic and intestinal biomarkers in common carp (Cyprinus carpio) – Sidika Sakalli – Science of The Total Environment

Feminizing Wolbachia influence microbiota composition in the terrestrial isopod Armadillidium vulgare – Jessica Dittmer – Scientific Reports

Preprint: Intestinal microbiota of whitefish (Coregonus sp.) species pairs and their hybrids in natural and controlled environment – Maelle Sevellec – bioRxiv

Gut microbiomes of wild great apes fluctuate seasonally in response to diet – Allison L. Hicks – Nature Communications

Dietary polyphenols enhance optogenetic recall of fear memory in hippocampal dentate gyrus granule neuron subpopulations – Chad Smith – Communications Biology


Built Environments

The Reestablishment of Microbial Communities after Surface Cleaning in Schools – Sarah E. Kwan – Journal of Applied Microbiology


Bioinformatics and Genomics

SHI7 Is a Self-Learning Pipeline for Multipurpose Short-Read DNA Quality Control – Gabriel A. Al-Ghalith – mSystems

Phylogenetic Placement of Exact Amplicon Sequences Improves Associations with Clinical Information – Stefan Janssen – mSystems

Identifying Group-Specific Sequences for Microbial Communities Using Long k-mer Sequence Signatures – Ying Wang – Frontiers in Microbiology


Plant/Soil Microbiomes

The role of bacteria in pine wilt disease: insights from microbiome analysis – Marta Alves – FEMS Microbiology Ecology


Other (Microbiome-related)

Review: Food Intake and Eating Behavior After Bariatric Surgery – Werd Al-Najim – Physiological Reviews

Review: Microfluidic Organ-on-a-Chip Models of Human Intestine – Amir Bein – Cellular and Molecular Gastroenterology and Hepatology

Preprint: CRISPR-Cas blocks antibiotic resistance plasmid transfer between Enterococcus faecalis strains in the gastrointestinal tract – Valerie J Price – bioRxiv


April 27, 2018

Have a good Friday! Today’s Digest include a set of interesting reviews about the Hologenome concept, Clostridium difficile, the relation between microbiota and tuberculosis and microbiota transplantation. This digest also contains interesting articles about the use of dietary studies to control diet in microbiota studies, microbiome in cancer, microbiome and depression in rats and microbiome in soil from the Atacama’s desert.


Human and General Microbiome

Bile Acids and the Gut Microbiome as Potential Targets for NAFLD Treatment – Lixin Zhu – Journal of Pediatric Gastroenterology and Nutrition

Review: The role of fecal microbiota transplantation in inflammatory bowel disease – Irene D’Odorico – Journal of Digestive Diseases

Review: Put “gender glasses” on the effects of phenolic compounds on cardiovascular function and diseases – Ilaria Campesi – European Journal of Nutrition

Use of dietary indices to control for diet in human gut microbiota studies – Ruth C. E. Bowyer – Microbiome

Review: The hologenome concept of evolution after 10 years – Eugene Rosenberg – Microbiome

Pharmabiotic Manipulation of the Microbiota in Gastrointestinal Disorders: A Clinical Perspective – Fanny Giron – Journal of Neurogastroenterology and Motility

Microbiota potential for the treatment of sexual dysfunction – Hassan Tirandaz – Medical Hypotheses

Gut microbiome analysis identifies potential aetiological factors in acute gastroenteritis – Natalia Castaño-Rodríguez – Immunity and Infection

Skin microbiota and allergic symptoms associate with exposure to environmental microbes – Jenni Lehtimäki – PNAS

Gut microbiome of Moroccan colorectal cancer patients – Imane Allali – Medical Microbiology and Immunology

Systematic Review: Safety and efficacy of encapsulated fecal microbiota transplantation for recurrent Clostridium difficile infection: a systematic review – Umair Iqbal – European Journal of Gastroenterology & Hepatology

Alterations in Enteric Virome Associate With Colorectal Cancer and Survival Outcomes – Geicho Nakatsu – Gastroenterology

High relative abundance of firmicutes and increased TNF-α levels correlate with obesity in children – Yaneth C Orbe-Orihuela – Salud Pública de México (Article in English)

Perspective: Why does the microbiome affect behaviour? – Katerina V.-A. Johnson – Nature Reviews Microbiology

Research Highlight: Exercise affects gut microbiota and bone – Claire Greenhill – Nature Reviews Endocrinology

Review: Clostridium difficile – From Colonization to Infection – Holger Schäffler – Frontiers in Microbiology

MiniReview: New Players in Immunity to Tuberculosis: The Host Microbiome, Lung Epithelium, and Innate Immune Cells – Nancy Gupta – Frontiers in Immunology


Animal Microbiome

A meta-barcoding approach to assess and compare the storage temperature-dependent bacterial diversity of gilt-head sea bream (Sparus aurata) originating from fish farms from two geographically distinct areas of Greece – Foteini F.Parlapani – International Journal of Food Microbiology

High-fat diet induces depression-like behaviour in mice associated with changes in microbiome, neuropeptide Y, and brain metabolome – Ahmed M. Hassan – Nutritional Neuroscience

Cascading effects on bacterial communities: cattle grazing causes a shift in the microbiome of a herbivorous caterpillar – Tali S. Berman – The ISME Journal

Microbiomes associated with bovine periodontitis and oral health – Ana C.Borsanelli – Veterinary Microbiology

Microbiota-accessible carbohydrates suppress Clostridium difficile infection in a murine model – Andrew J. Hryckowian – Nature Microbiology

High-Fat Diet Induces Dysbiosis of Gastric Microbiota Prior to Gut Microbiota in Association With Metabolic Disorders in Mice – Cong He – Frontiers in Microbiology

Differential Microbial Communities of Omnivorous and Herbivorous Cattle in Southern China – Susanna K.P.Lau – Computational and Structural Biotechnology Journal


Plant/Soil Microbes

A microorganisms’ journey between plant generations – Nathan Vannier – Microbiome

MYB72-dependent coumarin exudation shapes root microbiome assembly to promote plant health – Ioannis A. Stringlis – PNAS

Bacterial potentials for uptake, solubilization and mineralization of extracellular phosphorus in agricultural soils are highly stable under different fertilization regimes – Martin Grafe – Environmental Microbiology Reports



Microbiome analysis and bacterial isolation from Lejía Lake soil in Atacama Desert – Dinka Mandakovic – Extremophiles


Beneficial Microbes and Compounds

Current and future uses of probiotics – Georgia Tanner – JAAPA

Barley β-glucan improves metabolic condition via short-chain fatty acids produced by gut microbial fermentation in high fat diet fed mice – Junki Miyamoto – PLoS One

Systematic Review: Are probiotic treatments useful on fibromyalgia syndrome or chronic fatigue syndrome patients? A systematic review – P. Roman – Beneficial Microbes

Review: The application of in vitro human intestinal models on the screening and development of pre- and probiotics – V.T. Pham – Beneficial Microbes


Antimicrobial Resistance

Acquisition of multidrug-resistant organisms in the absence of antimicrobial exposure – E M C D’Agata – Clinical Infectious Diseases


Food Microbiome

Variation in the Microbiome, Trichothecenes, and Aflatoxins in Stored Wheat Grains in Wuhan, China – Qing-Song Yuan – Toxins



Review: Single-cell metagenomics: challenges and applications – Yuan Xu – Protein & Cell


April 24, 2018

Today, after a hiatus, we have a new and big digest. Have a good Tuesday!

Gut Or General Microbiome

Editorial: Metagenomics, culturomics, and the human gut microbiota – Sophie Amrane – Expert Review of Anti-infective Therapy

Review: Disruptions in gut microbial-host co-metabolism and the development of metabolic disorders – Cynthia Rajani – Clinical Science

Metabolic retroconversion of trimethylamine N-oxide and the gut microbiota – Lesley Hoyles – Microbiome

Review: Factors influencing horizontal gene transfer in the intestine – Ximin Zeng – Animal Health Research Reviews

Commentary: Help, hope and hype: ethical considerations of human microbiome research and applications – Yonghui Ma – Protein & Cell

A System Biology Perspective on Environment-Host-Microbe Interactions – Lianmin Chen – Human Molecular Genetics

Comment on: effects of sleeve gastrectomy on the composition and diurnal oscillation of gut microbiota related to the metabolic improvements – Tammy L.Kindel – Surgery for Obesity and Related Diseases

Dietary Interventions to Modulate the Gut Microbiome—How Far Away Are We From Precision Medicine – Francesca De Filippis – Inflammatory Bowel Diseases

Targeting the gut microbiome to treat the osteoarthritis of obesity – Eric M. Schott – JCI Insight

Increased prevalence of pathogenic bacteria in the gut microbiota of infants at risk of developing celiac disease: the PROFICEL study – Marta Olivares –  Gut Microbes

Genome sequence and description of Gracilibacillus timonensis sp. nov. strain Marseille-P2481T , a moderate halophilic bacterium isolated from the human gut microflora – Awa Diop – Microbiology Open

Inflammasomes make the case for littermate-controlled experimental design in studying host-microbiota interactions – Michail Mamantopoulos – Gut Microbes

No Significant Association Between the Fecal Microbiome and the Presence of Irritable Bowel Syndrome-type Symptoms in Patients with Quiescent Inflammatory Bowel Disease – Oliver Shutkever –  Inflammatory Bowel Diseases

Research Highlight: Microbiome promotes pancreatic cancer – Iain Dickson – Nature Reviews Gastroenterology & Hepatology

Deciphering human gut microbiota-nutrient interactions: a role for biochemistry – Carina Chittim – Biochemistry

Letter: Defining the Impact of Host Genotypes on Microbiota Composition Requires Meticulous Control of Experimental Variables –  Andy Wullaert – Cell Immunity

Review: Engineered Human Gastrointestinal Cultures to Study the Microbiome and Infectious Diseases – Sarah E.Blutt – Cellular and Molecular Gastroenterology and Hepatology

The Role of Macrophage Migration Inhibitory Factor in the Function of Intestinal Barrier – Milica Vujicic- Scientific Reports

Perspective: Urbanization and the gut microbiota in health and inflammatory bowel disease – Tao Zuo – Nature Reviews Gastroenterology & Hepatology

A systems biology approach to predict and characterize human gut microbial metabolites in colorectal cancer – QuanQiu Wang – Scientific Reports

Review: The human gut microbiota: metabolism and perspective in obesity – Aline Corado Gomes – Gut Microbes

Association between the Dietary Inflammatory Index (DII) and urinary enterolignans and C-reactive protein from the National Health and Nutrition Examination Survey-2003-2008 – Nitin Shivappa – European Journal of Nutrition

Case Report: The Effect of Fecal Microbiota Transplantation on a Child with Tourette Syndrome – Huijun Zhao – Case Reports in Medicine

Current evidence linking diet to gut microbiota and brain development and function – Florencia Ceppa – International Journal of Food Sciences and Nutrition

Using standard microbiome reference groups to simplify beta-diversity analyses and facilitate independent validation – Marlena Maziarz – Bioinformatics

Review: Gut microbiota, metabolism and psychopathology: A critical review and novel perspectives – Robin N. Groen – Critical Reviews in Clinical Laboratory Sciences

The Role of Gut Microbiota in Obesity and Type 2 and Type 1 Diabetes Mellitus: New Insights into “Old” Diseases – Igor Alexander Harsch – Medical Sciences

Biogeography and environmental conditions shape bacteriophage-bacteria networks across the human microbiome – Geoffrey D. Hannigan – PLoS Computational Biology


Respiratory Microbiome

Prenatal antibiotic exposure and childhood asthma: a population-based study – Keely Loewen – European Respiratory Journal

Impact of gut colonization with butyrate producing microbiota on respiratory viral infection following allo-HCT – Bastiaan W. Haak – Blood

Oropharyngeal and nasopharyngeal decontamination with chlorhexidine gluconate in lung cancer surgery: a randomized clinical trial – Xavier Benoit D’Journo – Intensive Care Medicine

Impact of Long-Term Erythromycin Therapy on the Oropharyngeal Microbiome and Resistance Gene Reservoir in Non-Cystic Fibrosis Bronchiectasis – Jocelyn M. Choo – mSphere

Neonates colonized with pathogenic bacteria in the airways have a low-grade systemic inflammation – Nadia Rahman Fink – Allergy

Next-Generation Immune Repertoire Sequencing as a Clue to Elucidate the Landscape of Immune Modulation by Host–Gut Microbiome Interactions – Tatsuo Ichinohe – Frontiers in Immunology


Oral Microbiome

Metagenomic analysis of oral microbiome in young children aged 6‐8 y living in a rural isolated Chinese province – Yuan Xu – Oral Diseases

Microbiota and Metatranscriptome Changes Accompanying the Onset of Gingivitis – Emily M. Nowicki – mBio

Do we treat our patients or rather periodontal microbes with adjunctive antibiotics in periodontal therapy? A 16S rDNA microbial community analysis – Daniel Hagenfeld – PLoS One

The interplay between oral microbiome, lifestyle factors and genetic polymorphisms in the risk of oral squamous cell carcinoma – Jenn-Ren Hsiao – Carcinogenesis

Dynamic Alterations in Salivary Microbiota Related to Dental Caries and Age in Preschool Children With Deciduous Dentition: A 2-Year Follow-Up Study – Lei Xu – Frontiers in Physiology


Reproductive / Urinary tract Microbiome

How uterine microbiota might be responsible for a receptive, fertile endometrium – Marilen Benner – Human Reproduction Update

Culturing of female bladder bacteria reveals an interconnected urogenital microbiota – Krystal Thomas-White – Nature Communications


Fecal Microbiota Transplant

Editorial: Is fecal microbiota transplantation a temporary patch for treatment of Clostridium difficile infection or a new frontier of therapeutics? – Alexander Khoruts – Expert Review of Gastroenterology & Hepatology

Case Report: ANCA Vasculitis and Hemophagocytic Lymphohistiocytosis following a Fecal Microbiota Transplant – Adam Amlani – Case Reports in Rheumatology

Regional variability in fecal microbiota transplantation practices: a survey of the Southern Ontario Fecal Microbiota Transplantation Movement – Susy S. Hota – CMAJ Open

Commentary: Bacteriophage transfer during faecal microbiota transplantation in Clostridium difficile infection is associated with treatment outcome – Blessing O. Anonye – Frontiers in Cellular and Infection Microbiology

Fecal microbiota transplantation reverses antibiotic and chemotherapy-induced gut dysbiosis in mice – Quentin Le Bastard – Scientific Reports


Animal Microbiome and Animal Experiments

Evaluation of a therapy for Idiopathic Chronic Enterocolitis in rhesus macaques (Macaca mulatta) and linked microbial community correlates – Joshua M. Taylor​​ – PeerJ

Comparative analyses of the gut microbiota among three different wild geese species in the genus Anser – Wen Wang – Journal of Basic Microbiology

Exposure to concentrated ambient PM2.5 alters the composition of gut microbiota in a murine model – Wanjun Wang – Particle and Fibre Toxicology

Imidacloprid decreases honey bee survival but does not affect the gut microbiome – Kasie Raymann – Applied and Environmental Microbiology

Letter: Bile Acids and the Microbiome in the Cow: Lack of Deoxycholic Acid Hydroxylation – Alan F. Hofmann – Lipids

Akkermansia muciniphila can reduce the damage of gluco/lipotoxicity, oxidative stress, and inflammation and normalize intestine microbiota in streptozotocin-induced diabetic rats – Ling Zhang – Pathogens and Disease

The impact of genome variation and diet on the metabolic phenotype and microbiome composition of Drosophila melanogaster – Lisa Jehrke –  Scientific Reports

Fecal microbial composition associated with variation in feed efficiency in pigs depends on diet and sex – Lisanne M G Verschuren – Journal of Animal Science

Discovery of a mcr-1-bearing plasmid in commensal colistin-resistant Escherichia coli from healthy broilers in Faisalabad, Pakistan – Jiali Lv – Virulence

Pre-colonization with the commensal fungus Candida albicans reduces murine susceptibility to Clostridium difficile infection – Laura Markey – Gut Microbes

PCBs-high-fat diet interactions as mediators of gut microbiota dysbiosis and abdominal fat accumulation in female mice – Yulang Chi – Environmental Pollution

Metagenome and Culture-Based Methods Reveal Candidate Bacterial Mutualists in the Southern House Mosquito (Diptera: Culicidae) – Aparna Telang – Journal of Medical Entomology

Polysaccharide of Hericium erinaceus attenuates colitis in C57BL/6 mice via regulation of oxidative stress, inflammation-related signaling pathways and modulating the composition of the gut microbiota – Yilin Ren – The Journal of Nutritional Biochemistry

Potent SGLT1/2 Dual Inhibition Improves Glycemic Control Without Marked Gastrointestinal Adaptation or Colonic Microbiota Changes in Rodents – Fuyong Du – Journal of Pharmacology and Experimental Therapeutics

Similarity of the dog and human gut microbiomes in gene content and response to diet – Luis Pedro Coelho – Microbiome

Direct and Indirect Effects of Penguin Feces on Microbiomes in Antarctic Ornithogenic Soils – Yudong Guo – Frontiers in Microbiology

Stem Cell Transcription Factor FoxO Controls Microbiome Resilience in Hydra – Benedikt M. Mortzfeld – Frontiers in Microbiology

The effects of baicalein on cortical pro-inflammatory cytokines and the intestinal microbiome in senescence accelerated mouse prone 8 – Li Gao – ACS Chemical Neuroscience

Biases from different DNA extraction methods in intestine microbiome research based on 16S rDNA sequencing: a case in the koi carp, Cyprinus carpio var. Koi – Zhuoran Han – Microbiology Open


Built Environments

A comparison of methods used to unveil the genetic and metabolic pool in the built environment – Cinta Gomez-Silvan – Microbiome

Metabolism and Biodegradation of Spacecraft Cleaning Reagents by Strains of Spacecraft-Associated Acinetobacter – Mogul Rakesh – Astrobiology


Pathogen Research

The Critical Role of Zinc in a New Murine Model of Enterotoxigenic  E. coli 1 (ETEC) Diarrhea – DT Bolick  – Infection and Immunity

Review: Effects of antibiotic resistance (AR) and microbiota shifts on Campylobacter jejuni-mediated diseases – Phillip T. Brooks – Animal Health Research Reviews

A quality improvement initiative to reduce necrotizing enterocolitis across hospital systems – Amy T. Nathan – Journal of Perinatology

Quantitative Simulations Predict Treatment Strategies Against Fungal Infections in Virtual Neutropenic Patients – Sandra Timme – Frontiers in Immunology

Review: Helicobacter pylori the Latent Human Pathogen or an Ancestral Commensal Organism – Jackie Li – Frontiers in Microbiology

Heterogeneous ceramide distributions alter spatially resolved growth of Staphylococcus aureus on human stratum corneum – Joseph M. Cleary – Journal of the Royal Society Interface



Viral Diversity of House Mice in New York City – Simon H. Williams – mBio

Subclinical cytomegalovirus infection associates with altered host immunity, gut microbiota and vaccine responses – Clarissa Santos Rocha – Journal of Virology


Antimicrobial Research

Antimicrobial resistance: from basic science to translational innovation – Jun Lin –  Animal Health Research Reviews


Plant/Environment Microbiome

Drought delays development of the sorghum root microbiome and enriches for monoderm bacteria – Ling Xu – PNAS

Assessment of toxic impact of metals on proline, antioxidant enzymes, and biological characteristics of Pseudomonas aeruginosa inoculated Cicer arietinum grown in chromium and nickel-stressed sandy clay loam soils – Saima Saif – Environmental Monitoring and Assessment

The first Taxus rhizosphere microbiome revealed by shotgun metagenomic sequencing – Da‐Cheng Hao – Journal of Basic Microbiology

Exposure to nanoplastics disturbs the gut microbiome in the soil oligochaete Enchytraeus crypticus – Bo-Kai Zhu – Environmental Pollution

Comparative Microbiome Analysis of a Fusarium Wilt Suppressive Soil and a Fusarium Wilt Conducive Soil From the Châteaurenard Region – Katarzyna Siegel-Hertz – Frontiers in Microbiology


Food Microbes

Towards better microbial safety of fresh produce: Chlorophyllin-based photosensitization for microbial control of foodborne pathogens on cherry tomatoes – Egle Paskeviciute – Journal of Photochemistry and Photobiology B: Biology

Metaproteomics of Microbiota in Naturally Fermented Soybean Paste, Da‐jiang – Ping Zhang – Journal of Food Science


Drugs, Beneficial Microbes and Compounds

Age-Related Changes in the Natural Killer Cell Response to Seasonal Influenza Vaccination Are Not Influenced by a Synbiotic: a Randomised Controlled Trial – Agnieszka Przemska-Kosicka – Frontiers in Immunology

4G-β-D-galactosylsucrose as a prebiotics may improve underweight in inpatients with schizophrenia – Takahiko Nagamine – Nihon Shokuhin Men’eki Gakkai

An approach on the potential use of probiotics in the treatment of skin conditions: acne and atopic dermatitis – Vitória H. M. Mottin – International Journal of Dermatology

Effects of Prebiotic Fiber Xylooligosaccharide in Adenine induced Nephropathy in Mice – Jieping Yang – Molecular Nutrition and Food Research

Anti-inflammatory effect of multistrain probiotic formulation (L. rhamnosus, B. lactis, and B. longum) – Marzia Sichetti – Nutrition

A combination of Lactobacillus mali APS1 and dieting improved the efficacy of obesity treatment via manipulating gut microbiome in mice – Yung-Tsung Chen – Scientific Reports

The Potential Effect of Chinese Herbal Formula Hongqijiangzhi Fang in Improving NAFLD: Focusing on NLRP3 Inflammasome and Gut Microbiota – Shu Liang – Evidence-Based Complementary and Alternative Medicine

Cationic amphiphilic bolaamphiphile-based delivery of antisense oligonucleotides provides a potentially microbiome sparing treatment for C. difficile – Arun K. Sharma – The Journal of Antibiotics

A probiotic modulates the microbiome and immunity in multiple sclerosis – Stephanie K. Tankou – Annals of Neurology

Comprehensive comparison of polysaccharides from Ganoderma lucidum and G. sinense: chemical, antitumor, immunomodulating and gut-microbiota modulatory properties – Li-Feng Li – Scientific Reports

Anti-diabetic mechanism of dietary polysaccharides based on their gastrointestinal functions – Jie-Lun Hu – Journal of Agricultural and Food Chemistry

The Effects of Synbiotic Supplementation on Body Mass Index, Metabolic and Inflammatory Biomarkers, and Appetite in Patients with Metabolic Syndrome: A Triple-Blind Randomized Controlled Trial – Samira Rabiei – Journal of Dietary Supplements


Bioinformatics and Methods

MEGAN-LR: new algorithms allow accurate binning and easy interactive exploration of metagenomic long reads and contigs – Daniel H. Huson – Biology Direct

KDiamend: a package for detecting key drivers in a molecular ecological network of disease – Mengxuan Lyu – BMC Systems Biology

ViDiT-CACTUS: an inexpensive and versatile library preparation and sequence analysis method for virus discovery and other microbiology applications – Joost Theo Petra Verhoeven – Canadian Journal of Microbiology

Phylogenomic Analysis of β-Lactamase in Archaea and Bacteria Enables the Identification of Putative New Members – Vivek Keshri – Genome Biology and Evolution


April 3, 2018

Human Microbiome

Non-Ischemic Heart Failure With Reduced Ejection Fraction Is Associated With Altered Intestinal Microbiota – Themistoklis Katsimichas – Circulation Journal

The impact of antibiotics on the Intestinal microbiota needs to be re-defined in order to optimize the antibiotic usage – Bryan Coburn – Clinical Microbiology and Infection

The direct and indirect association of cervical microbiota with the risk of cervical intraepithelial neoplasia – Chaoting Zhang – Cancer Medicine

Review: The use of probiotics in different phases of diverticular disease – Veronica Ojetti – Reviews on Recent Clinical Trials

Fecal microbiota transplantation and its potential therapeutic uses in gastrointestinal disorders – Ryan D. Heath – Northern clinics of Istanbul

Dysbiosis of the salivary microbiota in pediatric-onset primary sclerosing cholangitis and its potential as a biomarker – Kentaro Iwasawa – Scientific Reports

Microbiota Composition May Predict Anti-Tnf Alpha Response in Spondyloarthritis Patients: an Exploratory Study – Thomas Bazin – Scientific Reports

Research Highlight: Obesity: ANGPTL4 — the link binding obesity and glucose intolerance – Alan Morris – Nature Reviews Endocrinology

Influence of intrauterine administration of Lactobacillus buchneri on reproductive performance and pro-inflammatory endometrial mRNA expression of cows with subclinical endometritis – S. Peter – Scientific Reports

Review: Overview of Current Concepts in Gastric Intestinal Metaplasia and Gastric Cancer – David S. Jencks – Gastroenterology & Hepatology


Animal Microbiome

Psychoneuroimmunology and immunopsychiatry of zebrafish – Murilo S.de Abreu – Psychoneuroendocrinology

Regulation of growth, intestinal microbiota, non-specific immune response and disease resistance of sea cucumber Apostichopus japonicus (Selenka) in biofloc systems – Jinghua Chen – Fish & Shellfish Immunology

Loss of microRNA-21 Influences the Gut Microbiota Causing Reduced Susceptibility in a Murine Model of Colitis – Daniel G W Johnston – Journal of Crohn’s and Colitis

Influence of Long-Term Feeding Antibiotics on the Gut Health of Zebrafish – Zhou Li – Zebrafish

Effects of Intestinal Microbiota on Brain Development in Humanized Gnotobiotic Mice – Jing Lu – Scientific Reports

Long-term Western diet fed apolipoprotein E-deficient rats exhibit only modest early atherosclerotic characteristics – Ida Rune – Scientific Reports



Guided Protocol for Fecal Microbial Characterization by 16S rRNA-Amplicon Sequencing – Ayelet Di Segni – Journal Of Visualized Experiments (It includes a video)


Food Microbes

Tetracycline resistance in lactobacilli isolated from Serbian traditional raw milk cheeses – Tijana Ledina – Journal of Food Science and Technology



Case Report: Successful Fecal Microbiota Transplantation in a Patient with Severe Complicated Clostridium difficile Infection after Liver Transplantation – Schneider K.M. – Case Reports in Gastroenterology

Review: Significance of Streptococcus gallolyticus subsp. gallolyticus Association With Colorectal Cancer – Ewa Pasquereau-Kotula – Frontiers in Microbiology

Review: Helicobacter pylori the Latent Human Pathogen or an Ancestral Commensal Organism – Jackie Li –  Frontiers in Microbiology

Fungi-Induced Upper and Lower Respiratory Tract Allergic Diseases: One Entity – Aleksandra Barac – Frontiers in Microbiology

Genetic and Virulent Difference Between Pigmented and Non-pigmented Staphylococcus aureus – Jing Zhang – Frontiers in Microbiology


Environmental Microbes

Exploring Biogeochemistry and Microbial Diversity of Extant Microbialites in Mexico and Cuba – Patricia M. Valdespino-Castillo – Frontiers in Microbiology

Direct and Indirect Effects of Penguin Feces on Microbiomes in Antarctic Ornithogenic Soils – Yudong Guo – Frontiers in Microbiology



Combination of peracetic acid and ultrasound reduces Salmonella Typhimurium on fresh lettuce (Lactuca sativa L. var. crispa) – Luiza Oliveira Silveira – Journal of Food Science and Technology

Recent advances in the physiopathology of IgA nephropathy – Renato C. Monteiro – Néphrologie & Thérapeutique