April 17, 2019

Today’s Digest contains quite a few news articles. Features for today include a review on the importance of proper controls in microbiome studies, a patent for one method of analyzing microbiome dynamics (really?), and the NASA Twins Study, how can one year in space change your gut microbiota and much more? Enjoy reading!

General microbiology

Guideline: Microbiology Investigation Criteria for Reporting Objectively (MICRO): a framework for the reporting and interpretation of clinical microbiology data – Paul Turner & Andrew Fox-Lewis et al. – BMC Medicine

** Patent: Method of analyzing microbiome – E Segal & E Elinav

Combined deterministic and stochastic processes control microbial succession in replicate granular biofilm reactors – R Liébana et al. – Environmental Science & Technology

** Uncorrected proof: Issues and current standards of controls in microbiome research – Bastian V.H. Hornung et al. – FEMS Microbiology Ecology

Pregnancy and early life

Review: Intestinal Microbiota in Early Life and Its Implications on Childhood Health – Lu Zhuang et al. – Genomics, Proteomics & Bioinformatics

Cancer microbiome

PDF: Gastric Microbiota in Helicobacter pylori-Negative and -Positive Gastritis Among High Incidence of Gastric Cancer Area – Boldbaatar Gantuya et al. – Cancers

Human respiratory microbiome

Review: Microbes, metabolites, and the gut–lung axis – Anh Thu Dang & Benjamin J. Marsland – Mucosal Immunology

Microbial contributions to bronchial asthma occurrence in children: A metagenomic study – Man Tian et al. – Journal of Cellular Biochemistry

Human gut microbiome

Review: A Review on Bile Acids: Effects of the Gut Microbiome, Interactions with Dietary Fiber, and Alterations in the Bioaccessibility of Bioactive Compounds – Jashbir Singh et al. – Journal of Agricultural and Food Chemistry

Increased mucosal neutrophil survival is associated with altered microbiota in HIV infection – Tiffany Hensley-McBain et al. – PLoS Pathogens

Review: Thinking bigger: How early life environmental exposures shape the gut microbiome and influence the development of asthma and allergic disease – Hind Sbihi et al. – Allergy

** The NASA Twins Study: A multidimensional analysis of a year-long human spaceflight – Francine E. Garrett-Bakelman et al. – Science


Review: Changes in the Human Metabolome Associated With Alcohol Use: A Review – Taija Voutilainen & Olli Kärkkäinen – Alcohol and Alcoholism

Animal microbiome

Dynamic changes in rumen fermentation and bacterial community following rumen fluid transplantation in a sheep model of rumen acidosis: implications for rumen health in ruminants – Junhua Liu et al. – The FASEB Journal

Rainbow trout (Oncorhynchus mykiss) gut microbiota is modulated by insect meal from Hermetia illucens prepupae in the diet – Genciana Terova et al. – Reviews in Fish Biology and Fisheries

Plant, root and soil microbiome

Effects of mycorrhizae and water conditions on perennial ryegrass growth in rare earth tailings – Qiao Yang et al. – RSC Advance

Niche separation of species of entomopathogenic fungi within the genera Metarhizium and Beauveria in different cropping systems in Mexico – J.A. Cabrera-Mora et al. – Fungal Ecology

Soil abiotic properties and plant functional traits mediate associations between soil microbial and plant communities during a secondary forest succession on the Loess Plateau – Yongfu Chai et al. – Frontiers in Microbiology

Microbial Diversity and Antimicrobial Resistance Profile in Microbiota from Soils of Conventional and Organic Farming Systems – Julija Armalytė et al. – Frontiers in Microbiology

Effects of elevated temperature and elevated CO2 on soil nitrification and ammonia-oxidizing microbial communities in field-grown crop – Linh T.T. Nguyen et al. – Science of The Total Environment

Tropical forest conversion to rubber plantation affects soil micro- & mesofaunal community & diversity – Dharmesh Singh et al. – Scientific Reports

Water and extremophile microbiome

Sulfate reduction by a haloalkaliphilic bench-scale sulfate-reducing bioreactor and its bacterial communities at different depths – Tingzhen Mu et al. – Biochemical Engineering Journal

Extremely acidic environment: Biogeochemical effects on algal biofilms – Ana Teresa Luís et al. – Ecotoxicology and Environmental Safety

Proliferation of hydrocarbon-degrading microbes at the bottom of the Mariana Trench – Jiwen Liu & Yanfen Zheng et al. – Microbiome

Metagenomic insights to understand transient influence of Yamuna River on taxonomic and functional aspects of bacterial and archaeal communities of River Ganges – Rachel Samson et al. – Science of The Total Environment

Distribution of microbial communities in metal-contaminated nearshore sediment from Eastern Guangdong, China – Mei Zhuang et al. – Environmental Pollution

Phages and viruses

Diversities and potential biogeochemical impacts of mangrove soil viruses – Min Jin et al. – Microbiome


Explore mediated co-varying dynamics in microbial community using integrated local similarity and liquid association analysis – Dongmei Ai et al. – BMC Genomics

Microbes in the news

Can changing the microbiome reverse lactose intolerance? – PATRICIA L. FOSTER – PhillyVoice

A Look at the Trillions of Microorganisms That Live in and on You – Shayla Love – Vice

Mode of delivery alters infants’ gut microbiota and this may impact respiratory health in first year of life – EurekAlert!

Fecal Transplant Reduces Nearly 50 Percent Of Autism Symptoms In Children – Allan Adamson – Tech Times

Edinburgh Science Festival: from gut bacteria and depression to how rice is risking the planet – Helen McArdle – The Herald

Gut microbiome changes emerge as a potential modulator of age-associated cardiovascular disease risk – Andreu Prados – Gut Microbiota for Health

The Gut Microbiome & Cancer Immunotherapy – Osman, Afaf E. G. & Luke, Jason J. – Oncology Times


April 16, 2019

Good morning everyone! Today’s digest will deal a lot of disturbance in various ecosystems- starvation of the oral microbiota, forest fires, elevated CO2 levels and rising temperatures and more. Additionally, interesting pieces about science communication and education are recommended (bottom of the post).

Animal microbiome

Effects of diet on gut microbiota of soil collembolans– Qian Xiang- Science of the Total Environment

Diel population and functional synchrony of microbial communities on coral reefs– Winda Wegley-Kelly- Nature Communications

Human microbiome

Klebsiella and Providencia emerge as lone survivors following long-term starvation of oral microbiota– Jonathon L. Baker- PNAS

Horizontal gene transfer in human-associated microorganisms inferred by phylogenetic reconstruction and reconciliation– Hyeonsoo Jeong- Scientific Reports

Dysbiosis patterns during re-induction/salvage versus induction chemotherapy for acute leukemia– Armin Rashidi- Scientific Reports

The personalized temporal dynamics of microbiome in the airways of cystic fibrosis patients– Giovanni Baci- bioRxiv

Plant, root and soil microbiome

Maize synthesized benzoxazinoids affect the host associated microbiome- Enoch Narh Kodjordjie- Microbiome

Utilization of carbon sources in the rice rhizosphere and non-rhizosphere soils with different long-term fertilization management– Tang H- J of Basic Microbiology

Effect of forest fire prevention treatments on bacterial communities associated with productive Boletus edulis sites- Olaya Mediavilla- Microbial Biotechnology

Effects of elevated temperature and elevated CO2 on soil nitrification and ammonia-oxidizing microbial communities in field-grown crop– Linh T.T Nguyen- Science of the Total Environment

Phyllosphere epiphytic and endophytic fungal community and network structures differ in a tropical mangrove ecosystem– Hui Yao- Microbiome

Changes in fungal communities across a forest disturbance gradient– Lingling Shi- AEM

Water microbiome

Wetland sediments host diverse microbial taxa capable of cycling alchohols- Paula Dalcin Martins- AEM

Review- The microbiomes of deep-sea hydrothermal vents: distributed globally, shaped locally– Gregory J. Dick- N. Reviews Microbiology


DeeplyEssential: A Deep Neural Network for Predicting Essential Genes in Microbes- Md Abid Hassan- bioRxiv

Microbiome news and science communication

Biotech company launches animal models with custom microbiome profiles

Microbial biotechnology for water treatment- A collection of high-quality websites (from Microbial Biotechnology)

Thematic series on scholarly communications in the digital age

The urgent need for microbiology literacy in society

8 April, 2019

General Microbiome

Coevolutionary dynamics shape the structure of bacteria-phage infection networks. Fortuna MA.Evolution.

High proportions of bacteria are culturable across major biomes. Martiny AC. ISME Journal

The complexity of an optimal vaginal biome. Eschenbach DA. BJOG

The lung microbiome, vitamin D, and the tuberculous granuloma: A balance triangle. Balcells ME. Microbial Pathogenesis

Gut Microbiome

The parasitic worm product ES-62 normalises the gut microbiota bone marrow axis in inflammatory arthritis. Doonan J. Nature Communications

Culture-enriched human gut microbiomes reveal core and accessory resistance genes. Raymond F.Microbiome.

Plant, Soil, Water, and Air Microbiome

Temperature and soil moisture control microbial community composition in an arctic-alpine ecosystem along elevational and micro-topographic gradients.Frindte K. ISME Journal

Root traits and belowground herbivores relate to plant-soil feedback variation among congeners.Wilschut RA. Nature Communications

A Polyphasic Approach for Assessing Eco-System Connectivity Demonstrates that Perturbation Remodels Network Architecture in Soil Microcosms.Stamou GP. Microbial Ecology

Effect of stock density on the microbial community in biofloc water and Pacific white shrimp (Litopenaeus vannamei) gut microbiota.Deng Y. Applied Microbiology Biotechnology

Rapid and stable microbial community assembly in the headwaters of third-order stream. Teachey ME. Applied Environmental Microbiology

Comparative Metagenomics Reveals Enhanced Nutrient Cycling Potential After Two Years of Biochar Amendment in a Tropical Oxisol. Yu J. Applied Environmental Microbiology

Animal Experiments and Microbiome

Effect of a low protein diet on chicken ceca microbiome and productive performances. De Cesare A. Poultry Science

Impact of a probiotic-based cleaning product on the microbiological profile of broiler litters and chicken caeca microbiota.De Cesare P. Poultry Science

Metagenomic Analysis of the Whole Gut Microbiota in Brazilian Termitidae Termites Cornitermes cumulans, Cyrilliotermes strictinasus, Syntermes dirus, Nasutitermes jaraguae, Nasutitermes aquilinus, Grigiotermes bequaerti, and Orthognathotermes mirim. Grieco MB. Current Microbiology.

The hemolymph microbiome of insects. Blow F. Journal Of Insect Physiology

Musa basjoo regulates the gut microbiota in mice by rebalancing the abundance of probiotic and pathogen. Wei T. Microbial Pathogenesis

Investigating the influence of organic acid marinades, storage temperature and time on the survival/inactivation interface of Salmonella on chicken breast fillets.

Lytou AE. International Journal of Food Microbiology.

April 05, 2019

Good morning everyone! In today’s microbiome digest, we have multiple research and review articles focusing on the role of microbiome in Prostate Cancer, Breast Cancer, Gastric Cancer, Allergy, Gut-Brain axis, Schizophrenia, Paediatric Crohn’s Disease, Nonalcoholic Fatty Liver Disease, Alveolar Osteitis, Renal Failure, Cholecystokinin Expression, Lipid Metabolism Disorder, Regulation of Blood Pressure and an independent section on Fecal Microbiota Transplantation. Additionally, two very interesting metagenomic studies have discovered specific microbial signature as well as link with choline degradation in the colorectal cancer patients. Enjoy reading.

General microbiome

Reivew: The Human Microbiota and Prostate Cancer: Friend or Foe? – Francesco Massari – Cancers

Microbiome—Microbial Metabolome—Cancer Cell Interactions in Breast Cancer—Familiar, but Unexplored – Edit Miko – Cells

Review: Fighting AMR in the Healthcare Environment: Microbiome-Based Sanitation Approaches and Monitoring Tools – Maria D’Accolti – Molecular Sciences

Gut microbiome

Gut microbial dysbiosis is associated with allergen-specific IgE responses in young children with airway allergies – Chih-Yung Chiu – World Allergy Organization Journal

Review: The gut virome: the ‘missing link’ between gut bacteria and host immunity? – Indrani Mukhopadhya – Therapeutic Advances in Gastroenterology

Regulatory T Cells and Plasmacytoid Dendritic Cells Within the Tumor Microenvironment in Gastric Cancer Are Correlated With Gastric Microbiota Dysbiosis: A Preliminary Study – Zongxin Ling – Frontiers in Immunology

Review: Impact of Different Types of Diet on Gut Microbiota Profiles and Cancer Prevention and Treatment – Rainer J. Klement – Medicina

Review: Glutamatergic Signaling Along The Microbiota-Gut-Brain Axis – Andreina Baj – Molecular Sciences

Investigation of the Gut Microbiome in Patients with Schizophrenia and Clozapine-Induced Weight Gain: Protocol and Clinical Characteristics of First Patient Cohorts –Gorbovskaya I. –  Neuropsychobiology

Review: Sex Differences in Gut Microbiota – Yong Sung Kim – The World Journal of MEN’s HEALTH

The Microbiome in Paediatric Crohn’s Disease—A Longitudinal, Prospective, 
Single-Centre Study – Shivani Kansal – Journal of Crohn’s and Colitis

A gut microbiome signature for cirrhosis due to nonalcoholic fatty liver disease – Cyrielle Caussy – Nature Communications

Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation – Andrew Maltez Thomas – Nature Medicine

Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer – Jakob Wirbel – Nature Medicine

Ceftriaxone and cefotaxime have similar effects on the intestinal microbiota in human volunteers treated by standard doses regimens – Charles Burdet – Antimicrobial Agents and Chemotherapy

Human respiratory microbiome

Mycobiome Sequencing and Analysis Applied to Fungal Community Profiling of the Lower Respiratory Tract During Fungal Pathogenesis – Lisa R. McTaggart – Frontiers in Microbiology

Reproductive tract microbiome

Identification and evaluation of the microbiome in the female and male reproductive tracts – Rivka Koedooder – Human reproduction update

Skin microbiome

Mast cell recruitment is modulated by hairless skin microbiome – Chia-Chi Wu – The Journal of Allergy and Clinical Immunology

Oral microbiome

A metagenomic study of patients with alveolar osteitis after tooth extraction. A preliminary case-control study – Laura Aguilar-Duran – Clinical Oral Investigations

Animal microbiome / Animal experiments

Interactions Between Commensal Bacteria and Enteric Neurons, via FPR1 Induction of ROS, Increase Gastrointestinal Motility in Mice – Bindu Chandrasekharan – Gastroenterology

Danshen can interact with intestinal bacteria from normal and chronic renal failure rats – Hongdie Cai – Biomedicine and Pharmacotherapy

Review: A place for taxonomic profiling in the study of the coral prokaryotic microbiome – Alejandra Hernandez-Agreda – FEMS Microbiology Letters

Fructose malabsorption induces cholecystokinin expression in the ileum and cecum by changing microbiota composition and metabolism – Xufei Zhang – THE FASEB JOURNAL

Spinach consumption ameliorates the gut microbiota and dislipaemia in rats with diet-induced non-alcoholic fatty liver disease (NAFLD) – Elvira-Torales LI – Food and Functions

Microbial Colonization in Adulthood Shapes the Intestinal Macrophage Compartment – Franziska Schmidt – Journal of Chron’s and Colitis

Feeding modes shape the acquisition and structure of the initial gut microbiota in newborn lambs – Yanliang Bi – Environmental Microbiology

Effects of dietary lipid sources on the intestinal microbiome and health of golden pompano (Trachinotus ovatus) – Cuihong You – Fish & Shellfish Immunology

Gut microbiota characterization and lipid metabolism disorder found in PCB77-treated female mice – Chi Y – Toxicology

Changes of gut microbiota between different weight reduction programs – Belle Yanyu Lin – Surgery for Obesity and Related Diseases

Microbiome-metabolomic analysis of the impact of Zizyphus jujuba cv. Muzao polysaccharides consumption on colorectal cancer mice fecal microbiota and metabolites – Xiaolong Ji – International Journal of Biological Macromolecules

Fecal Microbiota Transplantation

Critical Role of the Interaction Gut Microbiota – Sympathetic Nervous System in the Regulation of Blood Pressure – Marta Toral – Frontiers in Physiology

Faecal microbiota transplantation for the decolonisation of antibiotic-resistant bacteria in the gut: a systematic review and meta-analysis – Vera Tavoukjian – The Journal of Hospital Infection


Effect of a multistrain probiotic (Lactoflorene®Plus) on inflammatory parameters and microbiota composition in subjects with stress-related symptoms – Sara Soldi – Neurobiology of Stress

Probiotics, prebiotics, and low FODMAP diet for irritable bowel syndrome – What is the current evidence? – Soo Liang Ooi – Complementary Therapies in Medicine

Water and extremophile microbiome

Microbial Community of Saline, Alkaline Lakes in the Nebraska Sandhills Based on 16S rRNA Gene Amplicon Sequence Data – Nicole A. Fiore – Microbiology Resource Announcements


A Customized At-Home Stool Collection Protocol for Use in Microbiome Studies Conducted in Cancer Patient Populations – Stephanie R. Hogue – Microbial Ecology

Effect of storage and DNA extraction method on 16S rRNA-profiled fecal microbiota in Japanese adults – Yuki Kawada – Journal of Clinical Biochemistry and Nutrition


𝑊∗𝑑Wd∗-test: robust distance-based multivariate analysis of variance – Bashir Hamidi – Microbiome

Identification and reconstruction of novel antibiotic resistance genes from metagenomes – Fanny Berglund – Microbiome

April 04, 2019

In today’s microbiome digest, multiple research and review articles focusing on the role of host-associated microbiomes in various diseases including Type 2 Diabetes, Obesity, Urolithiasis, Bronchial Asthma, Cancer Immunotherapy, Hepatic Glycan Storage, Uveitis, Schizophrenia and the Development of the immune system. Enjoy reading.

General microbiome

Harnessing microbiota interactions to produce bioactive metabolites: communication signals and receptor proteins – Juan F Martin – Current Opinion in Pharmacology

Review: Prevention of allergy with diverse and healthy microbiota:an update – Diana Chernikova – Current Opinion in Pediatrics

State of the Art: Pharmacomicrobiomics: The holy grail to variability in drug response? – Anukriti Sharma – Clinical Pharmacology and Therapeutics

Gut microbiome

The alteration of gut microbiota in newly diagnosed type 2 diabetic patients – Pei-Chi Chen – Nutrition

Defining Dysbiosis in Patients with Urolithiasis – Anna Zampini – Scientific Reports

Review: Gut Microbiota, Host Organism, and Diet Trialogue in Diabetes and Obesity – Veronica Lazar – Frontiers in Nutrition

Metabolic activity of intestinal microflora in patients with bronchial asthma – Vladimir Irashkin – Clinics and Practice

Pharmacologic and Nonpharmacologic Therapies for the Gut Microbiota in Type 2 Diabetes – Robert Caesar – Canadian Journal of Diabetes

Review: Modulation of cancer immunotherapy efficacy by gut microbiota – Huo S – Discovery Medicine

Hepatic glycogen storage diseases are associated to microbial dysbiosis – Karina Colonetti – PLOS ONE

Implicating Dysbiosis of the Gut Fungal Microbiome in Uveitis, an Inflammatory Disease of the Eye – Rajagopalaboopathi Jayasudha – Immunology and Microbiology

Cohort profile: The LoewenKIDS Study – life-course perspective on infections, the microbiome and the development of the immune system in early childhood – Cornelia Gottschick – International Journal of Epidemiology

Case Report: Decreased Clostridium Abundance after Electroconvulsive Therapy in the Gut Microbiota of a Patient with Schizophrenia – Misako Kanayama – Case Reports in Psychiatry

Reproductive tract microbiome

Effects of oral probiotic supplements on vaginal microbiota during pregnancy: a randomised, double‐blind, placebo‐controlled trial with microbiome analysis – S Husain – BJOG 

Skin microbiome

Review: The Cutaneous Microbiome: Implications for Dermatology Practice – Megan A. Sander

Animal microbiome / Animal experiments

Intestinal microbiota of broilers submitted to feeding restriction and its relationship to hepatic metabolism and fat mass: Fast-growing strain – Raquel Lunedo – Journal of Animal Physiology and Animal Nutrition

Phytate degradation, intestinal microbiota, microbial metabolites and immune values are changed in growing pigs fed diets with varying calcium–phosphorus concentration and fermentable substrates – Charlotte Maria Elisabeth Heyer – Journal of Animal Physiology and Animal Nutrition

Review: The importance of scale in comparative microbiome research: New insights from the gut and glands of captive and wild lemurs – Lydia K. Greene – American Journal of Primatology

A dietary isothiocyanate-enriched moringa (Moringa oleifera) seed extract improves glucose tolerance in a high-fat-diet mouse model and modulates the gut microbiome – Asha Jaja-Chimedza – Journal of Functional Foods

Musca domestica Cecropin (Mdc) Alleviates Salmonella typhimurium-Induced Colonic Mucosal Barrier Impairment: Associating With Inflammatory and Oxidative Stress Response, Tight Junction as Well as Intestinal Flora – Lun Zhang – Frontiers in Microbiology

The Effects of Unfermented and Fermented Cow and Sheep Milk on the Gut Microbiota – Elizabeth A. Rettedal – Frontiers in Microbiology

Water and extremophile microbiome

Microbiota of the Hickey Run Tributary of the Anacostia River – Robin Cagle – Microbiology Resource Announcements


Review: Statistical Analysis of Metagenomics Data – M. Luz Calle – Genomics and Informatics

March 28, 2019

Today’s digest covers interesting reviews on different aspects of host-microbiome interactions, research articles about how structural variation in gut microbiome affects host health, characterization of a simplified microbial community to study microbial interaction with diet in mice and viral diversity in soil metagenomes. Happy reading!

General microbiome

Review – Microbiome: Our opponents or allies in healthcare and medicine – Horst A von Recum – Experimental Biology and Medicine

Review –  To B12 or not to B12: Five questions on the role of cobalamin in host-microbial interactions – Carol A. Rowley – Plos Pathogens

Review – Can oral bacteria affect the microbiome of the gut? – Ingar Olsen – Journal of Oral Microbiology

Review –  Inter-kingdom signaling between gut microbiota and their host – Qing Li – Cellular and Molecular Life Sciences

Human gut microbiome

Structural variation in the gut microbiome associates with host health – David Zeevi – Nature

Effects of fermentable high fiber diet supplementation on gut derived and conventional nitrogenous product in patients on maintenance hemodialysis: a randomized controlled trial – Hamid Tayebi Khosroshahi – Nutrition and Metabolism

Identification of the microbial diversity after fecal microbiota transplantation therapy for chronic intractable constipation using 16s rRNA amplicon sequencing – Tadashi Ohara – PlosOne

The microbiome and tuberculosis: state of the art, potential applications, and defining the clinical research agenda – Charissa C Naidoo – Lancet Respiratory medicine

Fecal Microbiota Transplantation: An Update on Clinical Practice – Kyeong Ok Kim – Clinical Endoscopy

Aryl hydrocarbon receptor and uremic toxins from gut microbiota in chronic kidney disease patients: Is there a relationship? – Jessyca Brito – Biochemistry

Animal experiments

Bacterial AB5 toxins inhibit the growth of gut bacteria by targeting ganglioside-like glycoconjugates – Robert T. Patry – Nature Communications

Simplified Intestinal Microbiota to Study Microbe-Diet-Host Interactions in a Mouse Model – Petia Kovatcheva-Datchary – Cell Reports

Pomegranate ellagitannin-gut microbial-derived metabolites, urolithins, inhibit neuroinflammation in vitro – Nicholas A. DaSilva – Nutritional Neuroscience

Endogenous Enterobacteriaceae underlie variation in susceptibility to Salmonella infection – Eric M. Velazquez – Nature Microbiology

Plant, root, soil microbiome

Thickness determines microbial community structure and function in nitrifying biofilms via deterministic assembly – Carolina Suarez – Scientific Reports

Untapped viral diversity in global soil metagenomes – Emily B. Graham – BioRxiv

Water microbiome and extremophiles

Fate of antibiotic resistance genes in two Arctic tundra wetlands impacted by municipal wastewater – Jennifer L. Hayward – Science of the Total Environment


Importance of probiotics in the prevention and treatment of colorectal cancer – Majid Eslami – Journal of Cellular Physiology

Non-microbiology picks

Artificial womb technology breaks its four minute mile – Science Daily

March 25, 2019

Good morning everyone! In today’s microbiome digest, we have multiple research and review articles about the role of microbiome in various diseases including neurodevelopmental, biliary Cholangitis, obesity-associated CRC, bariatric surgery, atopic dermatitis, schizophrenia, respiratory tract infection and autoimmunity, and an independent section on Fecal Microbiota Transplantation. Enjoy reading.

General microbiome

Talking about a microbiome revolution – John F. Cryn – Nature Microbiology

Review: Crosstalk between neutrophils and the microbiota – Dachuan Zhang – Blood

 Gut microbiome

Alteration of gut microbiota by a westernized lifestyle and its correlation with insulin resistance in non‐diabetic Japanese men – Mami Yamashita – Journal of Diabetes Investigation

Association of the Infant Gut Microbiome With Early Childhood Neurodevelopmental Outcomes – Joanne E. Sordillo – JAMA Netw Open

Comprehensive Analysis of Serum and Fecal Bile Acid Profiles and Interaction with Gut Microbiota in Primary Biliary Cholangitis – Weihua Chen – Clinical Reviews in Allergy & Immunology

Gut microbiome meta-analysis reveals dysbiosis is independent of body mass index in predicting risk of obesity-associated CRC – K Leigh Greathouse – BMJ Open Gastroenterology

Gut microbiota specific signatures are related to the successful rate of bariatric surgery – Gutiérrez-Repiso C – American Journal of Transplantation Research

Differences in Systemic IgA Reactivity and Circulating Th Subsets in Healthy Volunteers With Specific Microbiota Enterotypes – Christina Grosserichter-Wagener – Frontiers in Immunology

Gut microbiota profile in children affected by atopic dermatitis and evaluation of intestinal persistence of a probiotic mixture – Sofia Reddel – Scientific Reports

Prebiotic effect of predigested mango peel on gut microbiota assessed in a dynamic in vitromodel of the human colon (TIM-2) – Sonia G. Sáyago-Ayerdi – Food Research International

Review: The gut microbiota promotes the pathogenesis of schizophrenia via multiple pathways – Xiuxia Yuan – Biochemical and Biophysical Research Communications

Evidence for an association of gut microbial Clostridia with brain functional connectivity and gastrointestinal sensorimotor function in patients with irritable bowel syndrome, based on tripartite network analysis – Jennifer S. Labus – Microbiome

A multi-omic cohort as a reference point for promoting a healthy human gut microbiome – Zhuye Jie – bioRxiv

Human respiratory microbiome

The microbiological characteristics of lower respiratory tract infection in patients with neuromuscular disorders: An investigation based on a multiplex polymerase chain reaction to detect viruses and a clone library analysis of the bacterial 16S rRNA gene sequence in sputum samples – Masato Ogawa – Journal of Microbiology, Immunology and Infection

Vaginal micorbiome

Cervicovaginal microbiota and local immune response modulate the risk of spontaneous preterm delivery – Michal A. Elovitz – Nature Communications

Animal microbiome / Animal experiments

Autoimmunity-Associated Gut Commensals Modulate Gut Permeability and Immunity in Humanized Mice – Baskar Balakrishnan – Military Medicine

Microbe and host interaction in gastrointestinal homeostasis – Rachael Horne – Psychopharmacology

Broiler gut microbiota and expressions of gut barrier genes affected by cereal type and phytogenic inclusion – VasileiosParaskeuas – Animal Nutrition

Manipulation of gut microbiota blunts the ventilatory response to hypercapnia in adult rats – Karen M. O’Connor – EbioMedicine

Beneficial Effects of Potentilla discolor Bunge Water Extract on Inflammatory Cytokines Release and Gut Microbiota in High-Fat Diet and Streptozotocin-Induced Type 2 Diabetic Mice – Lihua Han – Nutrients

Effects of gut-derived endotoxin on anxiety-like and repetitive behaviors in male and female mice – Christopher T. Fields – Biology of Sex Differences

Fecal Microbiota Transplantation

Recent Research on Fecal Microbiota Transplantation in Inflammatory Bowel Disease Patients – Monika Fischer – Gastroenterology and Hepatology

Assessing the viability of transplanted gut microbiota by sequential tagging with D-amino acid-based metabolic probes – Wei Wang – Nature Communications

Do we really understand how faecal microbiota transplantation works? Authors’ reply – Lito E. Papanicolas – EbioMeidicine

Water and extremophile microbiome

Mobile antibiotic resistome in wastewater treatment plants revealed by Nanopore metagenomic sequencing – You Che – Microbiome

Evolution of microbial community and drug resistance during enrichment of tetracycline-degrading bacteria – Qiang Wang – Ecotoxicology and Environmental Safety


A generic multivariate framework for the integration of microbiome longitudinal studies with other data types – Antoine Bodein – bioRxiv