September 4, 2020

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Good morning and get ready to enjoy a small, but diverse microbiome digest. Enjoy!

COVID-19
Commentary: Misconceptions about weather and seasonality must not misguide COVID-19 response – Colin J Carlson et al. – Nature Communications

Multi-site human microbiome
Relationship between the composition of the intestinal microbiota and the tracheal and intestinal colonization by opportunistic pathogens in intensive care patients – Candice Fontaine et al. – PLOS One

Human gut microbiome
Widespread transfer of mobile antibiotic resistance genes within individual gut microbiomes revealed through bacterial Hi-C – Alyssa G. Kent et al. – Nature Communications

Animal experiments
Review: Modulation of gut microbiota in healthy rats after exposure to nutritional supplements – Mirna Cool et al. – Gut Microbes

Animal microbiome
Anthrax toxin component, Protective Antigen, protects insects from bacterial infection – Saleem Alarme – PLOS Pathogens

Environmental gut bacteria in European honey bees (Apis mellifera) from Australia and their relationship to the chalkbrood disease – Sheba Khan et al. – PLOS One

Gut Microbiome Composition is Associated with Age and Memory Performance in Pet Dogs – Eniko Kubinyi et al. – Animals

Plant, root, and soil microbiome
Characterizing the nectar microbiome of the non-native tropical milkweed, Asclepias curassavica, in an urban environment – Magdalena L. Warren et al. – PLOS One

Water and extremophile microbiome
Book chapter: Analyzing the Diversity of Microbial Communities Residing in Marine Ecosystems – Piyush Chandna et al. – In: Marine Biotechnology

Bioinformatics
Ten simple rules to power drug discovery with data science – Enrico Ferrero et al. – PLOS Computational Biology

Techniques
Review: Sample pre-treatment procedures for the omics analysis of human gut microbiota: turning points, tips and tricks for gene sequencing and metabolomics – Elisa Zubeldia-Varela et al. – Journal of Pharmaceutical and Biomedical Analysis

Publishing
Research Topic: Beyond Conventional Models: Expanding Experimental Systems for Animal-Microbiome Interaction Research

September 3, 2020

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At the beginning of todays post I wanted to highlight some interesting recent articles on COVID-19 and in particular a recent trial demonstrating the utility of BCG for a trained immunity response to protect against respiratory infections in the elderly. Enjoy!

COVID-19 & Vaccines

Tracking the COVID-19 pandemic in Australia using genomics – Seemann et al. Nature Communications. 

A comparison of four serological assays for detecting anti–SARS-CoV-2 antibodies in human serum samples from different populations – Grzelak et al. Science Translational Medicine

Phase 1–2 Trial of a SARS-CoV-2 Recombinant Spike Protein Nanoparticle Vaccine – Keech et al. New England Journal of Medicine

ACTIVATE: Randomised clinical trial of BCG vaccination against infection in the elderly – Giamarellos-Bourboulis et al. Cell

 

General microbiome

Multi-omic Analysis of the Interaction between Clostridioides difficile Infection and Pediatric Inflammatory Bowel Disease – Bushman et al. Cell Host & Microbe

Gut mycobiome and its interaction with diet, gut bacteria and alzheimer’s disease markers in subjects with mild cognitive impairment: A pilot study – Nagpal et al. EBioMedicine

Relationship between the composition of the intestinal microbiota and the tracheal and intestinal colonization by opportunistic pathogens in intensive care patients – Fontaine et al. PLOS One

Human respiratory microbiome

Respiratory Bacteria Stabilize and Promote Airborne Transmission of Influenza A Virus – Rowe et al. mSystems

Animal microbiome

Uncovering the microbiome of invasive sympatric European brown hares and European rabbits in Australia – Shanmuganandam et al. PeerJ

Water and extremophile microbiome

Microbiome dynamics in the tissue and mucus of acroporid corals differ in relation to host and environmental parameters – Marchioro et al. PeerJ

Microbial Communities across Global Marine Basins Show Important Compositional Similarities by Depth – Miller et al. mBio. 

Phages and viruses

Metagenome Data on Intestinal Phage-Bacteria Associations Aids the Development of Phage Therapy against Pathobionts – Fujimoto et al. Cell Host & Microbe

Bioinformatics

BLAST-QC: automated analysis of BLAST results – Torkian et al. Environmental Microbiome

 

September 2, 2020

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Greetings for the month of September: the Haervest-monath (Harvest Month). Today’s microbiome digest consists of a cool editorial article on hidden theatre of microbes. The digest also features two interesting reviews; first one detailing the role of skin microbiota in forensic sciences and the second one with focus on association of sponges and their microbiome.

Let’s celebrate the month of September with some fascinating microbiome studies.

There are flowers enough in the summertime,
More flowers than I can remember—
But none with the purple, gold, and red
That dye the flowers of September!
—Mary Howitt (1799-1888)

General microbiome
*Editorial: Unveiling the Hidden Theatre of Microbes – Böttcher T – ChemBioChem

Chitosan-chelated zinc modulates cecal microbiota and attenuates inflammatory response in weaned rats challenged with Escherichia coli – Feng et al – Journal of Microbiology

Multi-site human microbiome
Potential Associations Among Alteration of Salivary miRNAs, Saliva Microbiome Structure, and Cognitive Impairments in Autistic Children – Ragusa et al – Int. J. Mol. Sci.

Human respiratory microbiome
Review: The importance of airway and lung microbiome in the critically ill – Martin-Loeches et al – Critical Care

Human skin microbiome
A Novel Mycovirus Evokes Transcriptional Rewiring in the Fungus Malassezia and Stimulates Beta Interferon Production in Macrophages – Clancey et al – mBio

A Novel Virus Alters Gene Expression and Vacuolar Morphology in Malassezia Cells and Induces a TLR3-Mediated Inflammatory Immune Response – Park et al – mBio

*Review: Challenges in Human Skin Microbial Profiling for Forensic Science: A Review – Neckovic et al – Genes

Human gut microbiome
Context-aware dimensionality reduction deconvolutes gut microbial community dynamics – Martino et al – Nat Biotechnol

Animal microbiome
*The relationship between microbiomes and selective regimes in the sponge genus Ircinia – Kelly et al – bioRxiv

Techniques
Flow cytometry with cell sorting and sequencing as a tool for the study of the Humboldt Current krill stomach microbiota – Henriquez-Castillo et al – bioRxiv

Microbes in the news
EurekAlert News: Researchers receive $3 million NSF grant to ‘understand the rules of life – Zhou J

September 1, 2020

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Today’s post consists of review article on short chain fatty acids, research articles on efficacy of fecal microbiota transplant in patients with C. difficle infection and comorbities, identification of potential microbial biomarkers for preterm birth and a new technique to perform ultrafast microbial community analysis. Happy reading!

General microbiome

A systematic review of the effect of dietary pulses on microbial populations inhabiting the human gut – C.P.F. Marinangeli – Beneficial Microbes

Short chain fatty acids in human gut and metabolic health – E E Blaak – Beneficial Microbes

Human microbiome

The gut microbiome–derived metabolite trimethylamine N-oxide modulates neuroinflammation and cognitive function with aging – Vienna E. Brunt – Geroscience

Impact of investigational microbiota therapeutic RBX2660 on the gut microbiome and resistome revealed by a placebo-controlled clinical trial – Suryang Kwak – Microbiome

Fecal Microbiota Transplantation for Recurrent Clostridium difficile Infection in Patients With Multiple Comorbidities: Long-Term Safety and Efficacy Results From a Tertiary Care Community Hospital – Charumathi Raghu Subramanian – Gastroenterology Research

Gut commensal microbiota and decreased risk for Enterobacteriaceae bacteriuria and urinary tract infection – Matthew Magruder – Gut Microbes

Leveraging sequence‐based faecal microbial community survey data to identify alterations in gut microbiota among patients with Parkinson’s disease – Tianyi Ji – European Journal of Neuroscience

Plasma enterobacterial ClpB levels and ClpB- and α-MSH–reactive immunoglobulins in lung cancer patients with and without anorexia – Alessio Molfino – Nutrition

Identification of Potential Biomarkers in the Cervicovaginal Fluid by Metabolic Profiling for Preterm Birth – AbuZar Ansari – Metabolites

Plant microbiome

Suppression of rice planthopper populations without affecting the rice microbiota by the entomopathogenic fungus Metarhizium anisopliae – Yifan Peng – Applied and Environmental Microbiology

Cold Plasma Treatment of Sunflower Seeds Modulates Plant-Associated Microbiome and Stimulates Root and Lateral Organ Growth – Inga Tamošiūnė – Frontiers in Plant Science

Water microbiome

Bradymonabacteria, a novel bacterial predator group with versatile survival strategies in saline environments – Da-Shuai Mu – Microbiome

Techniques

Ultrafast and accurate 16S rRNA microbial community analysis using Kraken 2 – Jennifer Lu – Microbiome

Non-microbiology picks

Clinical characteristics of children and young people hospitalised with covid-19 in the United Kingdom: prospective multicentre observational cohort study – Olivia V Swann – BMJ

August 31, 2020

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Human gut microbiome

Keystone taxa indispensable for microbiome recovery – Sean M. Gibbons – Nature Microbiology

Metagenomics analysis of gut microbiota in response to diet intervention and gestational diabetes in overweight and obese women: a randomised, double-blind, placebo-controlled clinical trial – Mokkala et al. – Gut

Environmental microbiome

Preprint: Bacterial Community Assemblages in Classroom Floor Dust of 50 Public Schools in a Large City: Characterization Using 16s rRNA Sequences and Associations with Environmental Factors – Park et al.

A nitrogenase-like enzyme system catalyzes methionine, ethylene, and methane biogenesis – North et al. – Science

Animal microbiome

Effect of glycerol feed-supplementation on seabass metabolism and gut microbiota – Louvado et al. – Applied Microbiology and Biotechnology

Food microbiome

Secrets of the cheese microbiome – Danilo Ercolini – Nature Food

Biotechnology

A heterogeneous microbial consortium producing short-chain fatty acids from lignocellulose – Shahab et al. – Science

Non-microbiology pics

One Health(y) Cities: Cities are pandemic ecosystems and that’s where the action ought to happen – Evelyne de Leeuw – Cities and Health

August 30, 2020

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Good morning everyone! In today’s microbiome digest we have several reviews and research articles focused on the human microbiome, some animal studies, few interesting methods such as Kraken2 for 16S rRNA analysis, and Convolutional Neural Network for prediction of host phenotypes from microbial samples. Enjoy reading!!

General microbiome

Review: CRISPR screens in the era of microbiomes – François Rousset – Current Opinion in Microbiology

Chapter: Genetic Transformation of Fusobacterium nucleatum – Akihiro Yoshida – Methods in Molecular Biology

Perspective: Gut microbiota: a potential therapeutic target for Parkinson’s disease – José Fidel Baizabal-Carvallo – Neural Regeneration Research

Processing has differential effects on microbiota accessible carbohydrates in whole grains during in vitro fermentation – Caroline Smith – Applied Environmental Microbiology

Human gut microbiome

Gut microbiota and oral contraceptive use in overweight and obese patients with polycystic ovary syndrome – Nesrin Damla Eyupoglu – The Journal of Clinical Endocrinology and Metabolism

Diversity analysis of gut microbiota between healthy controls and those with atopic dermatitis in a Chinese population – Siqi Ye – The Journal of Dermatology

Faecal microbiota transplantation for the treatment of diarrhoea induced by tyrosine-kinase inhibitors in patients with metastatic renal cell carcinoma – Gianluca Ianiro – Nature Communications

Integrated microbiota and metabolite profiles link Crohn’s disease to sulfur metabolism – Amira Metwaly – Nature Communications

Review: The potential role of the gut microbiota in shaping host energetics and metabolic rate – Elle C Lindsay – Journal of Animal Ecology

Oral and respiratory microbiome

Microbiological analysis of endodontically treated teeth with apical periodontitis before and after endodontic retreatment– Marlos Barbosa-Ribeiro – Clinical Oral Investigation

2000-year-old pathogen genomes reconstructed from metagenomic analysis of Egyptian mummified individuals – Judith Neukamm – BMC Biology

Comparing the nasal bacterial microbiome diversity of allergic rhinitis, chronic rhinosinusitis and control subjects – Weigang Gan – European Archives of Oto-Rhino-Laryngology

Maternal Oral Health Influences Infant Salivary Microbiome – K. Ramadugu – Journal of Dental Research

Animal microbiome / Animal experiments

Dietary supplementation of sodium sulfate improves rumen fermentation, fiber digestibility and plasma metabolome through modulating rumen bacterial communities in steers – Yuchao Zhao – Applied Environmental Microbiology

Salmonella enterica serovar Typhimurium Temporally Modulates the Enteric Microbiota and Host Responses to Overcome Colonization Resistance in Swine – Danisa M Bescucci – Applied Environmental Microbiology

Germ-Free Conditions Modulate Host Purine Metabolism, Exacerbating Adenine-Induced Kidney Damage – Eikan Mishima – Toxins

Conventional Co-Housing Modulates Murine Gut Microbiota and Hematopoietic Gene Expression – Jichun Chen – International Journal of Molecular Sciences

Plant, root, and soil microbiome

Suppression of rice planthopper populations without affecting the rice microbiota by the entomopathogenic fungus Metarhizium anisopliae – Yifan Peng – Applied Environmental Microbiology

Water and extremophile microbiome

Dissolved microcystin release coincident with lysis of a Microcystis-dominated bloom in western Lake Erie attributed to a novel cyanophage – McKindles et al – Applied Environmental Microbiology

Methods

Ultrafast and accurate 16S rRNA microbial community analysis using Kraken 2 – Jennifer Lu – Microbiome

Chapter: Predicting Host Phenotype Based on Gut Microbiome Using a Convolutional Neural Network Approach – Derek Reiman – Artificial Neural Networks

Techniques

Review: Application of Next Generation Sequencing in Laboratory Medicine – Yiming Zhong – Annals of laboratory medicine

 

 

August 29, 2020

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Good morning! Today’s post features a wide variety of interesting topics ranging from the role of the microbiome in attacking cancerous tumors, the potential use of extremophiles in Mars’ habitability and the association of worsening of NAFLD with cardiometabolic function. There is also a nice symposium report on the role of probiotics to a healthy microbiota and a fascinating look into the bacterial nano-universe using Cryo-ET.

Enjoy!!

COVID-19

An adenovirus-vectored COVID-19 vaccine confers protection from SARS-COV-2 challenge in rhesus macaques OPEN. Liqiang Feng, et al. Nature

HUMAN GUT MICROBIOME

Association of worsening of nonalcoholic fatty liver disease with cardiometabolic function and intestinal bacterial overgrowth: A cross-sectional study. Marília Marques Pereira Lira, et al. PLOS ONE

[HTML] Bifidobacterium adolescentis as a key member of the human gut microbiota in the production of GABA. S Duranti, et al. – Scientific Reports

[PDF] The role of probiotics on the roadmap to a healthy microbiota: a symposium report. S Lockyer, et al. – Gut Microbiome

PLANT, ROOT AND SOIL MICROBIOME

Preprint: [PDF] Geological Characteristics of Close Geographical Related Vineyards Influence Microbiomes of Two Soil Depth Profiles With Potential Impacts on Wine Quality. L Nerva, et al. Research Square

ANIMAL EXPERIMENTS

How the environment and the microbiome jointly shape the body. Phys.Org

ANIMAL EXPERIMENTS

News article: New insight into microbiome’s role in attacking cancerous tumours. THE WEEK

PHAGES AND VIRUSES

News article: HIV enters deep sleep in people who naturally control the virus. Nature

Preprint: Induction of selective cell death in HIV-1-infected cells by DDX3 inhibitors leads to depletion of the inducible reservoir. Shringar Rao, et al. bioRxiv

WATER AND EXTREMOPHILE MICROBIOME

[PDF] Can Halophilic and Psychrophilic Microorganisms Modify the Freezing/Melting Curve of Cold Salty Solutions? Implications for Mars Habitability. L Garcia-Descalzo, et al.- Astrobiology

BUILT ENVIRONMENT

Metagenomic characterization of microbial communities on plasticized fabric materials exposed to harsh tropical environments. O Radwan, et al. – International Biodeterioration & Biodegradation

BIOINFORMATICS

Gut metagenomics-derived genes as potential biomarkers of Parkinson’s disease. Y Qian, et al. – Brain

[HTML] CRISPR screens in the era of microbiomes. F Rousset, et al. – Current Opinion in Microbiology

[HTML] Microbial single-cell omics: the crux of the matter. AK Kaster, et al. – Applied Microbiology and Biotechnology

[HTML] Bionetworks, system biology, and superorganisms. M Nicoletti – Insect-Borne Diseases in the 21st Century

TECHNIQUES

[HTML] Exploring the bacterial nano-universe. N Söderholm, et al. – Current Opinion in Structural Biology

August 28, 2020

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Greetings!

Today’s microbiome digest has something for everyone. We have several articles focused on the human microbiome, a few animal studies, and quite a few articles focused on environmental bacteria found in soil, water, and even a cave! I want to highlight one article focused on the impact of spatial proximity on territory among bacteria. Although the article specifically focuses on skin bacteria, it’s relevant to anyone studying microbial communities!

Enjoy!

General microbiome

Horizontal transmission and recombination maintain forever young bacterial symbiont genomes – Russel et al. – PLOS GENETICS

Human skin microbiome

Impact of spatial proximity on territoriality among human skin bacteria – Hernandez-Valdes et al. – npj BIofilms and Microbiomes

Human gut microbiome

Gut microbiota and dysbiosis in Alzheimer’s disease: Implications for pathogenesis and treatment – Liu et al. – Molecular Neurobiology

Animal experiments

Caecal microbiota compositions from 7-day-old chicks reared in high-performance and low-performance industrial farms and systematic culturomics to select strains with anti-Campylobacter activity – Duquenoy et al. – PLOS ONE

Effect of FHA and Prn on Bordetella pertussis colonization of mice is dependent on vaccine type and anatomical site – Zeddeman et al. – PLOS ONE

Animal microbiome

Lactobacilli and other gastrointestinal microbiota of Peromyscus leucopus, reservoir host for agents of Lyme disease and other zoonoses in North America – Milovic et al. – PLOS ONE

Plant, root, and soil microbiome

Simple kinetics, assay, and trends for soil microbial catalases – Chabot et al. – Analytical Biochemistry

Sustaining the growth of Pinaceae trees under nutrient-limited edaphic conditions via plant-beneficial bacteria – Puri et al. – PLOS ONE

Soil properties, bacterial and fungal community compositions and the key factors after 5-year continuous monocropping of three minor crops – Yang et al. – PLOS ONE

Water and extremophile microbiome

Oleaginous potential of indigenously isolated fresh water microalgae for biofuel production – Saraf & Dutt – International Journal of Sustainable Energy

Bacteria and archaea communities in Cerrado natural pond sediments – Silveira et al. – Microbiology of Aquatic Systems

The microbial community of a biofilm lining the wall of a pristine cave in Western New Guinea – Turrini et al. – Microbiological Research

On microbial community of Pyropia haitanensis by metagenomic analysis – Wang et al. – Journal of Oceanology and Limnology

August 27, 2020

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Good morning! Today has a great nature paper on bacterial metabolic crossfeeding that can result in altered egg laying and reproducing behaviour, and additionally a paper showing how bacterial probiotics induce anergy in mice with Cow’s Milk allergy.

General microbiome

Metabolic cross-feeding in imbalanced diets allows gut microbes to improve reproduction and alter host behaviour, Henriques et al, Nature.

The Impact of the Postpartum “Doing-the-Month” Practice on Human Milk Microbiota: A Pilot Study in Taiwan, Chen et al. Microorganisms.

Vaginal microbiota

Glycan cross-feeding supports mutualism between Fusobacterium and the vaginal microbiota, Agarwal et al, PLOS biology.

Human gut microbiome

How Serotonin Level Fluctuation Affects the Effectiveness of Treatment in Irritable Bowel Syndrome, Vahora et al. Cureus.

Animal experiments

Three Candidate Probiotic Strains Impact Gut Microbiota and Induce Anergy in Mice with Cow’s Milk Allergy. Esber et al. Public and environmental Health Microbiology.

Plant, root and soil microbiome

Role of environmental factors in shaping the soil microbiome, Islam et al. Environmental Science and Pollution research.

Bioinformatics

Predictive analysis methods for human microbiome data with application to Parkinson’s disease, Dong et al, PLOS One.

August 26, 2020

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Shalom from Israel! Today’s digest has some great review papers, as well as research articles focusing on citures disease, vaginal microbiome, gut virome and some cool bioinformatic tools.

Also, check out this great event for the soil microbilogists out there: Non-academic Careers in Soil Ecology: a virtual career panel, hosted by MSU.

Enjoy your summer holiday if you managed to get one and as always- find yourself the time to rest and re-energize.

General

**review: Compartmentalization drives the evolution of symbiotic cooperation, Guillaume Chomicki, Phil. Tran. B

Marine microbiomoe

Assessing the strength and sensitivity of the core microbiota approach on a highly diverse sponge reef, Carmen Astudillo-Garica , Env. Micro.

Plant microbiome

Cooperation, Competition, and Specialized Metabolism in a Simplified Root Nodule Microbiome, Bridget L. Hansen , mBio

Stable isotope informed genome-resolved metagenomics uncovers potential trophic interactions in rhizosphere soil, Evan P. Starr, bioRxiv

Disease-Induced Microbial Shifts in Citrus Indicate Microbiome-Derived Responses to Huanglongbing Across the Disease Severity Spectrum, Nichole A. Ginnan , Phytobiomes

Human microbiome and virome

Cervicovaginal Microbiome Composition Is Associated with Metabolic Profiles in Healthy Pregnancy, Andrew Oliver , mBio

The Gut Virome Database Reveals Age-Dependent Patterns of Virome Diversity in the Human Gut, Ann C. Gregory , Cell Host Microbe

Bioinformatics

BiG-SLiCE: A Highly Scalable Tool Maps the Diversity of 1.2 Million Biosynthetic Gene Clusters, Satria Kutsar, bioRxiv

**mini-review: Natural product discovery through microbial genome mining, Emma Kenshole, Cur. Op. Chem. Bio.

Available Benchmarking Bacterial Promoter Prediction Tools: Potentialities and Limitations, Murilo Henrique Anzolini Cassiano, mSystems