Category Archives: Extremophiles

January 16, 2020

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Good morning/night everyone!

What I love about writing for MD is the huge diversity of topics we’re meeting along the process of making the daily digest. Even though I’m mostly working on plant and root microbiome, it’s amazing to see how diverse is the world of microbiome and how much more there is to accomplish. Check out today’s digest- and don’t forget the News section as well! it is highly interesting!

General Microbiology

Detection of phylogenetic core groups in diverse microbial ecosystems, Marcos Parras Molto, bioRxiv

Isolation of an archaeon at the prokaryote–eukaryote interface, Hiroyuki Imachi, Nature

Ferrosomes are iron storage organelles formed by broadly conserved gene clusters in bacteria and archaea, Carly R. Grant , bioRxiv

Human microbiome

Distribution of microbial communities and core microbiome in successive wound grades of diabetic foot ulcer individuals, Apoorva Jnana, AEM

Animal microbiome

Parasites modulate the gut-microbiome in insects: A proof-of-concept study, Brian Fredensborg, PlosONE

The effect of diet on the gastrointestinal microbiome of juvenile rehabilitating green turtles (Chelonia mydas), Jennifer Bloodgood ,PlosONE

Rotten-skin disease significantly changed giant spiny frog(Paa spinosa) gut microbiota, Tuoyu He, bioRxiv

Bacterial Biogeography of the Colon in Dogs With Chronic Inflammatory Enteropathy, Paula Giaretta, Veterniary Pathology

Plant and environmental microbiome

Biostimulants applied to maize seeds modulate the enzymatic activity and metaproteome of the rhizosphere, Monica Mattarozzi, Applied Soil Ecology

Biological inhibition of soil nitrification by forest tree species affects Nitrobacter populations, Amandine Laffite, Environmental Microbiology

Extremophile microalgae: An overview, Veronica Malavasi , Journal of Phycology

Methods in microbiome

**Taxonomic classification method for metagenomics based on
core protein families with Core-Kaiju, Anna Tovo, bioRxiv

**Metagenomic sequencing with spiked primer enrichment for viral diagnostics and genomic surveillance, Xianding Deng , Nature Microbiology

Quantitative PCR provides a simple and accessible method for quantitative microbiota profiling, Ching Jian, PlosONE

The effect of storage conditions on microbial communities in stool, Kristien Nel Van Zyl, PlosONE

Beyond mass spectrometry, the next step in proteomics, Winston and Gregory Timp, Science Advances

Microbiome in the news

Illumina Announces New Sequencing System, Partnership with Roche and Software Suite to Accelerate Adoption of Genomics

Integrating microbiomes into clinical trials – the importance of time

Bayer and Azitra partnership looks to develop skin microbiome products for eczema

**Please read! our mental health is the MOST important thing in our life! Researchers facing ‘shocking’ levels of stress, survey reveals

October 16, 2019

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Happy Wednesday! Today’s digest includes the human gut virome, microbiome recovery after antibiotics, and the fungi growing on museum skeletons. Enjoy!

Pregnancy and early life

The vaginal microbial communities of healthy expectant Brazilian mothers and its correlation with the newborn’s gut colonization – Dobbler – World Journal of Microbiology and Biotechnology

Human skin microbiome

In vitro Antimicrobial Activity of Acne Drugs Against Skin-Associated Bacteria – Blaskovich – Scientific Reports

Human gut microbiome

Review: The Human Gut Virome Is Highly Diverse, Stable, and Individual Specific – Shkoporov – Cell Host & Microbe

Review: Inflammatory Bowel Disease: A Potential Result from the Collusion between Gut Microbiota and Mucosal Immune System – Yue – Microorganisms

Individualized recovery of gut microbial strains post antibiotics – Koo – npj Biofilms and Microbiomes

Animal experiments

Depletion of dietary aryl hydrocarbon receptor ligands alters microbiota composition and function – Brawner – Scientific Reports

Rat H1 parvovirus infection leads to alterations in gut microbiota – Xiang – Pathogens and Disease

Positive effect of an electrolyzed reduced water on gut permeability, fecal microbiota and liver in an animal model of Parkinson’s disease – Bordoni – PLoS One

The Sulfate-Reducing Microbial Communities and Meta-Analysis of Their Occurrence during Diseases of Small–Large Intestine Axis – Kushkevych – Journal of Clinical Medicine

Plant, root, and soil microbiome

Spatial gradients in the characteristics of soil-carbon fractions are associated with abiotic features but not microbial communities – Sengupta – Biogeosciences

Water and extremophile microbiome

Diversity, Distribution, and Ecology of Fungi in the Seasonal Snow of Antarctica – Menezes – Microorganisms

Interaction and assembly processes of abundant and rare microbial communities during a diatom bloom process – Zhang – Environmental Microbiology

Built environment

Changes in the Bacterioplankton Community Structure from Southern Gulf of Mexico During a Simulated Crude Oil Spill at Mesocosm Scale – Valencia-Agami – Microorganisms

Increased loading leads to convergence of microbial communities and high methane yield in adapted anaerobic co-digesters – Wang – Water Research

Skeleton bones in museum indoor environments offer niches for fungi and are affected by weathering and deposition of secondary minerals – Pinzari – Environmental Microbiology

Bioinformatics

Species abundance information improves sequence taxonomy classification accuracy – Kaehler – Nature Communications

October 5, 2019

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This weekend, read about how cooking food modifies the microbiome, how bacteria ‘strip off’ to evade antibiotics, and more. Check out an interesting pilot study looking at potential inclusion and exclusion criteria of donors for safe vaginal microbiota transplant. Enjoy!

Events

Bioinformatics for the Microbiome Symposium 2019, Stanford University, Monday October 28.
Some tickets are still available!

General microbiome

Mobile phones as fomites for potential pathogens in hospitals: microbiome analysis reveals hidden contaminants – Rebecca Simmonds – Journal of Hospital Infection

Review: Microbiomes as sources of emergent host phenotypes – J. B. Lynch and E. Y. Hsiao – Science

Vaginal microbiome

*Conceptual Design of a Universal Donor Screening Approach for Vaginal Microbiota Transplant – Kevin DeLong – Frontiers in Cellular and Infection Microbiology

Highly diverse anaerobe-predominant vaginal microbiota among HIV-infected pregnant women in Zambia – Joan T. Price – PlosOne

Urinary microbiome

*Possible role of L-form switching in recurrent urinary tract infection – Katarzyna M. Mickiewicz – Nature Communications

Aerococcus urinae and Globicatella sanguinis Persist in Polymicrobial Urethral Catheter Biofilms Examined in Longitudinal Profiles at the Proteomic Level – Yanbao Yu – Biochemistry Insights

Gut microbiome

*Cooking shapes the structure and function of the gut microbiome – Rachel N. Carmody – Nature Microbiology

Integrated paired-end enhancer profiling and whole-genome sequencing reveals recurrent CCNE1 and IGF2 enhancer hijacking in primary gastric adenocarcinoma – Wen Fong Ooi – Gut

Effects of Low-FODMAP Diet on Symptoms, Fecal Microbiome, and Markers of Inflammation in Patients With Quiescent Inflammatory Bowel Disease in a Randomized Trial – Selina R.Cox – Gastroenterology

Water microbiome

Trophic networks improve the performance of microbial anodes treating wastewater – Christin Koch – npj Biofilms and Microbiomes

Application of a novel molecular technique to characterise the effect of settling on microbial community composition of activated sludge – Luong N.Nguyen – Journal of Environmental Management

Bacterial diversity in Icelandic cold spring sources and in relation to the groundwater amphipod Crangonyx islandicus – Ragnhildur Guðmundsdóttir – PlosOne

Animal microbiome

Looking like the locals – gut microbiome changes post-release in an endangered species – Rowena Chong – Animal microbiome

Animal experiment

Letrozole treatment of pubertal female mice results in activational effects on reproduction, metabolism and the gut microbiome – Pablo Arroyo – PlosOne

Microbiota of MR1 deficient mice confer resistance against Clostridium difficile infection – Ashley D. Smith – PlosOne

Exploring the microbiota of upper respiratory tract during the development of pneumonia in a mouse model – Yoshitomo Morinaga – PlosOne

Plant microbiome

Microbiome profiling of the onion thrips, Thrips tabaci Lindeman (Thysanoptera: Thripidae) – Suresh J. Gawande – PlosOne

Food

Comparison of the microbial composition of African fermented foods using amplicon sequencing – Maria Diaz – Scientific Reports

The impact of grape processing and carbonic maceration on the microbiota of early stages of winemaking – Raffaele Guzzon – Journal of Applied Microbiology

Fungi

Phyllosphere Fungal Communities of Plum and Antifungal Activity of Indigenous Phenazine-Producing Pseudomonas synxantha Against Monilinia laxa – Tamara Janakiev – Frontiers in Microbiology

Microbial communities associated with the black morel Morchella sextelata cultivated in greenhouses – Gian Maria Niccolò Benucci – PeerJ

Viruses

The gut virome in inflammatory bowel disease pathogenesis: From metagenomics to novel therapeutic approaches – Federica Ungaro – United European Gastroenterology Journal

Association of the Eukaryotic Vaginal Virome with Prophylactic Antibiotic Exposure and Reproductive Outcomes in a Subfertile Population Undergoing In Vitro Fertilization: A Prospective Exploratory Study – Ashley M. Eskew – Obstetrics and Gynaecology

Bioinformatics

ProphET, prophage estimation tool: A stand-alone prophage sequence prediction tool with self-updating reference database – João L. Reis-Cunha – PlosOne

September 26, 2019

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Have a nice day! Today, in this digest we have a good number of papers, including those associated with beneficial microbes, compounds, and interventions. Some highlights: host-microbiome evolution, microbiome and urinary tract infections, the first reported bloodstream infection caused by gut-habiting Prevotella species, microbiome activity in halitosis, and more! Enjoy.   

 

General or Human Microbiome

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

Review: Diagnosis of Urinary Tract Infection in the Neuropathic Bladder: Changing the Paradigm to Include the Microbiome – Catherine S. Forster – Topics in Spinal Cord Injury Rehabilitation 

Review: A critical review on diet-induced microbiota changes and cardiovascular diseases – Muthukumaran Jayachandran – Critical Reviews in Food Science and Nutrition 

Review: Microbiota: a novel regulator of pain – Manon Defaye – Journal of Neural Transmission

Relationship of tongue coating microbiome on volatile sulfur compounds in healthy and halitosis adults – Wei Ye – Journal of Breath Research

An Infectious Diseases Perspective on Fecal Microbiota Transplantation for Clostridioides difficile Infection in Children – Jillian M Cotter – Journal of the Pediatric Infectious Diseases Society

First bloodstream infection caused by Prevotella copri in a heart failure elderly patient with Prevotella-dominated gut microbiota: a case report – Patrizia Posteraro – Gut Pathogens

Pain regulation by gut microbiota: molecular mechanisms and therapeutic potential – Ran Guo – British Journal of Anaesthesia

The Dysbiosis and Inter-Kingdom Synergy Model in Oropharyngeal Candidiasis, a New Perspective in Pathogenesis – Martinna Bertolini – Journal of Fungi

Microbiome Influence in the Pathogenesis of Prion and Alzheimer’s Diseases – Valeria D’Argenio – International Journal of Molecular Sciences

Protein Intake at Twice the RDA in Older Men Increases Circulatory Concentrations of the Microbiome Metabolite Trimethylamine-N-Oxide (TMAO) – Sarah M. Mitchell – Nutrients

Potential Strategies in the Prevention of Nonsteroidal Anti-inflammatory Drugs-Associated Adverse Effects in the Lower Gastrointestinal Tract – Chuan-Guo Guo – Gut and Liver

 

Composition of gut microbiota of children and adolescents with perinatal HIV infection taking antiretroviral therapy in Zimbabwe – Trym T Flygel – The Journal of Infectious Diseases

Gut Microbiome in Psoriasis is Perturbed Differently During Secukinumab and Ustekinumab Therapy and Associated with Response to Treatment – Nai-Lun Yeh – Clinical Drug Investigation

The association between gut microbiota development and maturation of intestinal bile acid metabolism in the first 3 y of healthy Japanese infants – Masaru Tanaka – Gut Microbes

 

Animal Microbiome

Food Preservatives Induce Proteobacteria Dysbiosis in Human-Microbiota Associated Nod2-Deficient Mice – Lucia Hrncirova – Microorganisms

Maternal Dietary Protein Intake Influences Milk and Offspring Gut Microbial Diversity in a Rat (Rattus norvegicus) Model –  Matthew F. Warren – Nutrients

Microbiota, Gut Health and Chicken Productivity: What Is the Connection? – Juan M. Diaz Carrasco – Microorganisms

Microbiota Composition and Functional Profiling Throughout the Gastrointestinal Tract of Commercial Weaning Piglets – Raphaële Gresse – Microorganisms 

Microbiota fingerprints within the oral cavity of cetaceans as indicators for population biomonitoring – Pedro Soares-Castro – Scientific Reports

Core gut microbial communities are maintained by beneficial interactions and strain variability in fish – Fotini Kokou – Nature Microbiology

Beneficial Microbes and Compounds

Role of Dietary Flavonoid Compounds in Driving Patterns of Microbial Community Assembly – Kerry L. Ivey – mBio

Oral Administration of β-Glucan and Lactobacillus plantarum Alleviates Atopic Dermatitis-like Symptoms – In Sung Kim – Journal of Microbiology and Biotechnology

Protective Effect of Probiotic Bacteria and Estrogen in Preventing HIV-1-Mediated Impairment of Epithelial Barrier Integrity in Female Genital Tract – Sara Dizzell – Cells (MPDI)

Fish Oil, but Not Olive Oil, Ameliorates Depressive-Like Behavior and Gut Microbiota Dysbiosis in Rats under Chronic Mild Stress – Te-Hsuan Tung – Biomolecules

The Potential Impact of Probiotics on the Gut Microbiome of Athletes – Laura Wosinska – Nutrients

Royal Jelly and Its Components Promote Healthy Aging and Longevity: From Animal Models to Humans – Hiroshi Kunugi – International Journal of Molecular Sciences

Postbiotics and Their Potential Applications in Early Life Nutrition and Beyond – Carrie A. M. Wegh – International Journal of Molecular Sciences

Antifungal and Antivirulence Activity of Vaginal Lactobacillus Spp. Products against Candida Vaginal Isolates – Camilla Itapary dos Santos – Pathogens

Metabolic and Vascular Effect of the Mediterranean Diet – Antonino Tuttolomondo – International Journal of Molecular Sciences

 

Environmental Microbiome

Unveiling resistome profiles in the sediments of an Antarctic volcanic island – V.B. Centurion – Environmental Pollution

Functional metagenomic analysis of dust-associated microbiomes above the Red Sea – Nojood A. Aalismail – Scientific Reports

 

Bioinformatics

The EFI Web Resource for Genomic Enzymology Web Tools: Leveraging Protein, Genome, and Metagenome Databases to Discover Novel Enzymes and Metabolic Pathways – Rémi Zallot – Biochemistry

Pavian: Interactive analysis of metagenomics data for microbiome studies and pathogen identification – Florian P Breitwieser – Biochemistry

 

Methods

Review: Common principles and best practices for engineering microbiomes – Christopher E. Lawson – Nature Reviews Microbiology

Sample Preservation and Storage Significantly Impact Taxonomic and Functional Profiles in Metaproteomics Studies of the Human Gut Microbiome – Oskar Hickl – Microorganisms

Optimizing bacterial DNA extraction in urine – Matthew M. Munch – PLoS One

 

September 20, 2019

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Have a nice day! In this digest, an interesting study about the relationship between peripheral serotonin synthesis and host glucose homeostasis, as well as another study showing the long-term maintained high levels of Proteobacteria in Crohn’s disease. And, of course, more papers!

 

Human and General Microbiome

Are we Ready for a “Microbiome-Guided Behaviour” Approach? – Andrea Lavazza – Cambridge Quarterly of Healthcare Ethics

The gut microbiome regulates host glucose homeostasis via peripheral serotonin – Alyce M. Martin – PNAS

Increased abundance of proteobacteria in aggressive Crohn’s disease seven years after diagnosis – M. K. Vester-Andersen – Scientific Reports

The Gut Microbiome and Pediatric Cancer: Current Research and Gaps in Knowledge – Roma Bhuta – JNCI Monographs

Time to test antibacterial therapy in Alzheimer’s disease – Francesco Panza – Brain

Discrepant gut microbiota markers for the classification of obesity-related metabolic abnormalities – Qiang Zeng – Scientific Reports

Altered Fecal Small RNA Profiles in Colorectal Cancer Reflect Gut Microbiome Composition in Stool Samples – Sonia Tarallo – mSystems

Analysis of gut microbiome, nutrition and immune status in autism spectrum disorder: a case-control study in Ecuador – María Fernanda Zurita – Gut Microbes 

Association of the Eukaryotic Vaginal Virome with Prophylactic Antibiotic Exposure and Reproductive Outcomes in a Subfertile Population Undergoing In Vitro Fertilization: A Prospective Exploratory Study – Ashley M. Eskew – BJOG

Development of an Index Score for Intestinal Inflammation-Associated Dysbiosis Using Real-World Stool Test Results – Lihong Chen – Digestive Diseases and Sciences

Benchmarking urine storage and collection conditions for evaluating the female urinary microbiome – Carrie E. Jung – Scientific Reports

Dysbiotic microbiota in autistic children and their mothers: persistence of fungal and bacterial wall-deficient L-form variants in blood – N. Markova – Scientific Reports

Features of Fecal and Colon Microbiomes Associate With Responses to Biologic Therapies for Inflammatory Bowel Diseases: a Systematic Review – Maria Manuela Estevinho – Clinical Gastroenterology and Hepatology

Loss of microbial diversity and pathogen domination of the gut microbiota in critically ill patients – Anuradha Ravi – Microbial Genomics

Complex interactions between the microbiome and cancer immune therapy – Drew J. Schwartz – Critical Reviews in Clinical Laboratory Sciences

Disentangling the effect of host genetics and gut microbiota on resistance to an intestinal parasite – Bruno Faivre – International Journal for Parasitology

Small talk: microbial metabolites involved in the signaling from microbiota to brain – Giorgia Caspani – Current Opinion in Pharmacology

Sputum microbiota and inflammation at stable state and during exacerbations in a cohort of chronic obstructive pulmonary disease (COPD) patients – Solveig Tangedal – PLoS One

 

Animal Microbiome / Animal Experiments

Microbiome composition shapes rapid genomic adaptation of Drosophila melanogaster – Seth M. Rudman – PNAS

Abnormal composition of gut microbiota is associated with resilience versus susceptibility to inescapable electric stress – Kai Zhang – Translational Psychiatry

Adenovirus infection is associated with altered gut microbial communities in a non-human primate – Wasimuddin – Scientific Reports

 

Beneficial Microbes and Compounds

Honey Polyphenols Ameliorate DSS-induced Ulcerative Colitis Via Modulating Gut Microbiota in Rats – Haoan Zhao – Molecular Nutrition and Food Research

ω-3 PUFAs Alleviate High-fat Diet Induced Circadian Intestinal Microbes Dysbiosis – Lifeng Gui – Molecular Nutrition and Food Research

Additional Candida albicans administration enhances the severity of dextran sulfate solution induced colitis mouse model through leaky gut-enhanced systemic inflammation and gut-dysbiosis but attenuated by Lactobacillus rhamnosus L34 – Wimonrat Panpetch – Gut Microbes

Equol: A Bacterial Metabolite from The Daidzein Isoflavone and Its Presumed Beneficial Health Effects –  Baltasar Mayo – Nutrients

Dietary cranberry suppressed colonic inflammation and alleviated gut microbiota dysbiosis in dextran sodium sulfate-treated mice – Xiaokun Cai – Food and Function

 

Food Microbiome

Deciphering the microbiome shift during fermentation of medicinal plants – Martina Köberl – Scientific Reports

 

Plant Microbiome

The aeroponic rhizosphere microbiome: community dynamics in early succession suggest strong selectional forces – Jennifer W. Edmonds – Antonie van Leeuwenhoek

 

Extremophiles

A shared core microbiome in soda lakes separated by large distances – Jackie K. Zorz – Nature Communications

 

Methods

Phylogenetic microbiota profiling in fecal samples depends on combination of sequencing depth and choice of NGS analysis method – Sukithar K. Rajan – PLoS One

Gut microbiome comparability of fresh-frozen versus stabilized-frozen samples from hospitalized patients using 16S rRNA gene and shotgun metagenomic sequencing – Emma E. Ilett – Scientific Reports

 

September 17, 2019

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Happy Tuesday! Today’s digest includes wastewater treatment biofilms, the microbiome during Crohn’s disease remission, and the bacteria associated with acid mine drainage. Enjoy!

Human oral microbiome

Succession of oral microbiota community as a tool to estimate postmortem interval – Dong – Scientific Reports

Human gut microbiome

Remission in Crohn’s disease is accompanied by alterations in the gut microbiota and mucins production – Magro – Scientific Reports

Specific gut microbiome members are associated with distinct immune markers in pediatric allogeneic hematopoietic stem cell transplantation – Ingham – Microbiome

Effect of a Chinese medical nutrition therapy diet on gut microbiota and short chain fatty acids in the simulator of the human intestinal microbial ecosystem (SHIME) – Wu – Journal of Functional Foods

A comprehensive assessment of demographic, environmental, and host genetic associations with gut microbiome diversity in healthy individuals – Scepanovic – Microbiome

Animal experiments

Dietary Bovine Milk Exosomes Elicit Changes in Bacterial Communities in C57BL/6 Mice – Zhou – American Journal of Physiology

Microbial Metabolism Modulates Antibiotic Susceptibility within the Murine Gut Microbiome – Cabral – Cell Metabolism

Animal microbiome

Maternal vs artificial rearing shapes the rumen microbiome having minor long‐term physiological implications – Belanche – Environmental Microbiology

Plant, root, and soil microbiome

Impact of continuous Panax notoginseng plantation on soil microbial and biochemical properties – Zhang – Scientific Reports

Three Bermudagrass-suppression techniques have little effect on soil-nutrient availability and microbial communities 200 days after application – Farthing – Applied Soil Ecology

Water and extremophile microbiome

Effect of salinity on mature wastewater treatment biofilm microbial community assembly and metabolite characteristics – Wang – Science of the Total Environment

Diversity and functional profile of bacterial communities at Lancaster acid mine drainage dam, South Africa as revealed by 16S rRNA gene high-throughput sequencing analysis – Lukhele – Extremophiles

Abiotic stress resistance, plant growth promotion and antifungal potential of halotolerant bacteria from a Tunisian solar saltern – Masmoudi – Microbiological Research

Built environment

Effective removal of antibiotic resistance genes and potential links with archaeal communities during vacuum-type composting and positive-pressure composting – Fan – Journal of Environmental Science

Hydraulically Fractured Natural-Gas Well Microbial Communities Contain Genomic Halogenation and Dehalogenation Potential – Evans – Environmental Science & Technology Letters

Successional trophic complexity and biogeographical structure of eukaryotic communities in waterworks rapid sand filters – Harder – FEMS Microbiology Ecology

September 3, 2019

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Happy Tuesday and best of luck to those headed back to school! In today’s Digest, you’ll find the virome of the mosquito gut, leveraging blood metabolomics to predict gut alpha diversity, and a comparison of bacterial taxa consumed in organic vs. conventional apples.

General microbiome
Changes in microbial community structure during dark fermentative hydrogen production – Guang Yang – International Journal of Hydrogen Energy

Pregnancy and early life
Effect of the vaginal microbiome on the pregnancy rate in women receiving assisted reproductive treatment – Andrea Bernabeu – Journal of Assisted Reproduction and Genetics

Maturation of the infant rhesus macaque gut microbiome and its role in the development of diarrheal disease – Nicholas Rhoades – Genome Biology

Human gut microbiome
Blood metabolome predicts gut microbiome α-diversity in humans – Nature Biotechnology – Tomasz Wilmanski

B cell superantigens in the human intestinal microbiota – Jeffrey J. Bunker – Science Translational Medicine

Long-read metagenomic exploration of extrachromosomal mobile genetic elements in the human gut – Yoshihiko Suzuki – Microbiome

Microbiome of death
Preprint: Manner of death and demographic effects on microbial community composition in organs of the human cadaver – Holly L Lutz – bioRxiv

Animal experiments
Diet-induced remission in chronic enteropathy is associated with altered microbial community structure and synthesis of secondary bile acids – Shuai Wang – Microbiome

Animal microbiome
Testing the relationship between microbiome composition and flux of carbon and nutrients in Caribbean coral reef sponges – Shelby E. Gantt – Microbiome

Plant, root, and soil microbiome
A new family of uncultivated bacteria involved in methanogenesis from the ubiquitous osmolyte glycine betaine in coastal saltmarsh sediments – Helen J. Jones – Microbiome

Top-down Enrichment Guides in Formation of Synthetic Microbial Consortia for Biomass Degradation – Sean P. Gilmore – ACS Synthetic Biology

Microbial community response to environmental changes in a technosol historically contaminated by the burning of chemical ammunitions – Hugues Thouin – Science of the Total Environment

Preprint: Intra-genus metabolic diversity facilitates co-occurrence of multiple Ferrovum species at an acid mine drainage site – Christen L Grettenberger – bioRxiv

Water and extremophile microbiome
Exploring the effects of operational mode and microbial interactions on bacterial community assembly in a one-stage partial-nitritation anammox reactor using integrated multi-omics – Yulin Wang – Microbiome

Fungi in salterns – Dawoon Chung – Journal of Microbiology

Distinct temporal dynamics of planktonic archaeal and bacterial assemblages in the bays of the Yellow Sea – Jong-Geol Kim – Plos One

Food microbiology
An Apple a Day: Which Bacteria Do We Eat With Organic and Conventional Apples? – Birgit Wassermann – Frontiers in Microbiology

Preprint: Molecular characterization of bacterial communities in sheep cheese through 16S rRNA gene sequencing – Creciana Maria Endres – bioRxiv

Phages and viruses
Stable distinct core eukaryotic viromes in different mosquito species from Guadeloupe, using single mosquito viral metagenomics – Chenyan Shi – Microbiome

The virome of cerebrospinal fluid: viruses where we once thought there were none – Chandrabali Ghose – Frontiers in Microbiology

Detecting viral sequences in NGS data – Paul G. Cantalupo – Current Opinion in Virology

Bioinformatics
Identification of discriminatory antibiotic resistance genes among environmental resistomes using extremely randomized tree algorithm – Suraj Gupta – Microbiome

August 24, 2019

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This weekend, read about the microbial index of skin health for children with eczema, gut microbiome of koalas, and interactions between the gut bacterial microbiome and virome of rhesus monkey. Happy reading!

General microbiome

Why we need a small data paradigm – Eric B. Hekler – BMC Medicine

Correspondence: The importance of genome sequence quality to microbial comparative genomics – Theo H. M. Smits – BMC Genomics

The applications of Big Data in molecular diagnostics – Yin Kwan Evelyn Wong – Expert Review of Molecular Diagnostics

Tiny Hidden Genes within Our Microbiome – Karin Mittelman & David Burstein – Cell

Skin microbiome

*A Microbiome-Based Index for Assessing Skin Health and Treatment Effects for Atopic Dermatitis in Children – Zheng Sun – mSystems

Gut microbiome

Reproducible changes in the gut microbiome suggest a shift in microbial and host metabolism during spaceflight – Peng Jiang – Microbiome

Review: Gut Microbiota, Dietary Phytochemicals, and Benefits to Human Health – Ran Yin – Current Pharmacology Reports

Mild cognitive impairment has similar alterations as Alzheimer’s disease in gut microbiota – Binyin Li – Alzheimer’s & Dementia

Design of synthetic microbial consortia for gut microbiota modulation – Jorge F. Vázquez-Castellanos – Current Opinion in Pharmacology

Intestinal microbiota and colorectal cancer: changes in the intestinal microenvironment and their relation to the disease – Sandra Aparecida dos Reis – Journal of Medical Microbiology

Review: Celiac disease: a comprehensive current review – Giacomo Caio – BMC Medicine

Pregnancy and early life

Maternal IgA protects against the development of necrotizing enterocolitis in preterm infants – Kathyayini P. Gopalakrishna – Nature Medicine

Oral microbiome

Oral Microbiome and Cancer Therapy-Induced Oral Mucositis – Jean-Luc C Mougeot – JNCI Monographs

Respiratory microbiome

Deciphering the Ecology of Cystic Fibrosis Bacterial Communities: Towards Systems-Level Integration – Annamaria Bevivino – Trends in Molecular Medicine

Water and extremophile microbiome

Effects of water recirculation rate on the microbial community and water quality in relation to the growth and survival of white shrimp (Litopenaeus vannamei) – Zhao Chen – BMC Microbiology

Pseudomethylobacillus aquaticus gen. nov., sp. nov., a new member of the family Methylophilaceae isolated from an artificial reservoir – Ceshing Sheu – International Journal of Systematic and Evolutionary Microbiology

Bacterial Communities from Extreme Environments: Vulcano Island – Camilla Fagorzi – Diversity

Diversity and biogeography of SAR11 bacteria from the Arctic Ocean – Susanne Kraemer – bioRxiv

Review: Metal and organic pollutants bioremediation by extremophile microorganisms – Patricia Giovanella – Journal of Hazardous Material

Animal microbiome

*Faecal inoculations alter the gastrointestinal microbiome and allow dietary expansion in a wild specialist herbivore, the koala – Michaela D. J. Blyton – Animal microbiome

Impact of pine leaf biochar amendment on bacterial dynamics and correlation of environmental factors during pig manure composting – Jiao Li – Bioresource Technology

Animal experiment

Potential roles of gut microbiome and metabolites in modulating ALS in mice – Eran Blacher – Nature

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

Inhibitory and nutrient use phenotypes among co‐existing Fusarium and Streptomyces populations suggest local coevolutionary interactions in soil – Adil Essarioui – Environmental Microbiology

Phages and viruses

*The altered gut virome community in rhesus monkeys is correlated with the gut bacterial microbiome and associated metabolites – Heng Li – Virology Journal

August 10, 2019

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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

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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