May 28, 2021

Posted on May 28, 2021 by Rich Abdill

Good morning from New Jersey! A broad selection of papers to share with you today—highlights include several new bioinformatics papers and an examination of the effect of storage method on the composition of microbiome samples:

April 23, 2021

Posted on April 23, 2021 by Rich Abdill

Good morning from New Jersey! Lots of papers to share today, particularly regarding animal microbiota and new bioinformatics tools.

General microbiome

Human breast microbiome correlates with prognostic features and immunological signatures in breast cancer, Alice Tzeng et al., Genome Medicine

Pregnancy and early life

The infant gut resistome associates with E. coli, environmental exposures, gut microbiome maturity, and asthma-associated bacterial composition, Xuanji Li et al., Cell Host & Microbe

Multi-site human microbiome

Review: Microbiome-immune interactions in tuberculosis, Giorgia Mori et al., PLOS Pathogens

Human gut microbiome

Dynamic Changes in Microbiome Composition Following Mare’s Milk Intake for Prevention of Collateral Antibiotic Effect, Almagul Kushugulova et al., Frontiers in Cellular and Infection Microbiology

Review: The aging gut microbiome and its impact on host immunity, Bosco and Noti, Genes & Immunity

Animal experiments

Ingestion of Bifidobacterium longum changes miRNA levels in the brains of mice, DeVries and Horstman et al., PLOS ONE

Heat-inactivated Lactobacillus plantarum nF1 promotes intestinal health in Loperamide-induced constipation rats, Seon-Ah Park et al., PLOS ONE

The pregnane X receptor drives sexually dimorphic hepatic changes in lipid and xenobiotic metabolism in response to gut microbiota in mice, Sharon Ann Barretto et al., Microbiome

One dog’s waste is another dog’s wealth: A pilot study of fecal microbiota transplantation in dogs with acute hemorrhagic diarrhea syndrome, Arnon Gal et al., PLOS ONE

Animal microbiome

Diversity and functional landscapes in the microbiota of animals in the wild, Levin, Raab, Pinto, and Rothschild et al., Science

Microbiome reduction and endosymbiont gain from a switch in sea urchin life history, Tyler J. Carrier et al., PNAS

Diet and gut microbiome enterotype are associated at the population level in African buffalo, Claire E. Couch et al., Nature Communications

Coral microbiome changes over the day–night cycle, Alicia M. Caughman et al., Coral Reefs

An investigation of conventional microbial culture for the Naja atra bite wound, and the comparison between culture-based 16S Sanger sequencing and 16S metagenomics of the snake oropharyngeal bacterial microbiota, Mao and Chuang et al., PLOS Neglected Tropical Diseases

Plant, root, and soil microbiome

Preprint: Genome-centric analyses of seasonal phyllosphere microbiome activities in perennial crops, Adina Howe et al., bioRxiv

Influence of Plant Host and Organ, Management Strategy, and Spore Traits on Microbiome Composition, Kristi Gdanetz et al., Phytobiomes Journal

Built environment

Categorisation of culturable bioaerosols in a fruit juice manufacturing facility, Shirleen M. Theisinger et al., PLOS ONE

Bioinformatics

Preprint: Deconstructing taxa x taxa x environment interactions in the microbiota: A theoretical examination, Senay Yitbarek et al., bioRxiv

Preprint: Extended taxonomic profiling of diverse environments with mOTUs 2.6, Hans-Joachim Ruscheweyh et al., bioRxiv

Evaluation of the Microba Community Profiler for Taxonomic Profiling of Metagenomic Datasets From the Human Gut Microbiome, Donovan H. Parks et al., Frontiers in Microbiology

Supervised extraction of near-complete genomes from metagenomic samples: A new service in PATRIC, Bruce Parrello et al., PLOS ONE

March 26, 2021

Posted on March 26, 2021 by Rich Abdill

Good morning from New Jersey! Tons of papers to share with you today, including three about the role of the microbiome in COVID-19 and multiple new analysis tools and techniques.

Human respiratory microbiome

Functional profiling of COVID-19 respiratory tract microbiomes, Niina Haiminen et al., Scientific Reports

[Preprint] Mild CF Lung Disease is Associated with Bacterial Community Stability, Thomas H. Hampton et al., bioRxiv

Human skin microbiome

[Preprint] On-person adaptive evolution of Staphylococcus aureus during atopic dermatitis increases disease severity, Felix M. Key et al., bioRxiv

Human gut microbiome

[Mini-Review] The Unique Impact of COVID-19 on Human Gut Microbiome Research, Ella Burchill et al., Frontiers in Medicine

Variability in digestive and respiratory tract Ace2 expression is associated with the microbiome, Koester and Li et al., PLOS ONE

[Review] Towards a mechanistic understanding of reciprocal drug–microbiome interactions, Michael Zimmermann et al., Molecular Systems Biology

[Review] The Microbiome Meets Nanotechnology: Opportunities and Challenges in Developing New Diagnostic Devices, Celia Fuentes‐Chust et al., Advanced Materials

[Preprint] The capacity to produce hydrogen sulfide (H2S) via cysteine degradation is ubiquitous in the human gut microbiome, Domenick J Braccia et al., bioRxiv

Model experiments

[Preprint] Species richness determines C. difficile invasion outcome in synthetic human gut communities, Susan Hromada et al., bioRxiv

Gut microbiota determines the social behavior of mice and induces metabolic and inflammatory changes in their adipose tissue, Oryan Agranyoni et al., npj Biofilms and Microbiomes

Improvement of loperamide-induced slow transit constipation by Bifidobacterium bifidum G9-1 is mediated by the correction of butyrate production and neurotransmitter profile due to improvement in dysbiosis, Yutaka Makizaki et al., PLOS ONE

Animal microbiome

A Preliminary Comparison on Faecal Microbiomes of Free-Ranging Large Baleen (Balaenoptera musculus, B. physalus, B. borealis) and Toothed (Physeter macrocephalus) Whales, Stefanie P. Glaeser et al., Microbial Ecology

Host–microbial systems as glass cannons: Explaining microbiome stability in corals exposed to extrinsic perturbations, Courtney M. Dunphy et al., Journal of Animal Ecology

Fish predation on corals promotes the dispersal of coral symbionts, Carsten G. B. Grupstra et al., Animal Microbiome

Plant, root, and soil microbiome

Global analysis of the apple fruit microbiome: Are all apples the same?, Ahmed Abdelfattah et al., Environmental Microbiology

Evaluating domestication and ploidy effects on the assembly of the wheat bacterial microbiome, Wipf and Coleman-Derr, PLOS ONE

Water and extremophile microbiome

[Preprint] Uncharted biosynthetic potential of the ocean microbiome, Lucas Paoli et al., bioRxiv

The microbiome of the Black Sea water column analyzed by shotgun and genome centric metagenomics, Pedro J. Cabello-Yeves et al., Environmental Microbiome

Revealing taxon-specific heavy metal-resistance mechanisms in denitrifying phosphorus removal sludge using genome-centric metaproteomics, Yuan Lin et al., Microbiome

Bioinformatics

Forensic Microbiome Database: A Tool for Forensic Geolocation Meta-Analysis Using Publicly Available 16S rRNA Microbiome Sequencing, Singh and Clarke et al., Frontiers in Microbiology

ProgPerm: Progressive permutation for a dynamic representation of the robustness of microbiome discoveries, Liangliang Zhang et al., BMC Bioinformatics

Model-Based Microbiome Data Ordination: A Variational Approximation Approach, Yanyan Zeng et al., Journal of Computational and Graphical Statistics

Techniques

Blue poo: impact of gut transit time on the gut microbiome using a novel marker, Francesco Asnicar et al., Gut

Benchmarking DNA isolation kits used in analyses of the urinary microbiome, Lisa Karstens et al., Scientific Reports

Choice of library preparation affects sequence quality, genome assembly, and precise in silico prediction of virulence genes in shiga toxin-producing Escherichia coli, Julie Haendiges et al., PLOS ONE

February 19, 2021

Posted on February 19, 2021 by Rich Abdill

Good morning from New Jersey! There’s an amazing batch of microbiome papers to share with you today, including studies that use skin microbes to fight cancer, gut microbes to fight rotavirus, and evidence that the bird microbiome may harbor a mechanism that protects them from malaria. There’s also a fun story about dogs training a computer to detect prostate cancer.

General microbiome

Feasibility of integrating canine olfaction with chemical and microbial profiling of urine to detect lethal prostate cancer, Guest, Harris and Sfanos et al., PLOS ONE

Human skin microbiome

Preprint: Eliciting a potent antitumor immune response by expressing tumor antigens in a skin commensal, Yiyin Erin Chen et al., bioRxiv

Human nearly-sterile sites

Preprint: Fetal gut colonization: meconium does not have a detectable microbiota before birth, Katherine M. Kennedy et al., bioRxiv

Human gut microbiome

The gut microbiome modulates the protective association between a Mediterranean diet and cardiometabolic disease risk, Dong D. Wang et al., Nature Medicine

Gut microbiome pattern reflects healthy ageing and predicts survival in humans, Tomasz Wilmanski et al., Nature Metabolism

The composition of the gut microbiome differs among community dwelling older people with good and poor appetite, Cox and Bowyer et al., Journal of Cachexia, Sarcopenia and Muscle

Animal microbiome

The uropygial gland microbiome of house sparrows with malaria infection, Elin Videvall et al., Journal of Avian Biology

The amphibian microbiome exhibits poor resilience following pathogen-induced disturbance, Andrea J. Jani et al., The ISME Journal

Plant, root and soil microbiome

Carbon Fluxes and Microbial Activities from Boreal Peatlands Experiencing Permafrost Thaw, M.P. Waldrop et al., JGR Biogeosciences

Probiotics/prebiotics

Escherichia coli Nissle 1917 administered as a dextranomar microsphere biofilm enhances immune responses against human rotavirus in a neonatal malnourished pig model colonized with human infant fecal microbiota, Husheem Michael et al., PLOS ONE

Impact of Probiotic B. infantis EVC001 Feeding in Premature Infants on the Gut Microbiome, Nosocomially Acquired Antibiotic Resistance, and Enteric Inflammation, Marielle Nguyen et al., Frontiers in Pediatrics

January 22, 2021

Posted on January 22, 2021 by Rich Abdill

Good morning from New Jersey! A wide range of microbiome research to share with you today. Highlights include fecal microbiota transplantation in horses with colitis and a review on the foggy relationship between microbes and plastics. There are also a couple papers on metabolic modeling and an examination of how much black soldier flies like human food waste (hint: a lot).

Jobs

New postdoctoral positions were just announced at the University of Minnesota for “research at the interface of microbiome + human genomics” in the lab of Dr. Ran Blekhman (disclosure: my Ph.D. advisor).

Human skin microbiome

Potential role of the skin and gut microbiota in premenarchal vulvar lichen sclerosus: A pilot case-control study, Chattopadhyay and Arnold et al., PLOS ONE

Human gut microbiome

Degradation of complex arabinoxylans by human colonic Bacteroidetes, Gabriel V. Pereira et al., Nature Communications

Review – The complexities of the diet-microbiome relationship: advances and perspectives, Emily R. Leeming et al., Genome Medicine

Review – Understanding the host-microbe interactions using metabolic modeling, Jansma and El Aidy, Microbiome

Microbial Species that Initially Colonize the Human Gut at Birth or in Early Childhood Can Stay in Human Body for Lifetime, Li and Nelson, Microbial Ecology

Animal experiments

Preprint – The Predicted Metabolic Function of the Gut Microbiota of Drosophila melanogaster, Nana Ankrah et al, bioRxiv

Animal microbiome

Assessment of clinical and microbiota responses to fecal microbial transplantation in adult horses with diarrhea, Caroline A. McKinney et al., PLOS ONE

Climate change alters the haemolymph microbiome of oysters, Elliot Scanes et al., Marine Pollution Bulletin

Functional screening of a Caatinga goat (Capra hircus) rumen metagenomic library reveals a novel GH3 β-xylosidase, Betulia de Morais Souto et al., PLOS ONE

Built environment

Impact of Processed Food (Canteen and Oil Wastes) on the Development of Black Soldier Fly (Hermetia illucens) Larvae and Their Gut Microbiome Functions, Thomas Klammsteiner et al., Frontiers in Microbiology

Review – Plastics and the microbiome: impacts and solutions, G. Lear et al., Environmental Microbiome

Bioinformatics

Real-time resolution of short-read assembly graph using ONT long reads, Son Hoang Nguyen et al., PLOS Computational Biology

Covariance matrix filtering with bootstrapped hierarchies, Bongiorno and Challet, PLOS ONE

December 10, 2020

Posted on December 10, 2020 by Rich Abdill

Good morning from New Jersey! Only a few new research articles to share with you today, but FOUR new reviews on the microbiome’s role in cancers and periodontal disease. And if you’re feeling adventurous, PLOS ONE just published an article on human postmortem decomposition that includes a brief evaluation of the buried corpse microbiome.

Jobs

A new postdoctoral position was just posted at the University of Minnesota for research on new methods of fecal microbiota transplantation.

General microbiome

Review – Unexpected guests in the tumor microenvironment: microbiome in cancer, Abigail Wong-Rolle et al., Protein Cell

Review – Understanding the microbial components of periodontal diseases and periodontal treatment-induced microbiological shifts, Ioannis Fragkioudakis et al., Journal of Medical Microbiology

Human gut microbiome

Identification of a Novel Cobamide Remodeling Enzyme in the Beneficial Human Gut Bacterium Akkermansia muciniphila, Kenny C. Mok et al., mBio

Interpretable Machine Learning Framework Reveals Robust Gut Microbiome Features Associated With Type 2 Diabetes, Wanglong Gou et al., Diabetes Care

Gut microbial ecosystem in Parkinson’s disease: New clinico‐biological insights from multi‐omics, Ai Huey Tan et al., Annals of Neurology

Review – Intervention on Gut Microbiota May Change the Strategy for Management of Colorectal Cancer, Sedigheh Taghinezhad‐S et al., Gastroenterology and Hepatology

Short-Chain Fatty Acid-Producing Gut Microbiota Is Decreased in Parkinson’s Disease but Not in Rapid-Eye-Movement Sleep Behavior Disorder, Hiroshi Nishiwaki et al., mSystems

Animal experiments

Respiratory tissue-associated commensal bacteria offer therapeutic potential against pneumococcal colonization, Soner Yildiz et al., eLife

Effects of Pinus massoniana pollen polysaccharides on intestinal microenvironment and colitis in mice, Niu and Shang et al., Food & Function

A Subset of Roux-en-Y Gastric Bypass Bacterial Consortium Colonizes the Gut of Nonsurgical Rats without Inducing Host-Microbe Metabolic Changes, Zhigang Liu et al., mSystems

Plant, root, and soil microbiome

Preprint – Rapid evolution of bacterial mutualism in the plant rhizosphere, Erqin Li et al., bioRxiv

Review – Coffee Microbiota and Its Potential Use in Sustainable Crop Management, Benoit Duong et al., Frontiers in Sustainable Food Systems

Bioinformatics

Review – Tissue-associated microbial detection in cancer using human sequencing data, Rebecca M. Rodriguez et al., BMC Bioinformatics

Techniques

Preprint – BIOME-Preserve: A Novel Storage and Transport Medium for Preserving Anaerobic Microbiota Samples for Culture Recovery, Embriette R. Hyde et al., bioRxiv

November 12, 2020

Posted on November 12, 2020 by Rich Abdill

Good morning! There’s a really exciting collection of papers to share with you this morning. Among them, a study of gut archaea across multiple host domains, a link between F. nucleatum and esophageal cancer, and two new databases of shotgun metagenomic data. (There’s also a fun paper about environmental transmission of microbes aboard the International Space Station.)

General microbiome

Preprint – Strong influence of vertebrate host phylogeny on gut archaeal diversity, Nicholas D Youngblut et al., bioRxiv

A genomic catalog of Earth’s microbiomes, Stephen Nayfach et al., Nature Biotechnology

Human vaginal microbiome

Review – Vaginal microbiota and the potential of Lactobacillus derivatives in maintaining vaginal health, Wallace Jeng Yang Chee, Microbial Cell Factories

Human gut microbiome

Preprint – Fusobacterium Nucleatum Predicts a Risk for Esophageal Squamous Cell Carcinoma, Chao Shi et al., Research Square

Preprint – Human reference gut microbiome comprising 5,414 prokaryotic species, including newly assembled genomes from under-represented Asian metagenomes, Kim and Lee et al., bioRxiv

Preprint – Genetic Evidence for Selective Transfer of Microbes Between the International Space Station and an Astronaut, David C. Danko et al., bioRxiv

Review: An infectious diseases perspective on the microbiome and allogeneic stem cell transplant, Olivia C. Smibert et al., Current Opinion in Infectious Diseases

Animal experiments

Preprint – Longitudinal effects of antibiotics and fecal transplant on lemur gut microbiota structure, associations, and resistomes, Sally L. Bornbusch et al., bioRxiv

Pinto beans modulate the gut microbiome, augment MHC II protein, and antimicrobial peptide gene expression in mice fed a normal or western-style diet, Babajide A. Ojo et al., Journal of Nutritional Biochemistry

Preprint – Contagious Antibiotic Resistance: Plasmid Transfer Among Bacterial Residents of the Zebrafish Gut, Wesley Loftie-Eaton et al., bioRxiv

Animal microbiome

Shifts in microbial diversity, composition, and functionality in the gut and genital microbiome during a natural SIV infection in vervet monkeys, Anna J. Jasinska et al., Microbiome

A multi-disciplinary comparison of great ape gut microbiota in a central African forest and European zoo, Narat and Amato et al., Scientific Reports

Bioinformatics

Preprint – AGORA2: Large scale reconstruction of the microbiome highlights wide-spread drug-metabolising capacities, Almut Heinken et al., bioRxiv

Techniques

Preprint – Benchmarking DNA isolation kits used in analyses of the urinary microbiome, Lisa Karstens et al., bioRxiv

October 22, 2020

Posted on October 22, 2020 by Rich Abdill

Good morning! A relatively short collection of articles to share with you today—highlights include a human microbiome study that evaluated disease markers in more than 3,000 subjects, a study of emerging antibiotic resistance in melting Alaskan permafrost, and a preprint that found multiple immune responses typically associated with the microbiome may actually be more closely linked to viruses.

Human gut microbiome

Health and disease markers correlate with gut microbiome composition across thousands of people, Ohad Manor et al., Nature Communications

Newly Explored Faecalibacterium Diversity Is Connected to Age, Lifestyle, Geography, and Disease, Francesca De Filippis et al., Current Biology

Preprint: Extraintestinal pathogenic (ExPEC) lineages explain prolonged faecal carriage of travel-acquired extended-spectrum β-lactamase-producing Escherichia coli, Boas CL van der Putten et al., bioRxiv

Intestinal microbiology shapes population health impacts of diet and lifestyle risk exposures in Torres Strait Islander communities, Fredrick M Mobegi et al., eLife

Animal experiments

A longitudinal study reveals the alterations of the Microtus fortis colonic microbiota during the natural resistance to Schistosoma japonicum infection, Du Zhang et al., Experimental Parasitology

Animal microbiome

Seasonal variation in the gut microbiota of rhesus macaques inhabiting limestone forests of southwest Guangxi, China, Yuhui Li et al., Archives of Microbiology

Preprint: Persistence of the ground beetle (Coleoptera: Carabidae) microbiome to diet manipulation, Anita Silver et al., bioRxiv

Plant, root, and soil microbiome

Preprint: Unearthing the Boreal Soil Resistome Associated with Permafrost Thaw, Haan and Drown, bioRxiv

Phages and viruses

Preprint: Enteric viruses evoke broad host immune responses resembling bacterial microbiome, Simone Dallari et al., bioRxiv

September 17, 2020

Posted on September 17, 2020 by Rich Abdill

Another broad selection of microbiome papers for you this morning. Several papers today show how microbial communities are influenced by pollution, water depth, and El Niño, plus a study that found ants use signals from soil microbes to decide where to nest.

Human gut microbiome

Lactobacillus strains vary in their ability to interact with human endometrial stromal cells, Shiroda and Manning, PLOS ONE

A predictive index for health status using species-level gut microbiome profiling, Vinod K. Gupta et al., Nature Communications

Gut Microbiota and Metabolome Alterations Associated with Parkinson’s Disease, Sarah Vascellari et al., mSystems

Human nearly sterile sites

Metagenome analysis using serum extracellular vesicles identified distinct microbiota in asthmatics, Lee and Choi et al., Scientific Reports

Animal microbiome

The nesting preference of an invasive ant is associated with the cues produced by actinobacteria in soil, Hongmei Huang et al., PLOS Pathogens

Influence of host genetics in shaping the rumen bacterial community in beef cattle, Abbas and Howard et al., Scientific Reports

Bacteria Contribute to Plant Secondary Compound Degradation in a Generalist Herbivore System, Charlotte B. Francoeur et al., mBio

Plant, root, and soil microbiome

Diazotrophic bacteria from maize exhibit multifaceted plant growth promotion traits in multiple hosts, Shawn M. Higdon et al., PLOS ONE

Water and extremophile microbiome

Pollution shapes the microbial communities in river water and sediments from the Olifants River catchment, South Africa, Angel Valverde et al., Archives of Microbiology

Persistent El Niño driven shifts in marine cyanobacteria populations, Alyse A. Larkin et al., PLOS ONE

Depth-Dependent Variables Shape Community Structure and Functionality in the Prince Edward Islands, Phoma and Makhalanyane, Environmental Microbiology

Bioinformatics

Preprint: Tracking strains predicts personal microbiomes and reveals recent adaptive evolution, Shijie Zhao et al., bioRxiv

August 6, 2020

Posted on August 6, 2020 by Rich Abdill

Good morning from Minnesota! A broad selection of papers to share with you today: Immune responses in lung transplant patients, an examination of how hurricanes can alter the soil microbiome, and a cool preprint on host–microbe interactions in stickleback, plus 10 more—