September 7th, 2020

God morgon!

Good morning from Sweden. Today’s digest is a loaded one with a lot of new preprints and news from the world of microbiology.

As someone who suffers from allergic rhinitis my mind was blown when I read the article that linked gut microbiota to allergic rhinitis! I am waiting for someone to come up with a gut microflora based treatment now! Further in the area of microbiome are preprints on assessment of antibiotic use in neonates and barcoding of about 1000 new marine yeast isolates.

A new preprint details the mechanism of action of a very effective new antibiotic armeniaspirol against Gram positive bacteria. Yet another preprint describes the potent antimycobaterial activity of synthetic Azetidines derivatives, which could be a great tool in our fight against tuberculosis. Further in bacteriology are preprints providing new information about host-pathogen interactions during Helicobacter infections, dynamics in persisting and resuscitating bacteria, RNA metabolism and metabolic homeostasis in bacteria.

A super interesting preprint describes a new form of on-chip microscopy and I must confess that the authors did a great job at giving their manuscript a catchy, short and yet informative title!

Bioinformatic studies using thousands of nCoV genomes have unearthed some mutations that might be responsible for its human adaptation (although computational studies without any experimental biological evidence are not my favourite, it might provide a starting point for scientists interested in COVID19.

There are a lot of more interesting articles and I wish I could write about all of them! I hope you will enjoy today’s selection.

COVID-19

Preprint: The discovery of gene mutations making SARS-CoV-2 well adapted for humans: host-genome similarity analysis of 2594 genomes from China, the USA and Europe – Weitao Sun

Preprint: Mutation in position of 32 (G>U) of S2M differentiate human SARS-CoV2 from Bat Coronavirus – Majid Vahed, et al.

Preprint: Development of SARS-CoV-2 Nucleocapsid Specific Monoclonal Antibodies – James S. Terry, et al.

Preprint: A Mental Health Paradox: Mental health was both a motivator and barrier to physical activity during the COVID-19 pandemic – Maryam Marashi, et al.

Bacteria Hysteria

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

Preprint: Armeniaspirols inhibit the AAA+ proteases ClpXP and ClpYQ leading to cell division arrest in Gram-positive bacteria – Puneet Labana, et al.

Preprint: Effect of polyethylene glycol on growth of Escherichia coli DH5α and Bacillus subtilis NRS-762 – Wenfa Ng

Preprint: Essentiality of c-di-AMP in Bacillus subtilis: Bypassing mutations converge in potassium and glutamate homeostasis – Larissa Krüger, et al.

Preprint: Comparative genomics of Clostridium species associated with vacuum-packed meat spoilage – Nikola Palevich, et al.

Preprint: Antibiotics and the developing intestinal microbiome, metabolome and inflammatory environment: a randomized trial of preterm infants – Jordan T. Russell, et al.

Preprint: Azetidines kill Mycobacterium tuberculosis without detectable resistance by blocking mycolate assembly – Alice Lanne, et al.

Preprint: Proteome dynamics in persisting and resuscitating bacterial cells – Maja Semanjski, et al.

Preprint: Limitation of phosphate assimilation maintains cytoplasmic magnesium homeostasis – Roberto E. Bruna, et al.

Preprint: RecA levels modulate biofilm development in Acinetobacter baumannii – Carly Ching, et al.

Preprint: Distinct survival, growth lag, and ribosomal RNA degradation kinetics during long-term starvation for carbon or phosphate – Yusuke Himeoka, et al.

General microbiome

Gut microbial characteristics of adult patients with allergy rhinitis – Libing Zhu, et al., Microbial Cell Factories

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

Preprint: Soil characteristics constrain the response of bacterial and fungal communities and hydrocarbon degradation genes to phenanthrene soil contamination and phytoremediation with poplars – Sara Correa-García, et al.

Preprint: Microbial bioprospecting for lignocellulose degradation at a unique Greek environment – Daphne N. Georgiadou, et al.

Preprint: DNA barcoding analysis of more than 1000 marine yeast isolates reveals previously unrecorded species – Chinnamani PrasannaKumar, et al.

Viruses

Preprint: Mammalian ANP32A and ANP32B proteins drive alternative avian influenza virus polymerase adaptations – Thomas. P. Peacock, et al.

Preprint: Development of Resistance to 4′-Ethynyl-2-Fluoro-2′-Deoxyadenosine (EFdA) by Wild-Type and Nucleoside Reverse Transcriptase Inhibitor Resistant Human Immunodeficiency Virus Type 1 – Maria E Cilento, et al.

Host-pathogen interactions

Preprint: NHR-49/PPAR-α and HLH-30/TFEB promote C. elegans host defense via a flavin-containing monooxygenase – Khursheed A. Wani, at al.

Preprint: Role of ERK activation in H. pylori-induced disruption of cell-cell tight junctions – Amita Sekar and Bow Ho

Preprint: Cellular co-infection can modulate the efficiency of influenza A virus production and shape the interferon response – Brigitte E Martin, et al.

Preprint: Non-permissive human conventional CD1c+ dendritic cells enable trans-infection of human primary renal tubular epithelial cells and protect BK polyomavirus from neutralization – Mathieu Sikorski, et al.

Techniques

Preprint: Nanoscopy on the Chea(i)p – Benedict Diederich, et al.

Preprint: Visualizing Borrelia burgdorferi infection using a small molecule imaging probe – Madeline G Sell, et al.

Microbiology in News

Malibu Microbiome Meeting Virtual Prelude Shares New Data – PR Newswire

Human Microbiome-Based Drugs And Diagnostics Market An Insight On the Important Factors and Trends Influencing the Market – Daily Research Chronicle

Autism and the Microbiome – The New Indian Express

September 5, 2020

Have a nice weekend! Today, this Digest includes a good amount of reviews covering different topics (from the concept of inflammageing to the impact of the microbiome on cancer treatment), as well as a report covering the use of flow cytometry to search for microbiome markers in Crohn’s disease patients, and studies on microbiota and portal hypertension, the microbiome of pesticide-treated soils and the effect of natural microbes on hydrocarbon degradation.

Human and General Microbiome

Cytometric fingerprints of gut microbiota predict Crohn’s disease state –  Peter Rubbens – The ISME Journal

Review: Is inflammageing influenced by the microbiota in the aged gut? A systematic review – Cabirou M Shintouo – Experimental Gerontology

Review: The Gut Microbiome, Inflammation, and Salt-Sensitive Hypertension – Fernando Elijovich – Current Hypertension Reports 

Review: Intestinal microbial metabolites in human metabolism and type 2 diabetes – Hilde Herrema – Diabetologia

Review: Gut Microbiota Dysbiosis as a Target for Improved Post-Surgical Outcomes and Improved Patient Care. A Review of Current Literature – Fatema Mustansir Dawoodbhoy – Shock

Review: The Role of the Microbiome in Cancer and Therapy Efficacy: Focus on Lung Cancer – Adrienne Halley – Anticancer Research 

Review: Breast and Gut Microbiota Action Mechanisms in Breast Cancer Pathogenesis and TreatmentCancers (MDPI)

Review: Influence of Resveratrol on the Cardiovascular Health Effects of Chronic Kidney DiseaseInternational Journal of Molecular Sciences

Review: An RNA-centric view on gut Bacteroidetes – Daniel Ryan – Biological Chemistry

Exploratory Research on the Relationship between Human Gut Microbiota and Portal Hypertension – Keiji Yokoyama – Internal Medicine

Gut microbiome alterations in type 1 autoimmune pancreatitis after induction of remission by prednisolone – Ken Kamata – Clinical and Experimental Immunology

Type I IFNs and CD8 T cells increase intestinal barrier permeability after chronic viral infection – Lara Labarta-Bajo – Journal of Experimental Medicine

Plant-associated Microbiome

Prokaryotic and microeukaryotic communities in an experimental rice plantation under long-term use of pesticides – Maria Pilar Serbent – 

Environmental Microbiome

Effect of natural microbiome and culturable biosurfactants-producing bacterial consortia of freshwater lake on petroleum-hydrocarbon degradation – Irfan Ali Phulpoto – Science of The Total Environment

Animal Microbiome

Alterations in the gut-associated microbiota of juvenile Caribbean spiny lobsters Panulirus argus (Latreille, 1804) infected with PaV1 – Jesús Alejandro Zamora-Briseño – Journal of Invertebrate Pathology

Effects of Zinc Oxide and Arginine on the Intestinal Microbiota and Immune Status of Weaned Pigs Subjected to High Ambient Temperature – Se Young Yoon – Animals (MDPI)

The Microbiome of Neotropical Water Striders and Its Potential Role in Codiversification – Anakena M Castillo – Insects (MDPI)

Beneficial Microbes and Compounds

Effects of probiotic bacterium Weissella cibaria CMU on periodontal health and microbiota: a randomised, double-blind, placebo-controlled trial – Mi-Sun Kang – BMC Oral Health

Other

A 500-year tale of co-evolution, adaptation, and virulence: Helicobacter pylori in the Americas – Zilia Y Muñoz-Ramirez – The ISME Journal

September 4, 2020

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

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

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

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

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

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 MicrobiomeK. 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

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

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