In Sunday’s microbiome digest read about a genomic approach which identified large number of novel proteins from human microbiome, how gut microbiome modulates the pancreatic adenocarcinoma microbiome landscape, detailed investigation of host-microbiome interactions via screening of human microbiome-derived metabolites against G-protein-coupled receptors, homeostasis of brain-gut-microbiota axis in functional dyspepsia rats, modelling of microbial communities using artificial neural networks and in the techniques section Gupta et. al. compared the diagnostic efficacy of Amplicon sequencing and traditional culture methods. Happy weekend. Enjoy reading.

General microbiome

Review Essay: At the Intersection of Microbiota and Circadian Clock: Are Sexual Dimorphism and Growth Hormones the Missing Link to Pathology? – Benjamin D. Weger – BioEssays

Gut microbiome

Large-Scale Analyses of Human Microbiomes Reveal Thousands of Small, Novel Genes – Hila Sberro – Cell

Tumor Microbiome Diversity and Composition Influence Pancreatic Cancer Outcomes – Erick Riquelme – Cell

Mapping Interactions of Microbial Metabolites with Human G-Protein-Coupled Receptors – Dominic A. Colosimo – Cell Host & Micorbe

The Association between Gut Microbiota Composition and Body Mass Index in Chinese Male College Students, as Analyzed by Next-generation Sequencing – Yanrong Lv – British Journal of Nutrition

Influence of Helicobacter pylori Infection and Atrophic Gastritis on the Gut Microbiota in a Japanese Population – Iino C – Digestion

Gut microbiome response to a modern Paleolithic diet in a Western lifestyle context – Monica Barone – PLOS ONE

Early E. casseliflavus gut colonization and outcomes of allogeneic hematopoietic cell transplantation – Armin Rashidi – PLOS ONE

Vaginal microbiome

Review: The vaginal microbiome in uterine transplantation – BP Jones – BJOG

Animal microbiome / Animal experiments

16S rRNA Gene Amplicon Sequence Data from Chicken Cecal Feces from Vietnam and Thailand – Nachiko Takeshita – Microbiology Resource Announcements

Modification of the equine gastrointestinal microbiota by Jerusalem artichoke meal supplementation – M. Glatter – PLOS ONE

Effect of 1-Deoxynojirimycin Isolated from Mulberry Leaves on Glucose Metabolism and Gut Microbiota in a Streptozotocin-Induced Diabetic Mouse Model – Teng-Gen Hu – Journal of Natural Products

Different microbiomes are found in healthy breeder ducks and those with foot pad dermatitis – S M Qin – Poultry Science

Effects of early-life lactoferrin intervention on growth performance, small intestinal function and gut microbiota in suckling piglets – Ping Hu – Food and Function

Child compound Endothelium corneumattenuates gastrointestinal dysmotility through regulating the homeostasis of brain-gut-microbiota axis in functional dyspepsia rats – YixinHe – Journal of Ethnopharmacology

Water and extremophile microbiome

Modelling the influence of environmental parameters over marine planktonic microbial communities using artificial neural networks – F.H.Coutinho – Science of The Total Environment

Biomonitoring detoxification efficiency of an algal-bacterial microcosm system for treatment of coking wastewater: Harmonization between Chlorella vulgaris microalgae and wastewater microbiome – MariamHassan – Science of The Total Environment

Environmental Microbiome

Hospital Microbiome Variations As Analyzed by High-Throughput Sequencing – Marwa T. ElRakaiby – OMICS

Techniques

Amplicon sequencing provides more accurate microbiome information in healthy children compared to culturing – Shashank Gupta – Communications Biology

Microbiome news

The microbiome explained: how a vast army of gut bacteria regulates body’s functioning

How snuggling close affects bats’ microbiome

Good Morning! Highlights of today’s digest include a comprehensive analysis of biosynthetic gene clusters from Bacillus amyloliquifaciens that synthesize a lipopeptide with anticancer activity, another study conducted with African-origin adults confirms association of the oral and gut microbiota to cardiometabolic risks, a review about future applications of probiotics focusing on the characteristics of Bacteroides fragilis and an editorial article on environmental bacteriophages highlighting exciting future applications such as antibacterial therapies for antibiotic-resistant pathogens.

General Microbiology

* A comprehensive genomic and growth proteomic analysis of antitumor lipopeptide bacillomycin Lb biosynthesis in Bacillus amyloliquefaciens X030 – Jiao Yang Lu et al. – Applied Microbiology and Technology

Pregnancy and early life

Patterned progression of gut microbiota associated with necrotizing enterocolitis and late onset sepsis in preterm infants: a prospective study in a Chinese neonatal intensive care unit – Jiayi Liu et al. – PeerJ

Multi-site human microbiome

*The human microbiota is associated with cardiometabolic risk across the epidemiologic transition – Na Fei et al. – PLOS ONE

Human vaginal microbiome

The effect of antiretroviral therapy initiation on the vaginal microbiome in HIV-infected women – Cindy M Liu et al. – Open Forum Infectious Diseases

Competition among Gardnerella subgroups from the human vaginal microbiome – Salahuddin Khan et al. – bioRxiv

Human gut microbiome

Exposure to parasitic protists and helminths changes the intestinal community structure of bacterial microbiota but not of eukaryotes in a cohort of mother-child binomial from a semi-rural setting in Mexico – Oswaldo Partida-Rodriguez et al. – bioRxiv

Animal experiments

Metagenomic analysis of the effects of toll-like receptors on bacterial infection in the peritoneal cavity following cecum ligation and puncture in mice – Pao-Jen Kuo et al. – PLOS ONE

Animal microbiome

Social interactions across groups of colobus monkeys (Colobus vellerosus) explain similarities in their gut microbiomes – bioRxiv

Plant, root and soil microbiome

Phosphorus Input Alters the Assembly of Rice (Oryza sativa L.) Root-Associated Communities – Xi-En Long et al. – Microbial Ecology

Water and extremophile microbiome

Review: Microbial Diversity of Saline Habitats: An Overview of Biotechnological Applications – Shubhrima Ghosh et at. – Microorganisms in Saline Environments: Strategies and Functions

Built-environment microbiome

Rapid metagenomics analysis of EMS vehicles for monitoring pathogen load using nanopore DNA sequencing – Taylor Sheahan et al. – PLOS ONE

Food microbiology

Characterization and comparison of metaproteomes in traditional and commercial dajiang, a fermented soybean paste in northeast China – Mengxi Xie et al. – Food Chemistry

Probiotics / peribiotics

*Review: A potential species of next-generation probiotics? The dark and light sides of Bacteroides fragilis in health – X Li et al. – Food Research International

Phages and viruses

*Editorial: Environmental Bacteriophages: from Biological Control Applications to Directed Bacterial Evolution – Robert Czajkowski et al. – Frontiers in Microbiology

Techniques

Quantitative Stable Isotope Probing with H218O to Measure Taxon-Specific Microbial Growth – Alicia M. Purcell et al. – ACSESS Metods of Soil Analysis

Linking process performances and core microbial community structures in anaerobic membrane bioreactor with rotatory disk (ARMBR) system fed with high-strength food waste recycling wastewater – Hyunduk Seo et al. – Bioresource Technology

Nanopore sequencing for fast determination of plasmids, phages, virulence markers, and antimicrobial resistance genes in Shiga toxin-producing Escherichia coli – Narjol Gonzalez-Escalona et al. – PLOS ONE

Microbes in the news

Poop transplants can help prematurely old mice live longer – Eva Freserick – Science Magazine

Today we have covered several interesting studies including the effect of drugs such as levofloxacin and penconazole, vitamin E, and raw potato starch on the microbiome composition. Microbial diversity of bharals (Pseudois nayaur) is also explored under wild and captive conditions. Additionally, researchers from Gordon’s group have investigated the interactions between therapeutic diet, microbiota development, and growth recovery. Hope readers will enjoy today’s digest.

General microbiome

Review: The impact of microbiome in urological diseases: a systematic review – Joseph K. M. Li – International Urology and Nephrology

Impact of Pristine Graphene on Intestinal Microbiota Assessed Using a Bioreactor-Rotary Cell Culture System – Mohamed H. Lahiani – ACS Applied Materials & Interfaces

Review: Host–microbial dialogues in atopic dermatitis – Tetsuro Kobayashi – International Immunology

Human gut microbiome

A sparse covarying unit that describes healthy and impaired human gut microbiota development – Arjun S. Raman – Science

Effects of microbiota-directed foods in gnotobiotic animals and undernourished children – Jeanette L. Gehrig – Science

Insights: Gut Microbiota and Short Chain Fatty Acids: Influence on the Autonomic Nervous System – Jessica Bruning – Neuroscience Bulletin

Human gut microbiome changes during a 10 week Randomised Control Trial for micronutrient supplementation in children with attention deficit hyperactivity disorder – Aaron J. Stevens – Scientific Reports

Characterization of gut microbiota, bile acid metabolism, and cytokines in intrahepatic cholangiocarcinoma – Xiaodong Jia – Hepatology

Effect of Synbiotic Supplementation in a Very‐Low‐Calorie Ketogenic Diet on Weight Loss Achievement and Gut Microbiota: A Randomized Controlled Pilot Study – Carolina Gutiérrez‐Repiso – Molecular Nutrition and Food Research

Animal microbiome / Animal experiments

Effects of Potential Probiotic Strains on the Fecal Microbiota and Metabolites of d-Galactose-Induced Aging Rats Fed with High-Fat Diet – Lee-Ching Lew – Probiotics and Antimicrobial Proteins

Characterization of bacterial community changes and antibiotic resistance genes in lamb manure of different incidence – Ling-cong Kong – Scientific Reports

Comparison of gut microbiota diversity between wild and captive bharals (Pseudois nayaur) – Xiangwen Chi – BMC Veterinary Research

The effects of desynchronosis on the gut microbiota composition and physiological parameters of rats – Ksenia M. Klimina – BMC Microbiology

Low gut microbiota diversity and dietary magnesium intake are associated with the development of PPI-induced hypomagnesemia – Lisanne M. M. Gommers – The FASEB Journal

The role of commensal microbes in the lifespan of Drosophila melanogaster – Hye-Yeon Lee – Aging

The effect of levofloxacin on the lung microbiota of laboratory rats – Sade M. B. Finn – Experimental Lung Research

Impacts of penconazole and its enantiomers exposure on gut microbiota and metabolic profiles in mice – Zhiyuan Meng – Journal of Agricultural and Food Chemistry

Evaluation of the impact of in ovo administered bacteria on microbiome of chicks through 10 days of age – K M Wilson – Poultry Science

Vitamin E (α-tocopherol) consumption influences gut microbiota composition – Yukyung Choi – International Journal of Food Sciences and Nutrition

CRTAM Shapes the Gut Microbiota and Enhances the Severity of Infection – Araceli Perez-Lopez – The Journal of Immunology

Metaproteomic investigation to assess gut microbiota shaping in newborn mice: A combined taxonomic, functional and quantitative approach – Stefano Levi Mortera – Journal of Proteomics

Bacillus subtilis Strain DSM 29784 Modulates the Cecal Microbiome, Concentration of Short-Chain Fatty Acids, and Apparent Retention of Dietary Components in Shaver White Chickens during Grower, Developer, and Laying Phases – Mohamed Neijat – Applied and Environmental Microbiology

Effect of raw potato starch on the gut microbiome and metabolome in mice – So-Jung Bang – International Journal of Biological Macromolecules

Edgeworthia gardneri (Wall.) Meisn. water extract improves diabetes and modulates gut microbiota – Zhiwen Zhang – Journal of Ethnopharmacology

Plant, root, and soil microbiome

Review: Soil Aggregate Microbial Communities: Towards Understanding Microbiome Interactions at Biologically Relevant Scales – Regina L. Wilpiszeski – Applied and Environmental Microbiology

Water and extremophile microbiome

Metagenomic insights into microbial diversity in a groundwater basin impacted by a variety of anthropogenic activities – Prinpida Sonthiphand – Environmental Science and Pollution Research

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

Techniques

Tracing seafood at high spatial resolution using NGS-generated data and machine learning: Comparing microbiome versus SNPs – Massimo Milan – Food Chemistry

Microbiome news

The Gut Microbiome Can Be a Boon or a Bane for Cardiovascular Health – SHAWNA WILLIAMS

The human microbiome is a treasure trove waiting to be unlocked

Good Morning! Highlights of today’s digest include several AACR Cancer Research meeting abstracts on microbiome profiling which are promising for development of early detection cancer or treatment-associated-toxicity biomarkers and novel probiotics that can prevent HPV infections-associated cancers and oropharyngeal cancers, development of non-invasive health monitoring tools for endangered humpback whales from East Australia, and re-assemblage of rhizosphere microbiome of medicinal Chinese ginseng or Sanqi. Finally, check out the news about development of a food supplement, expected to be commercialized by 2021 and suggested only to be used as a complementary approach -not a replacement of appropriate dietary habits, that involves a probiotic gut bacterium Akkermansia muciniphila to improve metabolism and metabolic factors in obesity, type II diabetes and inflammatory bowel diseases.

Human oral microbiome

Meeting Abstract: Mucositis, candidiasis, and associations with the oral microbiome in treatment naive patients with oropharyngeal cancer – Pierce et al. – AACR Cancer Research

Multi-site human microbiome

Meeting Abstract: The microbiota associated to cervical and anal HPV infections in a Hispanic population – Vazquez-Sanchez et al. – AACR Cancer Research

Animal microbiome

Review: Coral microbiome dynamics, functions and design in a changing world – van Oppen et al. – Nature Reviews Microbiology

Interannual comparison of core taxa and community composition of the blow microbiota from East Australian humpback whales – Vendl et al. – FEMS Microbiology Ecology

Plant, root and soil microbiome

Ecological Processes Shaping Bulk Soil and Rhizosphere Microbiome Assembly in a Long-Term Amazon Forest-to-Agriculture Conversion – Goss-Souza et al. – Microbial Ecology

Mycorrhizal frequency, physiological parameters, and yield of strawberry plants inoculated with endomycorrhizal fungi and rhizosphere bacteria – Mikiciuk et al. – Mycorrhiza

Negative plant-soil feedback driven by re-assemblage of the rhizosphere microbiome with the growth of Panax notoginseng – Zhu et al. – Frontiers in Microbiology

Water and extermophile microbiome

Microbial communities in a flow-through fish farm for lumpfish (Cyclopterus lumpus L.) during healthy rearing conditions – Roalkvam et al. – Frontiers in Microbiology

Probiotics / prebiotics

Dietary Resistant Potato Starch Alters Intestinal Microbial Communities and Their Metabolites, and Markers of Immune Regulation and Barrier Function in Swine – Trachsel et al. – Frontiers in Immunology

Phages and viruses

Virome capture sequencing does not identify active viral infection in unicentric and idiopathic multicentric Castleman disease – Nabel et al. – PLOS ONE

Wide distribution of phage that infect freshwater SAR11 bacteria – Chen et al. – BioRxiv

Techniques

Meeting Abstract: Microbial sequencing using a single-pool target enrichment of multiple variable regions of the 16S rRNA gene, the nuclear ribosomal internal transcribed spacer (ITS) region, and antimicrobial resistance genes – Peck et al. – AACR Cancer Research

Microbes in the news

Microbiome Food Supplement Improves Metabolic Syndrome in Overweight People – Smith – Labiotech.eu Newsletter

Today’s microbiome digest featuring a variety of research and review articles highlighting the role of gut microbiota-derived signals to the beta cells are necessary for proper insulin trafficking, a microfluidic chip designed by Roberta et. al. to mimic interactions between microorganisms and host tissue, the innovative role of exosomes in the pathogenesis of CRC, and a very interesting study in mice shows the host mitochondrial genotype influence the gut microbiota species diversity. Happy weekend. Enjoy reading.

General microbiome

Review: Translating Recent Microbiome Insights in Otitis Media into Probiotic Strategies – Marianne F. L. van den Broek – Clinical Microbiology Reviews

Research Highlight : Microbiota guides insulin trafficking in beta cells – Ozren Stojanović – Cell Research

Human gut microbiome

Human-gut-microbiome on a chip – Roberta Poceviciute – Nature Biomedical Engineering

Gut microbial profile is altered in biliary atresia – Junfeng Wang – Biliary and Pancreatic

The specific use of alginate from Laminaria japonica by Bacteroidesspecies determined its modulation of the Bacteroides community – Chunging Ai – Food & Function

Lactose and Bovine Milk Oligosaccharides Synergistically Stimulate B. longum subsp. longum Growth in a Simplified Model of the Infant Gut Microbiome – Louise M.A. Jakobsen – Journal of proteome research

Review: Probiotics and constipation: mechanisms of action, evidence for effectiveness and utilisation by patients and healthcare professionals – Eirini Dimidi – Proceedings of the Nutrition Society

In Vitro Digestion and Fermentation of Three Polysaccharide Fractions from Laminaria japonica and Their Impact on Lipid Metabolism-Associated Human Gut Microbiota – Jie Gao – Journal of Agricultural and Food Chemistry

Review: Role of intestinal microbiota and metabolites in inflammatory bowel disease – Li-Na Dong – Chinese Medical Journal

Review: The malignant role of exosomes in the communication among colorectal cancer cell, macrophage and microbiome – Jinjie Wu – Carcinogenesis

Human respiratory microbiome

Microbial Composition of the Human Nasopharynx Varies According to Influenza Virus Type and Vaccination Status – Tao Ding – mBio

Animal microbiome / Animal experiments

Full‐length 16S rRNA gene classification of Atlantic salmon bacteria and effects of using different 16S variable regions on community structure analysis – Terje Klemetsen – MicrobiologyOpen

Protein and carbohydrate intakes alter gut microbial community structure in crickets: A Geometric Framework approach – Soon Hwee Ng – FEMS Microbiology Ecology

Caulerpa lentillifera polysaccharides enhance the immunostimulatory activity in immunosuppressed mice in correlation with modulating gut microbiota – Yujiao Sun – Food & Function

Diet Consisting of Balanced Yogurt, Fruit and Vegetables Modifies the Gut Microbiota and Protects Mice Against Nonalcoholic Fatty Liver Disease – Chao‐Yue Kong – Molecular Nutrition Food Research

Unraveling the effects of the gut microbiota composition and function on horse endurance physiology – Sandra Plancade – Scientific Reports

Inulin and metformin ameliorate polycystic ovary syndrome via anti-inflammation and modulating gut microbiota in mice – Jing Xue – Endocrine Journal

Antiretroviral therapy administration in healthy rhesus macaques is associated with transient shifts in intestinal bacterial diversity and modest immunological perturbations – Alexandra M. Ortiz – Journal of Virology

Microbiota-Driven Tonic Interferon Signals in Lung Stromal Cells Protect from Influenza Virus Infection– Konrad C.Bradley – Cell Reports

Microbial and metabolomic remodeling by a formula of Sichuan dark tea improves hyperlipidemia in apoE-deficient mice – Lingzhi Li – PLOS ONE

Effect of chronic and acute heat challenges on fecal microbiota composition, production and thermoregulation traits in growing pigs – M Le Sciellour – Journal of Animal Science

Metaproteomics characterization of the alphaproteobacteria microbiome in different developmental and feeding stages of the poultry red mite Dermanyssus gallinae (De Geer, 1778) – José Francisco Lima-Barbero – Journal of Animal Science

L. plantarum, L. fermentum, and B. breveBeads Modified the Intestinal Microbiota and Alleviated the Inflammatory Response in High-Fat Diet–Fed Mice – Qingshen Sun – Probiotics and Antimicrobial Proteins

Host mitochondria influence gut microbiome diversity: A role for ROS – Tal Yardeni – Science Signaling

Potential effects of rapeseed peptide Maillard reaction products on aging-related disorder attenuation and gut microbiota modulation in D-galactose induced aging mice – Shudong He – Food & Function

The piglet mycobiome during the weaning transition: a pilot study – Katie L Summers – Journal of Animal Science

A heritable subset of the core rumen microbiome dictates dairy cow productivity and emissions – R. John Wallace – Science Advances

Microbiome in news

Dairy cow microbiome could yield the key to eco-friendly agriculture 

Today’s microbiome digest featuring the milestones in the human microbiota research along with a very interesting stochastic model to explain microbiome composition in host organisms and a review focusing on the effect of antipsychotic medications on the microbiome and weight gain. Additionally, there are some interesting studies from animal microbiome/animal experiments section such as the role of rumen microbiota in altering average daily gain and feed efficiency and microbiome of deposit feeder Capitella teleta. Enjoy reading. 

General microbiome

Milestones in human microbiota research – Nature

Neutrality in the Metaorganism – Michael Sieber – PLOS Biology

Gut microbiome

Novel Inter‐omic Analysis Reveals Relationships Between Diverse Gut Microbiota and Host Immune Dysregulation in HLA‐B27‐Induced Experimental Spondyloarthritis – Tejpal Gill – Arthritis And Rheumatology

Review: The effects of antipsychotic medications on microbiome and weight gain in children and adolescents – Tali Bretler – BMC Medicine

Oral microbiome

Fretibacterium sp. human oral taxon 360 is a novel biomarker for periodontitis screening in the Japanese population – Thatawee Khemwong – PLOS ONE

Animal microbiome / Animal experiments

Effects of dietary supplementation with lysozyme on the structure and function of the cecal microbiota in broiler chickens – Yun Xia – PLOS ONE

Potential role of rumen microbiota in altering average daily gain and feed efficiency in meat goats fed simple and mixed pastures using bacterial tag-encoded FLX amplicon pyrosequencing – Byeng Ryel Min – Journal of Animal Science

Modulation of the gut microbiota by a galactooligosaccharide protects against heavy metal lead accumulation in mice – Qixiao Zhai – Food & Function

Modulating effects of polysaccharides from the fruits of Lycium barbarum on the immune response and gut microbiota in cyclophosphamide-treated mice – Yu Ding – Food & Function

Sinapine reduces non-alcoholic fatty liver disease in mice by modulating the composition of the gut microbiota – Youdong Li – Food & Function

Glycated fish protein supplementation modulated gut microbiota composition and reduced inflammation but increased accumulation of advanced glycation end products in high-fat diet fed rats – Zhenjie Mao – Food & Function

The deposit feeder Capitella teleta has a unique and relatively complex microbiome likely supporting its ability to degrade pollutants – RebeccaHochstein – Science of The Total Environment

Microbiome news

Study Finds Link Between Gut Microbiome and Spread of Breast Cancer