Category Archives: Animal experiments

July 28, 2022

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Today’s digest includes research on the gut microbiome of infants, ruminants, and sand flies! There is also a preprint about sewage microbiomes as well as a research article about photosynthetic bacterial communities in crop fields.

Happy reading!

Human skin microbiome

Lichen Planopilaris: The first biopsy layer microbiota inspection – Pinto et al. – PLOS One

Human gut microbiome

Adaptation of the infant gut microbiome during the complementary feeding transition – McKeen et al. – PLOS One

Animal microbiome

Metagenomic insights into the microbe-mediated B and K2 vitamin biosynthesis in the gastrointestinal microbiome of ruminants – Jiang et al. – Microbiome

Comparative analysis of the gut microbiota of sand fly vectors of zoonotic visceral leishmaniasis (ZVL) in Iran; host-environment interplay shapes diversity – Karimian et al. – PLOS Neglected Tropical Diseases

Plant, root, and soil microbiome

Metagenomic analysis of the dynamical conversion of photosynthetic bacterial communities in different crop fields over different growth periods – Cheng et al. – PLOS One

Built environment

Preprint: A metagenomic investigation of spatial and temporal changes in sewage microbiomes across a university campus – Fierer et al. – bioRxiv

July 14, 2022

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Today’s digest has multiple articles on statistical and bioinformatic techniques! Also included is a job ad from my research team, so check it out if you’re interested in gaining geomicrobiology research experience at a national laboratory.

Events and jobs

Our geomicrobiology research group at the National Energy Technology Lab – Pittsburgh is looking for a technician/researcher. Exact responsibilities are somewhat flexible depending on interest and education-level; we are accepting applications from current students at all levels as well as postdocs.

General microbiome

Mycobacteriophages: From Petri dish to patient – Hatfull – PLOS Pathogens

Animal microbiome

Reconstructing the ecosystem context of a species: Honey-borne DNA reveals the roles of the honeybee – Wirta et al. – PLOS One

Plant, root, and soil microbiome

Patterns of microbial communities were shaped by bioavailable P along the elevation gradient of Shergyla Mountain, as determined by analysis of phospholipid fatty acids – Ba et al. – PLOS One

Preprint: Soil chemistry and soil history significantly structure oomycete communities in Brassicaceae crop rotations – Blakney et al. – bioRxiv

Community succession and straw degradation characteristics using a microbial decomposer at low temperature – Zhang et al. – PLOS One

Built Environment

Indoor air microbial load, antibiotic susceptibility profiles of bacteria, and associated factors in different wards of Arba Minch General Hospital, southern Ethiopia – Kayta et al. – PLOS One

Techniques

moreThanANOVA: A user-friendly Shiny/R application for exploring and comparing data with interactive visualization – Jiang et al. – PLOS One

Preparation of biological monolayers for producing high-resolution scanning electron micrographs – Mentor et al. – PLOS One

The accuracy of absolute differential abundance analysis from relative count data – Roche & Mukherjee – PLOS Computational Biology

AC-PCoA: Adjustment for confounding factors using principal coordinate analysis – Wang et al. – PLOS Computational Biology

Microbes in the news

The Art of Science: Students Participate in University’s First-Ever Bio-Art Class – Bernardi – Syracuse University News

July 13, 2022

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Today’s digest features studies on the leaf-microbiome of 🍅 and 🍓 plants (+ bumblebees and mites), human gut and wastewater resistome, and more. Happy reading!

Reproductive tract

Female reproductive tract microbiota and recurrent pregnancy loss: a nested case-control study – Pirkko Peuranpää – Reproductive BioMedicine Online

Gut microbiome

Dynamic metabolic interactions and trophic roles of human gut microbes identified using a minimal microbiome exhibiting ecological properties – Sudarshan A. Shetty – Journal of the International Society for Microbial Ecology

*Within-patient evolution of plasmid-mediated antimicrobial resistance – Javier DelaFuente – bioRxiv

An expanded reference map of the human gut microbiome reveals hundreds of previously unknown species – Sigal Leviatan – Nature Communications

Animal microbiome

Carpenter Bees (Xylocopa) Harbor a Distinctive Gut Microbiome Related to That of Honey Bees and Bumble Bees – Jo-anne C. Holley – Applied and Environmental Microbiology

Animal experiments

Gardnerella Exposures Alter Bladder Gene Expression and Augment Uropathogenic Escherichia coli Urinary Tract Infection in Mice – Nicole M. Gilbert – Frontiers in Cellular and Infection Microbiology

Plant microbiome

*The Greenhouse Phyllosphere Microbiome and Associations with Introduced Bumblebees and Predatory Mites – Marie Legein – Microbiology Spectrum

Food microbiome

Longitudinal, multi-platform metagenomics yields a high-quality genomic catalog and guides an in vitro model for cheese communities – Christina C. Saak – bioRxiv

New insights of bacterial communities in fermented vegetables from shotgun metagenomics and identification of antibiotic resistance genes and probiotic bacteria – Muhammad Yasir – Food Research International

Water microbiome

*High-resolution characterisation of short-term temporal variability in the taxonomic and resistome composition of wastewater influent – Kevin Kaibond Chau – bioRxiv

Pilot investigation on biostability of drinking water distribution systems under water source switching – Kejia Zhang – Applied Microbiology and Biotechnology

Bioinformatics

*BinaRena: a dedicated interactive platform for human-guided exploration and binning of metagenomes – Michael J. Pavia – bioRxiv

getSequenceInfo: a suite of tools allowing to get genome sequence information from public repositories – Vincent Moco – BMC Bioinformatics

baseLess: Lightweight detection of sequences in raw MinION data – Ben Noordijk – bioRxiv

July 8, 2022

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A selection of some great microbiome research and I’ve highlighted some resources for spatial transcriptomics for my non-microbiome picks.

General microbiome

Host control and the evolution of cooperation in host microbiomes – Sharp & Foster. Nature Communications

Effect of Helicobacter pylori Eradication on Gastric Cancer Prevention: Updated Report From a Randomized Controlled Trial With 26.5 Years of Follow-up – Yan et al. Gastroenterology

Gut microbiome

Antibiotic exposure prevents acquisition of beneficial metabolic functions in the preterm infant gut microbiome – Xu et al. Microbiome

Long-Term Effects of Developmental Exposure to Oxycodone on Gut Microbiota and Relationship to Adult Behaviors and Metabolism – Lyu et al. mSystems

Biogeographic variation and functional pathways of the gut microbiota in celiac disease – Constante et al. Gastroenterology.

Animal experiments

Akkermansia muciniphila prevents cold-related atrial fibrillation in rats by modulation of TMAO induced cardiac pyroptosis – Luo et al. eBioMedicine

Diet and feeding pattern modulate diurnal dynamics of the ileal microbiome and transcriptome – Machado et al. Cell Reports.

Virome

Gut virome profiling identifies a widespread bacteriophage family associated with metabolic syndrome – Jonge et al. Nature Communications

Respiratory microbiome

Host lung microbiota promotes malaria-associated acute respiratory distress syndrome – Mukherjee et al. Nature Communications

Bioinformatics

Super-taxon in human microbiome are identified to be associated with colorectal cancer – Dai et al. BMC Bioinformatics

Non-microbiome picks

As spatial transcriptomics grows in popularity you might be interested in some recent reviews & examples of the technology in use

An introduction to spatial transcriptomics for biomedical research – Williams et al. Genome Medicine

Deciphering tissue structure and function using spatial transcriptomics – Walker et al. Communications biology

Method of the Year: spatially resolved transcriptomics – Marx. Nature Methods

Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays – Chen et al. Cell (The recent famous Cell cover using Stereo-Seq)

Museum of spatial transcriptomics – Moses & Pachter. Nature Methods

July 5, 2022

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Highlights!

A volatile from the skin microbiota of flavivirus-infected hosts promotes mosquito attractiveness – Hong Zhang – Cell → The production of acetophenone, a potent attractant for mosquitoes, is induced by Flavivirus by a microbiota-based mechanism. This finding shows an interesting example of the interplay between certain viral agents and the microbiota to influence host susceptibility to interact with other species. 

Human and General Microbiome

Dynamic Alterations in the Respiratory Tract Microbiota of Patients with COVID-19 and its Association with Microbiota in the Gut – Yifei Shen – Advanced Science

Interaction of n-3 polyunsaturated fatty acids with host CD36 genetic variant for gut microbiome and blood lipids in human cohorts – Zelei Miao – Clinical Nutrition 

A weight-loss model based on baseline microbiota and genetic scores for selection of dietary treatments in overweight and obese population – Amanda Cuevas-Sierra – Clinical Nutrition

Beneficial Microbes and Compounds

Restoration of cefixime-induced gut microbiota changes by a prebiotic blend in a mouse model – Jingyi Yuan – Applied Microbiology and Biotechnology

A synbiotics, long chain polyunsaturated fatty acids, and milk fat globule membranes supplemented formula modulates microbiota maturation and neurodevelopment – Tomás Cerdó – Clinical Nutrition

Animal Model Microbiome

Multi-omics data reveals the disturbance of glycerophospholipid metabolism caused by disordered gut microbiota in depressed mice – Tian Tian – Journal of Advanced Research

C-section increases cecal abundance of the archetypal bile acid and glucocorticoid modifying Lachnoclostridium [clostridium] scindens in mice – Sean H Adams – Physiological Reports

A single respiratory tract infection early in life reroutes healthy microbiome development and affects adult metabolism in a preclinical animal model – Soner Yildiz – NPJ Biofilms and Microbiomes

Non-Model Animal Microbiome

Microbiota mediated plasticity promotes thermal adaptation in the sea anemone Nematostella vectensis – Laura Baldassarre – Nature Communications

Dysbiosis and Predicted Functions of the Dental Biofilm of Dairy Goats with Periodontitis – Ana Carolina Borsanelli – Microbial Ecology

Houseflies harbor less diverse microbiota under laboratory conditions but maintain a consistent set of host-associated bacteria – Anna Voulgari-Kokota – Scientific Reports

Plant and Soil Microbiome

Salinity Influences Endophytic Bacterial Communities in Rice Roots from the Indian Sundarban Area – Gargi Das – Current Microbiology

Routes and rates of bacterial dispersal impact surface soil microbiome composition and functioning – Kendra E Walters – The ISME Journal

Leaf bacterial microbiota response to flooding is controlled by plant phenology in wheat (Triticum aestivum L.) – Davide Francioli – Scientific Reports

Bioinformatics and Microbiome Analysis

MB-SupCon: Microbiome-based predictive models via Supervised Contrastive Learning – Sen Yang – Journal of Molecular Biology

July 1, 2022

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We made it to the end of the week, we made it through the end of June. To celebrate, check out the two (!) articles about the pig gut microbiome, try out a new tool for network analysis (MicNet Toolbox), or enjoy an NPR Short Waves podcast episode about Agar Art. Or maybe you’re spending the afternoon preparing a research talk or fieldwork event? If that’s the case, check out the article presenting 10 rules for improving communication among scientists or the one on the hidden labor of managing threats to safety by women in fieldwork.

General microbiome

Assessment of disinfectant efficacy in reducing microbial growth – Alajlan et al. – PLOS One

Animal experiments

Metagenomic analysis of the gut microbiota in piglets either challenged or not with enterotoxigenic Escherichia coli reveals beneficial effects of probiotics on microbiome composition, resistome, digestive function and oxidative stress responses – Apiwatsiri et al. – PLOS One

Phylogenetic diversity analysis of shotgun metagenomic reads describes gut microbiome development and treatment effects in the post-weaned pig – Gaio et al. – PLOS One

Preprint: Using axenic and gnotobiotic insects to examine the role of different microbes on the development and reproduction of the kissing bug Rhodnius prolixus (Hemiptera: Reduviidae) – Gilliland et al. – bioRxiv

Bioinformatics

MicNet toolbox: Visualizing and unraveling a microbial network – Favila et al. – PLOS One
Techniques

Evaluating the impact of sample storage, handling, and technical ability on the decay and recovery of SARS-CoV-2 in wastewater – Beattie et al. – PLOS One

Microbes in the news

NPR’s Short Wave Podcast: Let’s Get Crafty With Agar Art (11 minute episode)!

Science, publishing, and career

Ten simple rules for improving communication among scientists – Bautista et al. – PLOS Computational Biology

You can’t report your feelings: The hidden labor of managing threats to safety by women in global public health fieldwork – McAuliffe et al. – PLOS Global Public Health

June 29, 2022

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General microbiome

Microbial Tracking-2, a metagenomics analysis of bacteria and fungi onboard the International Space Station – Urbaniak et al. – Microbiome

Engineering the human gut commensal Bacteroides thetaiotaomicron with synthetic biology – Lai, Hayashi & Lu – Current Opinion in Chemical Biology

Factors shaping the abundance and diversity of the gut archaeome across the animal kingdom – Thomas et al. – Nature Communications

Human oral microbiome

Increase in Bifidobacterium is a characteristic of the difference in the salivary microbiota of pregnant and non-pregnant women – Kato et al. – BMC Oral Health

Human urinary microbiome

Concordance of Urinary Microbiota Detected by 16S rRNA Amplicon Sequencing Versus Expanded Quantitative Urine Culture – Vaughan et al. – American Journal of Obstetrics and Gynecology

Human gut microbiome

Dietary variety relates to gut microbiota diversity and abundance in humans – Huang et al. – European Journal of Nutrition

The gut microbiota composition in patients with right- and left-sided colorectal cancer and after curative colectomy, as analyzed by 16S rRNA gene amplicon sequencing – Suga et al. – BMC Gastroenterology

Long-Term Dietary Effects on Human Gut Microbiota Composition Employing Shotgun Metagenomics Data Analysis – Troci et al. – Molecular Nutrition & Food Research

Functional changes of the gastric bypass microbiota reactivate thermogenic adipose tissue and systemic glucose control via intestinal FXR-TGR5 crosstalk in diet-induced obesity – Münzker et al. – Microbiome

Animal experiments (mouse/rat experiments, chickens/pigs on different diets)

Perinatal transmission of a probiotic Bifidobacterium strain protects against early life stress-induced mood and gastrointestinal motility disorders – Zhu et al. – Food & Function

Leveraging Existing 16SrRNA Microbial Data to Define a Composite Biomarker for Autism Spectrum Disorder – Xu et al. – Microbiology Spectrum

Animal microbiome (for animals in the wild)

Gut microbiome of century-old snail specimens stable across time in preservation – Chalifour, Elder & Li – Microbiome

Plant, root, and soil microbiome

Soil-derived bacteria endow Camellia weevil with more ability to resist plant chemical defense – Zhang et al. – Microbiome

Water and extremophile microbiome (sea, rivers, lakes, glaciers, permafrost, high-salt)

A genome and gene catalog of glacier microbiomes – Liu et al. – Nature Biotechnology

Bioinformatics / Data

Large Scale Genome-Centric Metagenomic Data from the Gut Microbiome of Food-Producing Animals and Humans – Lemos et al. – Scientific Data

Research Note: Choice of microbiota database affects data analysis and interpretation in chicken cecal microbiota – Campos et al. – Poultry Science

[PREPRINT]Predicting metabolomic profiles from microbial composition through neural ordinary differential equations – Wang et al. – bioRxiv

June 24, 2022

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Today we have a report in Science on bacterium which is 1cm long, a great review of the gut virome in human health, and a meta-analysis of mycobiota signatures in colorectcal cancer among some other great papers.

General microbiology

A centimeter-long bacterium with DNA contained in metabolically active, membrane-bound organelles – Volland et al. – Science

Virome

Filamentous bacteriophage delays healing of Pseudomonas-infected wounds – Bach et al. – Cell Reports Medicine

[REVIEW] The gut virome: A new microbiome component in health and disease – Cao et al. – eBioMedicine

Gut Microbiome

Presence of Blastocystis in gut microbiota is associated with cognitive traits and decreased executive function – Mayneris-Perxachs et al. – ISME

Altered mycobiota signatures and enriched pathogenic Aspergillus rambellii are associated with colorectal cancer based on multi-cohort fecal metagenomic analyses – Lin et al. – Gastroenterology

[REVIEW] Small molecules in the big picture of gut microbiome-host cross-talk – Ma et al. – eBioMedicine

Maternal gut microbiome–induced IgG regulates neonatal gut microbiome and immunity – Sanidad et al. – Science Immunology

Non-Microbiome picks

Time for better time-restricted eating trials to lessen the burden of metabolic diseases – Taub and Panda – Cell Reports Medicine

What SARS-CoV-2 does to our brains – Aschman et al. – Immunity

June 22, 2022

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General microbiome

A 16th century Escherichia coli draft genome associated with an opportunistic bile infection – Long et al. – Communications Biology

Pregnancy and early life

[PREPRINT]Strong pathogen competition in neonatal gut colonisation – Mäklin et al. – bioRxiv

Human skin microbiome

Dysbiosis of Skin Microbiota with Increased Fungal Diversity is Associated with Severity of Disease in Atopic Dermatitis – Schmid et al. – JEADV

Human gut microbiome

Loss of Novel Diversity in Human Gut Microbiota Associated with Ongoing Urbanization in China – Sun et al. – mSystems

A comprehensive analysis of the microbiota composition and host driver gene mutations in colorectal cancer – Yuan et al. – Investigational New Drugs

[REVIEW]Vegetarianism, Microbiota and Cardiovascular health: Looking back, and forward – Kumar et al. – European Journal of Preventive Cardiology

[REVIEW]Effects of a low FODMAP diet on the colonic microbiome in irritable bowel syndrome: a systematic review with meta-analysis – So, Loughman & Staudacher – The American Journal of Clinical Nutrition

Profiling gut microbiota and bile acid metabolism in critically ill children – Kean et al. – Scientific Reports

Super-taxon in human microbiome are identified to be associated with colorectal cancer – Dai et al. – BMC Bioinformatics

The gut metagenomics and metabolomics signature in patients with inflammatory bowel disease – Xu et al. – Gut Pathogenes

Animal experiments (mouse/rat experiments, chickens/pigs on different diets)

Immune checkpoint inhibitors unleash pathogenic immune responses against the microbiota – Hu et al. – PNAS

Deletion of both Dectin-1 and Dectin-2 affects the bacterial but not fungal gut microbiota and susceptibility to colitis in mice – Wang et al. – Microbiome

Animal microbiome (for animals in the wild)

Fecal microbiome of horses transitioning between warm-season and cool-season grass pasture within integrated rotational grazing systems – Weinert-Nelson, Biddle & Williams – Animal Microbiome

Water and extremophile microbiome (sea, rivers, lakes, glaciers, permafrost, high-salt)

Full-Length 16S rRNA Gene Sequences from Raw Sewage Samples Spanning Geographic and Seasonal Gradients in Conveyance Systems across the United States – LaMartina, Schmoldt & Newton – Microbiology Resource Announcements

Techniques

SRS-FISH: A high-throughput platform linking microbiome metabolism to identity at the single-cell level – Ge et al. – PNAS

June 18, 2022

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Have a nice weekend! Today, in this Digest: The effect of the gut dysbiosis on prostate cancer, microbial inheritance, bee microbiome, rhizosphere microbiota, a comparison of DNA isolation techniques for deep amplicon sequencing, and more…

Human and General Microbiome

Gut dysbiosis promotes prostate cancer progression and docetaxel resistance via activating NF-κB-IL6-STAT3 axis – Weibo Zhong – Microbiome

On the effect of inheritance of microbes in commensal microbiomes – Román Zapién-Campos – BMC Ecology and Evolution

Ureaplasma and Prevotella colonization with Lactobacillus abundance during pregnancy facilitates term birth – Sunwha Park – Scientific Reports

Deep Grouping Analysis of the Altered Cervical Canal Microbiota in Intrauterine Adhesion Patients – Xiangdong Hua – Reproductive Sciences

Intestinal microbiota transplantation: do not forget the metabolites – Benjamin H Mullish – The Lancet. Gastroenterology & Hepatology

Characterization of oral and gut microbiome and plasma metabolomics in COVID-19 patients after 1-year follow-up – Guang-Ying Cui – Military Medical Research

Congenitally underdeveloped intestine drives autism-related gut microbiota and behavior – Jie Li – Brain, Behavior, and Immunity

Beneficial Microbes and Compounds

Lacticaseibacillus rhamnosus HA-114 improves eating behaviors and mood-related factors in adults with overweight during weight loss: a randomized controlled trial – Béatrice S-Y Choi – Nutritional Neuroscience

Model Animal Microbiome

New Strains of Akkermansia muciniphila and Faecalibacterium prausnitzii are Effective for Improving the Muscle Strength of Mice with Immobilization-Induced Muscular Atrophy – Hye Rim Byeon – Journal of Medicinal food

Non-Model Animal Microbiome

Comparative metagenomics reveals expanded insights into intra- and interspecific variation among wild bee microbiomes – Wyatt A Shell – Communications Biology

Rumen multi-omics addressing diet-host-microbiome interplay in farm animals: a review – Sonam Dixit – Animal Biotechnology

Plant Microbiome

Spatio-temporal variation in the root-associated microbiota of orchard-grown apple trees – Maximilian Fernando Becker – Environmental Microbiome

Identifying plant genes shaping microbiota composition in the barley rhizosphere – Carmen Escudero-Martinez – Nature Communications

Disentangling the genetic basis of rhizosphere microbiome assembly in tomato – Ben O Oyserman – Nature Communications

Environmental Microbiome

Rapid changes in coastal ocean microbiomes uncoupled with shifts in environmental variables – Jessica L Gronniger – Environmental Microbiology

Microplastics alter nitrous oxide production and pathways through affecting microbiome in estuarine sediments – Cheng Chen – Water Research

500 metagenome-assembled microbial genomes from 30 subtropical estuaries in South China – Lei Zhou – Scientific Data

Food Microbiome

Microbiome and -omics application in food industry – Ilario Ferrocino – International Journal of Food Microbiology

Bioinformatic and Experimental Microbiome Analysis

A comparison of six DNA extraction protocols for 16S, ITS and shotgun metagenomic sequencing of microbial communities – Justin P Shaffer – BioTechniques

Review: Machine Learning Advances in Microbiology: A Review of Methods and Applications – Yiru Jiang – Frontiers in Microbiology