August 10, 2019

This weekend, read about the role that gut microbes play in inflammation, microbes in the placenta-maternal interface, BactMAP R package, and more. Happy reading!

General microbiome

High proportions of bacteria and archaea across most biomes remain uncultured – Andrew D. Steen – The ISME Journal

Isolation of an archaeon at the prokaryote-eukaryote interface – Hiroyuki Imachi – bioRxiv

Urinary microbiome

A Prospective Study of the Urinary and Gastrointestinal Microbiome in Prepubertal Males – Borna Kassir – Urology

Gut microbiome

*Review: The intestinal microbiota fuelling metabolic inflammation – Herbert Tilg – Nature Reviews Immunology

Long-term dietary intervention reveals resilience of the gut microbiota despite changes in diet and weight – Gabriela K Fragiadakis – bioRxiv

Recovery of the gut microbiota after antibiotics depends on host diet and environmental reservoirs – Katharine M. Ng – bioRxiv

Differential detection of Entamoeba species in stool samples collected from children in District Swat, Khyber Pakhtunkhwa Pakistan – Muhammad Iftikhar Khan – bioRxiv

Association network analysis identifies enzymatic components of gut microbiota that significantly differ between colorectal cancer patients and healthy controls – Dongmei Ai – PeerJ

Specific changes in faecal microbiota are associated with familial Mediterranean fever – Samuel Deshayes – Annals of the Rheumatic Diseases

Pregnancy and early life

*Functional characterization of Ralstonia insidiosa, a bona fide resident at the maternal-fetal interface – Lindsay A. Parnell – bioRxiv

The association between caesarean section delivery and later life obesity in 21-24 year olds in an Urban South African birth cohort – Eniola Sogunle – bioRxiv

Water and extremophile microbiome

Microbial community and geochemical analyses of trans-trench sediments for understanding the roles of hadal environments – Satoshi Hiraoka – bioRxiv

Metabolically-active obligate aerobes in anoxic (sulfidic) marine sediments – Sabyasachi Bhattacharya – bioRxiv

Plant microbiome

Shared mycorrhizae but distinct communities of other root-associated microbes on co-occurring native and invasive maples – Tonia DeBellis – PeerJ

Non-target Effects of Trichoderma on Plants and Soil Microbial Communities – Monika Jangi – Plant Microbe Interface

Bioinformatics

*BactMAP: an R package for integrating, analyzing and visualizing bacterial microscopy data – Renske van Raaphorst – bioRxiv

Podcast

The placental microbiome, and advances in artificial intelligence – Nick Howe and Noah Baker – Nature Podcast

August 1, 2019

Happy Thursday! Today’s digest includes fungi abundance in paddy fields, the microbial quality of treated wastewater, and the oral microbiome of cats. Enjoy!

Animal microbiome

The feline cutaneous and oral microbiota are influenced by breed and environment – Older – PLoS One

Microbial community modulates growth of symbiotic fungus required for stingless bee metamorphosis – Paludo – PLoS One

Preprint: Effects of the copper IUD on composition of the vaginal microbiota in the olive baboon – Eastman – bioRxiv

Plant, root, and soil microbiome

Nitrogen fertilization altered arbuscular mycorrhizal fungi abundance and soil erosion of paddy fields in the Taihu Lake region of China – Zhang – Environmental Science and Pollution Research

Reconciling disparate responses to grazing in the arbuscular mycorrhizal symbiosis – van Der Heyde – Rhizosphere

Redox-driven shifts in soil microbial community structure in the drawdown zone after construction of the Three Gorges Dam – Wang – Soil Ecology Letters

Water and extremophile microbiome

Biomarker Profiling of Microbial Mats in the Geothermal Band of Cerro Caliente, Deception Island (Antarctica): Life at the Edge of Heat and cold – Lezcano – Astrobiology

Microbial diversity analysis and screening for novel xylanase enzymes from the sediment of the Lobios Hot Spring in Spain – Knapik – Scientific Reports

Built environment

How does urban wastewater treatment affect the microbial quality of treated wastewater? – Lopez – Process Safety and Environmental Protection

Identifying microbial community evolution in membrane bioreactors coupled with anaerobic side-stream reactor, packing carriers and ultrasonication for sludge reduction by linear discriminant analysis – Zheng – Bioresource Technology

Food microbiology

Preprint: Deep microbial community profiling along the fermentation process of pulque, a major biocultural resource of Mexico – Rocha-Arriaga – bioRxiv

Bioinformatics

Preprint: µbialSim: constraint-based dynamic simulation of complex microbiomes – Popp and Centler – bioRxiv

July 29, 2019

Good Morning! Highlights of today’s digest include a revisited study that showed a significant alterations in the gut microbiome by the consumption of low/no-calorie sweeteners (LNCS), such as Splenda, and raising safety concerns, another work tells us development of Burkholderia-free host plant model to show how Burkholderia helps plant development, and finally a study finds a mechanistic link between the gut microbiome and early childhood asthma as shown with highthened expression of bacterial genes that make 12,13-diHOME which alters immune response.

Human gut microbiome

***Revisited: Assessing the in vivo data on low/no-calorie sweeteners and the gut microbiota – Susan S. Schiffman et al. – Food and Chemical Toxicology

A structured weight loss program increases gut microbiota phylogenetic diversity and reduces levels of Collinsella in obese type 2 diabetics: A pilot study – Fabian Frost et al. – PLOS ONE

Human respiratory microbiome

Chronic obstructive pulmonary disease upper airway microbiome is associated with select clinical characteristics – Alexa A. Pragman et al. – PLOS ONE

Animal experiments

***Elevated faecal 12,13-diHOME concentration in neonates at high risk for asthma is produced by gut bacteria and impedes immune tolerance – Sophia R. Levan et al. – Nature Microbiology

Effect of live yeast Saccharomyces cerevisiae supplementation on the performance and cecum microbial profile of suckling piglets – Tadele G. Kiros et al. – PLOS ONE

Low-dose inoculation of Escherichia coli achieves robust vaginal colonization and results in ascending infection accompanied by severe uterine inflammation in mice – Valerie P. O’Brien – PLOS ONE

Probiotic strains improve high-fat diet-induced hypercholesterolemia through modulating gut microbiota in ways different from atorvastatin – Dun Su et al. – bioRxiv

Host Genotype-shaped Gut Microbiome Modulate Atherosclerosis Development in Mice – Kazuyuki Kasahara et al. – Arteriosclerosis, Thrombosis, and Vascular Biology

Animal microbiome

Fecal microbiota of different reproductive stages of the central population of the lesser-long nosed bat, Leptonycteris yerbabuenae – Osiris Gaona et al. – PLOS ONE

Taxon appearance from extraction and amplification steps demonstrates the value of multiple controls in tick microbiome analysis – Emilie Lejal et al. – bioRxiv

Characterization of the gastrointestinal bacterial microbiome of farmed juvenile and adult white Cachama (Piaractus brachypomus) – Victor Alfonso et al. – Aquaculture

Biosynthesis and Characterization, Antioxidant and Antimicrobial Activities
of Selenium Nanoparticles from Ethanol Extract of Bee Propolis
– Shubharani R. et al. – Journal of Nanomedicine & Nanotechnology

Plant, root and soil microbiome

The role of inoculum dispersal and plant species identity in the assembly of leaf endophytic fungal communities – Kevin D. Ricks et al. – PLOS ONE

***Is the bacterial leaf nodule symbiosis obligate for Psychotria umbellata? The development of a Burkholderia-free host plant – Arne Sinnesael et al. – PLOS ONE

AOA and AOB communities respond differently to changes of soil pH under long-term fertilization – Rubio Sun et al. – Soil Ecology Letters

***Negative plant-microbiome feedback limits productivity in aquaponics – Jessica A. Day et al. – bioRxiv

Do plant–microbe interactions and aluminum tolerance influence
alpine sedge species’ responses to nitrogen deposition?
– Teal S. Potter et al. – Ecosphere

Plant diversity and fertilizer management shape the belowground microbiome of native grass bioenergy feedstocks – Daniel Revillini et al. – Frontiers in Plant Science

Microbial taxonomical composition in spruce phyllosphere, but not community functional structure, varies by geographical location – Yunshi Li et al. – PeerJ

Responses of plant growth, physiological, gas exchange parameters of super and non-super rice to rhizosphere temperature at the tillering stage – Shuying Li at al. – Nature Scientific Reports

Influence of introduced arbuscular mycorrhizal fungi and phosphorus sources on plant traits, soil properties, and rhizosphere microbial communities in organic legume-flax rotation – Yunliang Li et al. – Plant and Soil

Effects of arbuscular mycorrhizal fungi on inoculated seedling growth and rhizosphere soil aggregates – Zhongfeng Zhang et al. – Soil and Tillage Research

Properties of bacterial community in the rhizosphere soils of Achyranthes bidentata tolerant to consecutive monoculture – Juanying Wang et al. – Plant Growth Regulation

The role of volatile organic compounds and rhizosphere competence in the mode of action of the non-pathogenic Fusarium oxysporum FO12 towards Verticillium wilt – Mulero-Aparicio et al. – Frontiers in Microbiology

Dynamic changes in soil chemical properties and microbial community structure in response to different nitrogen fertilizers in an acidified celery soil – Yuping Wu et al. – Soil Ecology Letters

Improved rhizoremediation for decabromodiphenyl ether (BDE-209) in E-waste contaminated soils – Jiayin Feng et al. – Soil Ecology Letters

Review: Soil biofilms: microbial interactions, challenges, and advanced techniques for ex-situ characterization – Peng Cai et al. – Soil Ecology Letters

Organic amendment effects on nematode distribution within aggregate fractions in agricultural soils – Xiaoke Zhang et al. – Soil Ecology Letters

Water and extermophile microbiome

Book chapter: New Perspectives on the Distribution and Roles of Thermophilic Fungi – Miriam I. Hutchinson et al. – Fungi in Extreme Environments: Ecological Role and Biotechnological Significance

Diversity and biogeography of eukaryotic microorganism in the deepsea sediment of the Eastern Indian Ocean – Xiaoxia Ma et al. – International Journal of Science

Phages and viruses

Phage composition of a fermented milk and colostrum product assessed by microbiome array; putative role of open reading frames – Stefania Pacini et al. – bioRxiv

Techniques

Modelling approaches for studying the microbiome – Manish Kumar et al. – Nature Microbiology

Guest Editorial: Beyond sequencing: fast and easy microbiome profiling by flow cytometry – Charlotte Esser at al. – Archives of Toxicology

View Point: Opportunities at the Intersection of Synthetic Biology, Machine Learning, and Automation – Pablo Carbonell et al. – ACS Synthetic Biology

Microbes in the News

***Elevated Concentration of Lipid in Neonatal Microbiome Predicts Later Risk for Asthma, Allergy – Allison Inserro – AJMC Newsroom

July 18, 2019

Have a nice Thursday! Today in this Digest, we have papers with clinical implications for the use of microbiota in disease analysis; for example: a paper presenting a model for the use of gut microbiota for disease classification, or an article showing the impact of microbiota in cardiometabolic risk. Today we have several papers about animal microbiome or studies in animal models, including an interesting article showing a relationship between wasp adaptation and their microbiota. And, of course, more papers!

 

Human and General Microbiome

* Establishment and evaluation of prediction model for multiple disease classification based on gut microbial data – Sohyun Bang – Scientific Reports

* Gut microbiota composition explains more variance in the host cardiometabolic risk than genetic ancestry – Sandra J. Guzmán-Castañeda – Gut Microbes 

Species Deletions from Microbiome Consortia Reveal Key Metabolic Interactions between Gut Microbes – Natalia Gutiérrez – mSystems

The association between pneumococcal vaccination, ethnicity, and the nasopharyngeal microbiota of children in Fiji – Laura K. Boelsen – Microbiome

Crypt- and Mucosa-Associated Core Microbiotas in Humans and Their Alteration in Colon Cancer PatientsAzadeh Saffarian – mBio

A Bacteriophage Cocktail Eliminates Salmonella Typhimurium from the Human Colonic Microbiome while Preserving Cytokine Signaling and Preventing Attachment to and Invasion of Human Cells by Salmonella In Vitro – Zachary D. Moye – Journal of Food Protection

Discovery of potential genes contributing to the biosynthesis of short-chain fatty acids and lactate in gut microbiota from systematic investigation in E. coli – Chunhua Zhao – npj Biofilms and Microbiomes

Altered in Vitro Metabolomic Response of the Human Microbiota to Sweeteners – Emanuel Vamanu – Genes

Research Highlight: Microbiota supplements to improve metabolic health – Anna Kriebs – Nature Reviews Endocrinology

Review: Ketogenic Diet and Microbiota: Friends or Enemies? – Antonio Paoli – Genes

Review: Supporting a Healthy Microbiome for the Primary Prevention of Eczema – Sofia Szari – Clinical Reviews in Allergy & Immunology

A Comparative Analysis of Biosynthetic Gene Clusters in Lean and Obese Humans – Shengqin Wang – BioMed Research International

 

Animal Models / Animal Experiments

* Phylosymbiosis Impacts Adaptive Traits in Nasonia Wasps – Edward J. van Opstal – mBio

The microbiota protects from viral-induced neurologic damage through microglia-intrinsic TLR signaling – D Garrett Brown – eLife

Pregnancy and lactation interfere with the response of autoimmunity to modulation of gut microbiota – Qinghui Mu – Microbiome

Polysaccharide A-Dependent Opposing Effects of Mucosal and Systemic Exposures to Human Gut Commensal Bacteroides Fragilis in Type 1 Diabetes – M. Hanief – Diabetes

Heart failure developed after myocardial infarction does not affect gut microbiota composition in the rat – Renata Maria Lataro – Gastrointestinal and Liver Physiology

Effect of chrysin on changes in intestinal environment and microbiome induced by fructose-feeding in rats – Nelson Andrade – Food & Function

Microbiota of periodontal pockets and root canals in induced experimental periodontal disease in dogs – Cícero R. Gadê‐Neto – Journal of Investigative and Clinical Dentistry

Frontline Science: Abnormalities in the gut mucosa of non-obese diabetic mice precede the onset of type 1 diabetes – Mariana Camila Gonçalves Miranda – Journal of Leukocyte Biology

Early Feeding Regime of Waste Milk, Milk, and Milk Replacer for Calves Has Different Effects on Rumen Fermentation and the Bacterial Community – Rong Zhang – Animals

 

Beneficial Compounds and Microbes

Modified apple polysaccharide regulates microbial dysbiosis to suppress high-fat diet-induced obesity in C57BL/6J mice – Yuhua Li – European Journal of Nutrition

Mulberry leaves ameliorate obesity through enhancing brown adipose tissue activity and modulating gut microbiota – Yao Sheng – Food & Function

 

Plant Microbiome

Root-specific camalexin biosynthesis controls the plant growth-promoting effects of multiple bacterial strains – Anna Koprivova – PNAS

 

Environmental Microbiome

An RNA-based quantitative and compositional study of ammonium-oxidizing bacteria and archaea in Lake Taihu, a eutrophic freshwater lake – Tong-tong Liu – FEMS Microbiology Ecology

Exploring Biodiversity and Arsenic Metabolism of Microbiota Inhabiting Arsenic-Rich Groundwaters in Northern Italy – Lucia Cavalca – Frontiers in Microbiology

June 27, 2019

This Thursday, read about the well-to-well contamination in microbiome research, antibiotic resistance gene pool in avian microbiomes, a novel robust taxonomic framework (AutoTax), and more. Happy reading!

General microbiome

*Quantifying and Understanding Well-to-Well Contamination in Microbiome Research – Jeremiah J. Minich – mSystems

Controlling for Contaminants in Low-Biomass 16S rRNA Gene Sequencing Experiments – Lisa Karstens – mSystems

Skin microbiome

The impact of skin care products on skin chemistry and microbiome dynamics – Amina Bouslimani – BMC Biology

Animal microbiome

*Meta-transcriptomics reveals a diverse antibiotic resistance gene pool in avian microbiomes – Vanessa R. Marcelin – BMC Biology

Soil microbiome

Defoliation management and grass growth habits modulated the soil microbial community of turfgrass systems – Qing Xia – PlosOne

Comparative overview of red kidney bean (Phaseolus valgaris) rhizospheric bacterial diversity in perspective of altitudinal variations – Deep Chandra Suyal – Biologia

Animal experiments

Puerarin prevents high-fat diet-induced obesity by enriching Akkermansia muciniphila in the gut microbiota of mice – Lei Wang – PlosOne

Water and extremophile microbiome

The anaerobic digestion microbiome: a collection of 1600 metagenome-assembled genomes shows high species diversity related to methane production – Stefano Campanaroa – bioRxiv

In situ transformation of ethoxylate and glycol surfactants by shale-colonizing microorganisms during hydraulic fracturing – Morgan V. Evans – ISME Journal

Bioinformatics

*Comprehensive ecosystem-specific 16S rRNA gene databases with automated taxonomy assignment (AutoTax) provide species-level resolution in microbial ecology – Morten Simonsen Dueholm – bioRxiv

June 24, 2019

Happy Monday! In today’s Digest, you’ll find a primer on metabolomics, a description of the fungal and bacterial communities involved in coffee fermentation, and several studies on extremophile communities.

General Microbiome
Staring into the void: Demystifying microbial metabolomics – Cynthia M Grim – FEMS Microbiology Letters

Bacterial metabolism-inspired molecules to modulate antibiotic efficacy – Yuan Liu – Journal of Antimicrobial Chemotherapy

Deterministic processes structure bacterial genetic communities across an urban landscape – J. M. Hassell – Nature Communications

Gut Microbiome
Bifidobacterium dentium Fortifies the Intestinal Mucus Layer via Autophagy and Calcium Signaling Pathways – Melinda A. Engevik – mBio

Lipopolysaccharides modulate intestinal epithelial permeability and inflammation in a species-specific manner – Matthew Stephens – Gut Microbes

Fecal Microbiome Data Distinguish Liver Recipients with Normal and Abnormal Liver Function from Healthy Controls – Hai-feng Lu – Frontiers in Microbiology

Human Microbiota and Personalized Cancer Treatments: Role of Commensal Microbes in Treatment Outcomes for Cancer Patients – Stephen Gately – Precision Medicine in Cancer Therapy

Animal Experiments
Intervening Effects of Total Alkaloids of Corydalis saxicola Bunting on Rats With Antibiotic-Induced Gut Microbiota Dysbiosis Based on 16S rRNA Gene Sequencing and Untargeted Metabolomics Analyses – Xi Liu – Frontiers in Microbiology

Animal Microbiome
Gestation alters the gut microbiota of an oviparous lizard – Brian K Trevelline – FEMS Microbiology Ecology

Diversity of deep-water coral associated bacteria and comparison across depth gradients – Sigmund Jensen – FEMS Microbiology Ecology

Plant, Root, and Soil Microbiome
Bacterial and archaeal spatial distribution and its environmental drivers in an extremely haloalkaline soil at the landscape scale – Martha Adriana Martínez-Olivas – PeerJ

The microbial community in an alkaline saline sediment of a former maar lake bed – Claudia L. Ibarra-Sánchez – Journal of Soils and Sediments

Impacts on soil microbial characteristics and their restorability with different soil disinfestation approaches in intensively cropped greenhouse soils – Tianzhu Meng – Applied Microbiology and Biotechnology

Nonylphenol causes shifts in microbial communities and nitrogen mineralization in soil microcosms – Stefania Mattana – Ecotoxicology and Environmental Safety

Changes in Plant Rhizosphere Microbial Communities under Different Vegetation Restoration Patterns in Karst and Non-karst Ecosystems – Zhouzhou Fan – Scientific Reports

Water and Extremophile Microbiome
Culture independent bacterial diversity of Changme Khang and Changme Khangpu glaciers of North Sikkim, India – Mingma Thundu Sherpa – Environmental Sustainability

Selection of a Microbial Community in the Course of Formation of Acid Mine Drainage – V. V. Kadnikov – Microbiology

Thermophilic Bacteria in Lake Baikal Bottom Sediments Associated with Hydrocarbon Discharge – O. N. Pavlova – Microbiology

Bacterial alkylquinolone signaling contributes to structuring microbial communities in the ocean – Kristen E. Whalen – Microbiome

Food Microbiology
First description of bacterial and fungal communities in Colombian coffee beans fermentation analysed using Illumina-based amplicon sequencing – Ana C. de Oliveira Junqueira – Scientific Reports

Techniques
Functional Gene Array-Based Ultrasensitive and Quantitative Detection of Microbial Populations in Complex Communities – Zhou Shi – mSystems

June 11, 2019

Today’s digest is about microbiome and Alzheimer’s disease association, global survey of arsenic related genes in soil microbiome,  Bifidobacterium bifidus in infant gut and a preprint on selection in host microbiome evolution.

General microbiome

Understanding the Role of the Gut Microbiome and Microbial Metabolites in Obesity and Obesity-Associated Metabolic Disorders: Current Evidence and Perspectives – Natalia Vallianou – Current Obesity Reports

Alzheimer’s disease and symbiotic microbiota: an evolutionary medicine perspective – Molly Fox – Annals of the New York Academy of Sciences

Biogeography of the Oral Microbiome: The Site-Specialist Hypothesis – Jessica L. Mark Welch – Annual Review of Microbiology

Human microbiome

Colonic mucosal and exfoliome transcriptomic profiling and fecal microbiome response to a flaxseed lignan extract intervention in humans – Johanna W. Lampe – American journal of Clinical Nutrition

Analysis of Transcriptionally Active Bacteria Throughout the Gastrointestinal Tract of Healthy Individuals – Riccardo Vasapolli – Gastroenterology

Identification of Salivary Microbiota and its Association with Host Inflammatory Mediators in Periodontitis – Anna Lundmark – Frontiers in Cellular and Infection Microbiology

Effect of the Degree of Polymerization of Fructans on Ex Vivo Fermented Human Gut Microbiome – Erola Astó – Nutrients

Inflammatory skin is associated with changes in the skin microbiota composition on the back of severe acne patients – Marie-Ange Dagnelie – Experimental Dermatology

Gut microbiota development of preterm infants hospitalised in intensive care units – H. Tauchi – Beneficial Microbes

Animal experiments

Antibiotic treatment in feedlot cattle: a longitudinal study of the effect of oxytetracycline and tulathromycin on the fecal and nasopharyngeal microbiota – Devin B. Holman – Microbiome

Sequential changes in the host gut microbiota during infection with the intestinal parasitic nematode Strongyloides venezuelensis – Tanzila Afrin – Frontiers in Cellular and Infection Microbiology

Plant, root, soil microbiome

A global survey of arsenic-related genes in soil microbiomes – Taylor K. Dunivin – BMC Biology

Geochemical-Compositional-Functional Changes in Arctic Soil Microbiomes Post Land Submergence Revealed by Metagenomics – Nengfei Wang – Microbes and Environments

Water microbiome and extremophiles

Comparison of the microbiomes of two drinking water distribution systems—with and without residual chloramine disinfection – Michael B. Waak – Microbiome

Probiotics

Probiotics may not prevent the deterioration of necrotizing enterocolitis from stage I to II/III – Zheng-Li Wang – BMC Pediatrics

Bifidobacterium bifidum and the infant gut microbiota: an intriguing case of microbe‐host co‐evolution – Sabrina Duranti – Environmental Microbiology

Techniques

NanoARG: a web service for detecting and contextualizing antimicrobial resistance genes from nanopore-derived metagenomes – G.A.Arango-Argoty – Microbiome

Metabolic route computation in organism communities – Markus Krummenacker – Microbiome

The role of multilevel selection in host microbiome evolution – Simon van Vliet – BioRxiv

Microbes and the market

Human Microbiome Therapeutics Market Analysis 2019: With Top 20 Countries data, Product Types, Segmentation, Market Share Analysis, Influential Trends And Challenges, Forecast To 2023 – Saginaw Daily

Global Human Microbiome Based Drugs and Diagnostics Market Potential Growth 2019 | Second Genome Inc., Enterome Bioscience, Yakult – Business Tech Hub

Human Microbiome Market 2024 Significant Development | Future Trends of Key Players by Size and Share – The Warren Daily

In-Depth Research Report of Global Microbiome Sequencing Services Market (2019 Version), with Types, Application, and Manufactures – the Pueblo Daily

Microbiome Sequencing Services Market Key Players, Industry Overview, Demand & Supply Chain Analysis, Forecast To 2024 – Burbank Observer

Human Microbiome Market Growth, Trend and Forecast 2018-2026 – Business Herald