Category Archives: Human reproductive or urinary

June 7, 2024

Posted on by

Today’s digest features AMPSphere, Candida pathogenesis, rhizosphere microbiome in the Himalayas, imaging of oral microbiome, and more.
See you at #MVIF special event on women’s health!

Global microbiome

Discovery of antimicrobial peptides in the global microbiome with machine learning – Célio Dias Santos-Júnior and Marcelo D.T. Torres – Cell

Bioenergetic mapping of ‘healthy microbiomes’ via compound processing potential imprinted in gut and soil metagenomes – Craig Liddicoat – Science of The Total Environment

Infant microbiome

The impact of perinatal maternal stress on the maternal and infant gut and human milk microbiomes: A scoping review protocol – Niamh Ryan – Plos One

Oral microbiome

Improved Visualization of Oral Microbial Consortia – S.T. Ramirez-Puebla – Journal of Dental Research

Animal microbiome

Changes of faecal bacterial communities and microbial fibrolytic activity in horses aged from 6 to 30 years old – Marylou Baraille – Plos One

Compendium of 5810 genomes of sheep and goat gut microbiomes provides new insights into the glycan and mucin utilization – Ke Zhang – Microbiome

Animal experiments

Bacteroides uniformis CECT 7771 requires adaptive immunity to improve glucose tolerance but not to prevent body weight gain in diet-induced obese mice – Marina Romaní-Pérez – Microbiome

The impact of microplastics polystyrene on the microscopic structure of mouse intestine, tight junction genes and gut microbiota – Qi-Ling Su – Plos One

Epithelial hypoxia maintains colonization resistance against Candida albicans – Hannah P. Savage – Cell Host & Microbe

Viruses and phages

Characterizing the gut phageome and phage-borne antimicrobial resistance genes in pigs – Jun Hu – Microbiome

Water microbiome

Deep long-read metagenomic sequencing reveals niche differentiation in carbon cycling potential between benthic and planktonic microbial populations – Tomeu Viver – bioRxiv

Root, soil, plant microbiome

Altitude-Dependent Influence of Artemisia brevifolia on its Rhizosphere Microbiome in Ladakh Region of the Western Himalayas – Manzoor Hussain – Rhizosphere

Bioinformatics

Lightweight taxonomic profiling of long-read sequenced metagenomes with Lemur and Magnet – Nicolae Sapoval – bioRxiv

Comprehensive profiling of genomic invertons in defined gut microbial community reveals associations with intestinal colonization and surface adhesion – Xiaofan Jin – bioRxiv

May 29, 2024

Posted on by

Human microbiomes

Gut microbiome remodeling and metabolomic profile improves in response to protein pacing with intermittent fasting versus continuous caloric restriction – Alex E. Mohr – Nature Communications

[PREPRINT] Towards a Health-Associated Core Keystone (HACK) index for the human gut microbiome – Abishek Goel – bioRxiv

Exposure to environmental pollutants selects for xenobiotic-degrading functions in the human gut microbiome – Francesca De Fillipis – Nature Communications

The interrelation between microbial immunoglobulin coating, vaginal microbiota, ethnicity, and preterm birth – H.J. Schuster – BMC Microbiome

Porphyromonas gingivalis, a bridge between oral health and immune evasion in gastric cancer – Matías Muñoz-Medel – Frontiers in Oncology

Differences in maternal subgingival microbiome between preterm and term births: The MOHEPI study – Jung Soo Park – Journal of Periodontal Resaerch

Animal microbiome

Integrating uterine microbiome and metabolome to advance the understanding of the uterine environment in dairy cows with metritis – S. Casaro – BMC Animal Microbiome

Responses of nutrient utilization, rumen fermentation and microorganisms to different roughage of dairy buffaloes – Shichun He – BMC Microbiology

Identification of the mutual gliding locus as a factor for gut colonization in non-native bee hosts using the ARTP mutagenesis – Yujie Meng – BMC Microbiome

Co-habiting ants and silverfish display a converging feeding ecology – Thomas Parmentier – BMC Biology

Temperature-dependent differences in mouse gut motility are mediated by stress – Alvin Han – Nature Lab Animal

Food microbiome

Evaluation of microbiota-induced changes in biochemical, sensory properties and volatile profile of kombucha produced by reformed microbial community – Hilal Kilmanoglu – Food Chemistry X

Plant, soil, and root microbiome

Microbial polyphenol metabolism is part of the thawing permafrost carbon cycle – Bridget B. McGivern – Nature Microbiology

[PREPRINT] Soil viral community dynamics over seven years of heat disturbance: spatial variation exceeds temporal in annually sampled soils – Samuel E. Barnett & Ashley Shade – bioRxiv

Global soil metagenomics reveals distribution and predominance of Deltaproteobacteria in nitrogen-fixing microbiome – Yoko Masuda – BMC Microbiome

Water & extremophile microbiome

Bacterial dynamics of the plastisphere microbiome exposed to sub-lethal antibiotic pollution – Brune Jounnard & Concepcion Sanchez-Cid – BMC Microbiome

Exploring potential polysaccharide utilization loci involved in the degradation of typical marine seaweed polysaccharides by Bacteroides thetaiotaomicron – Biao Yu – Frontiers in Microbiology

Organic matter degradation in the deep, sulfidic waters of the Black Sea: insights into the ecophysiology of novel anaerobic bacteria – Subhash Yadav – BMC Microbiome

May 17, 2024

Posted on by

Today’s digest features bioinformatics binning methods, healthy dogs, lakes in South Africa, and more. For the human gut microbiome studies, check out the latest digest (May 15, 2024) by Grace Deitzler.

See you at #MVIF!

Skin microbiome

Intraspecies warfare restricts strain coexistence in human skin microbiomes – Christopher P. Mancuso – bioRxiv

Oral microbiome

Oral microbiota of patients with phenylketonuria: A nation-based cross-sectional study – Memduh Bingöl – Journal of Clinical Periodontology

Urinary microbiome

Microbroth dilution method for antibiotic susceptibility testing of fastidious and anaerobic bacteria of the urinary microbiome – Wilson Geaman – Microbiology Spectrum

Respiratory tract

Meta-analysis of the human upper respiratory tract microbiome reveals robust taxonomic associations with health and disease – Nick Quinn-Bohmann – BMC Biology

Food microbiome

Microbial community structure of plant-based meat alternatives – Franz-Ferdinand Rochn – pj Science of Food

Plan, root, soil

Functional team selection: a framework for local adaptation in plants and their belowground microbiomes – Nancy Collins Johnson and César Marín – ecoevoRxiv

Life on the edge: microbial diversity, resistome, and virulome in soils from the Union Glacier cold desert – Patricio Arros – bioRxiv

Animal microbiome

Microbiota of healthy dogs demonstrate a significant decrease in richness and changes in specific bacterial groups in response to supplementation with resistant starch, but not psyllium or methylcellulose, in a randomized cross-over trial – Silke Salavati Schmitz – Access Microbiology

Early-life factors shaping the gut microbiota of Common buzzard nestlings – Hugo Pereira – Animal Microbiome

Animal experiment

13C-Stable isotope resolved metabolomics uncovers dynamic biochemical landscape of gut microbiome-host organ communications in mice – Xia Xiao – Microbiome

Water microbiome

Metagenomics datasets of water and sediments from eutrophication-impacted artificial lakes in South Africa – Grace Nkechinyere Ijoma – Scientific Data

Bioinformatics

Fairy: fast approximate coverage for multi-sample metagenomic binning – Jim Shaw and Yun William Yu – bioRxiv

Highly accurate metagenome-assembled genomes from human gut microbiota using long-read assembly, binning, and consolidation methods – Daniel M Portik – biorXiv

Using short-read 16S rRNA sequencing of multiple variable regions to generate high-quality results to a species level – Amy S Graham – bioRxiv

Full factorial construction of synthetic microbial communities – Juan Diaz-Colunga – bioRxiv

ARGNet: using deep neural networks for robust identification and classification of antibiotic resistance genes from sequences – Yao Pei – Microbiome

May 15, 2024

Posted on by

Human gut microbiome

A shared group of bacterial taxa in the duodenal microbiota of undernourished Pakistani children with environmental enteric dysfunction – Najeeha T Iqbal – mSphere

Gut microbiota, blood metabolites, and left ventricular diastolic dysfunction in US Hispanics/Latinos – Kai Luo – BMC Microbiome

Co-localization of antibiotic resistance genes is widespread in the infant gut microbiome and associates with an immature gut microbial composition – Xuanji Li – BMC Microbiome

Impact of the gut microbiome composition on social decision-making – Marie Falkenstein – PNAS Nexus

Veillonella and Bacteroides are associated with gestational diabetes mellitus exposure and gut microbiota immaturity – Fernanda Valdez-Palomares – PLOS One

[REVIEW] The neonatal gut microbiome and global health – Pinaki Panigrahi – Gut Microbes

Functional characterization of helminth-associated Clostridiales reveals covariates of Treg differentiation – Shusan Sargisan – BMC Microbiome

Vaginal microbiome

16S rRNA female reproductive microbiome investigation reveals Dalfopristin, Clorgyline, and Hydrazine as potential therapeutics for the treatment of bacterial vaginosis – Sudeepti Kulshrestha – Diagnostic Microbiology and Infectious Disease

Fecal transplant from vaginally seeded infants decreases intraabdominal adiposity in mice – Sivaranjani Namasivayam – Gut Microbes

Animal microbiome

Viruses contribute to microbial diversification in the rumen ecosystem and are associated with certain animal production traits – Ming Yan & Zhongtang Yu – BMC Microbiome

Quantitative microbiome profiling of honey bee (Apis mellifera) guts is predictive of winter colony loss in northern Virginia (USA) – David B. Carlini – Nature Scientific Reports

How do phytophagous insects affect phyllosphere fungi? Tracking fungi from milkweed to monarch caterpillar frass reveals communities dominated by fungal yeast – Ryoko Oono – Environmental Microbiology

Beneficial microbes & compounds

The gut lactic acid bacteria metabolite, 10-oxo- cis-6, trans-11-octadecadienoic acid, suppresses inflammatory bowel disease in mice by modulating the NRF2 pathway and GPCR-signaling – Miki Ando – Frotiers in Immunology

Effect of weight loss program using prebiotics and probiotics on body composition, physique, and metabolic products: longitudinal intervention study – Nayera E Hassan – Nature Scientific Reports

Origin of the neonatal gut microbiota and probiotic intervention: a randomized controlled trial – Zhe Li – Frontiers in Nutrition

Effectiveness of probiotic- and fish oil-loaded water-in-oil-in-water (W1/O/W2) emulsions at alleviating ulcerative colitis – Qingzhao Gu – Food & Function

Plant, root, and soil microbiome

Competition mode and soil nutrient status shape the role of soil microbes in the diversity–invasibility relationship – Haokun Li – Ecology and Evolution

Dynamics and drivers of fungal communities in a multipartite ant-plant association – Veronica Barrajon-Santos – BMC Biology

Quorum sensing related activities of beneficial and pathogenic bacteria have important implications for plant and human health – Anton Hartmann – FEMS Microbiology Ecology

Impacts of vegetable processing and cheese making effluent on soil microbial functional diversity, community structure, and denitrification potential of land treatment systems – Geoffrey S. Siemering – Water Environment Research

Role of Bacillus subtilis exopolymeric genes in modulating rhizosphere microbiome assembly – Caroline Sayuri Nishisaka – BMC Environmental Microbiome

The predominant lactic acid bacteria and yeasts involved in the spontaneous fermentation of millet during the production of the traditional porridge Hausa koko in Ghana – Amy Atter – BMC Microbiology

Bioinformatics & Tools

Multi-class boosting for the analysis of multiple incomplete views on microbiome data – Andrea Simeon – BMC Bioinformatics

PrimerEvalPy: a tool for in-silico evaluation of primers for targeting the microbiome – Lara Vázquez-González – BMC Bioinformatics

Readsynth: short-read simulation for consideration of composition-biases in reduced metagenome sequencing approaches – Ryan Kuster – BMC Bioinformatics

March 6, 2024

Posted on by

Vaginal Microbiome

Modeling Healthy and Dysbiotic Vaginal Microenvironments in a Human Vagina-on-a-Chip – Aakanksha Gulati et al – JoVE Bioengineering

Cancer microbiome

Multi-omics analysis elucidates the relationship between intratumor microbiome and host immune heterogeneity in breast cancer – Jia Li et al – Microbiology Spectrum

Human gut microbiome

Protein combined with certain dietary fibers increases butyrate production in gut microbiota fermentation – Rachel Jackson et al – Food & Function

A human milk oligosaccharide prevents intestinal inflammation in adulthood via modulating gut microbial metabolism – Kasey M. Schalich et al – mBio

Taxonomic and metabolic development of the human gut microbiome across life stages: a worldwide metagenomic investigation – Leonardo Mancabelli et al – mSystems

Cadaver microbiome

Decomposer communities are universal in death – Michael S. Strickland – Nature Microbiology

Animal microbiome

The coral microbiome in sickness, in health and in a changing world – Christian R. Voolstra et al – Nature Reviews Microbiology

The effects of hydrolyzed protein on macronutrient digestibility, fecal metabolites and microbiota, oxidative stress and inflammatory biomarkers, and skin and coat quality in adult dogs – Clare Hsu et al – Journal of Animal Science

Host starvation and in hospite degradation of algal symbionts shape the heat stress response of the Cassiopea-Symbiodiniaceae symbiosis – Gaëlle Toullec et al – BMC Microbiome

An engineered bacterial symbiont allows noninvasive biosensing of the honey bee gut environment – Audam Chhun et al – PLOS Biology

From phyllosphere to insect cuticles: silkworms gather antifungal bacteria from mulberry leaves to battle fungal parasite attacks – Pengfei Zhao et al – BMC Microbiome

Phages and viruses

Discovery and characterization of novel DNA viruses in Apis mellifera: expanding the honey bee virome through metagenomic analysis – Dominika Kadlečková et al – mSystems

Taxonomic difference in marine bloom-forming phytoplanktonic species affects the dynamics of both bloom-responding prokaryotes and prokaryotic viruses – Hiroaki Takebe et al – mSystems

Plant, root, and soil microbiome

Microbiome sequencing revealed the abundance of uncultured bacteria in the Phatthalung sago palm-growing soil – Pumin Nutaratat et al – PLOS ONE

The rhizosphere microbiome reduces the uptake of arsenic and tungsten by Blechnum orientale by increasing nutrient cycling in historical tungsten mining area soils – Xiaolong Lan et al – Science of the Total Environment

Non-Microbiology/Science Communication

[PREPRINT] Sci-comm “behind the scenes”: Gendered narratives of scientific outreach activities in the life sciences – Perry G. Beasley-Hall et al – bioRxiv

February 23, 2024

Posted on by

Today’s digest features the MetaPhlAn v4.1 & viral module, early life gut microbiome and diabetes, human milk oligosaccharides study, and more.

NEWS
MVIF has launched their crowdfunding campaign https://www.gofundme.com/f/me-mvif

See you at #MVIF next week!

Oral microbiome

Favorable subgingival plaque microbiome shifts are associated with clinical treatment for peri-implant diseases – Davide Bazzani – npj Biofilms and Microbiomes

Nasal microbiome

Nasal commensals reduce Staphylococcus aureus proliferation by restricting siderophore availability – Y Zhao – bioRxiv

Semen microbiome

Characterisation and comparison of semen microbiota and sperm function in men with infertility, recurrent miscarriage, or proven fertility – Shahriar Mowla – bioRxiv

Gut microbiome

CRISPR-Cas-based identification of a sialylated human milk oligosaccharides utilization cluster in the infant gut commensal Bacteroides dorei – Sivan Kijner – Nature Communications

Microbiome features associated with performance measures in athletic and non-athletic individuals: A case-control study – Kinga Humińska-Lisowska – Plos One

The impact of iron supplementation on the preterm neonatal gut microbiome: A pilot study – Matthew VanOrmer – Plos One

Early-life exposures to specific commensal microbes prevent type 1 diabetes – Jamal Green – bioRxiv

Insights into gut microbiomes in stem cell transplantation by comprehensive shotgun long-read sequencing – Philipp Spohr – Scientific Reports

Donor-recipient intermicrobial interactions impact transfer of subspecies and fecal microbiota transplantation outcome – Qiyi Chen – Cell Host & Microbe

Animal experiment

The gut ileal mucosal virome is disturbed in patients with Crohn’s disease and exacerbates intestinal inflammation in mice – Zhirui Cao – Nature Communications

Animal microbiome

Gut microbiome diversity and function during hibernation and spring emergence in an aquatic frog – Ji-Eun Lee – Plos One

Unraveling the gut microbiota of Tibetan chickens: insights into highland adaptation and ecological advantages – Tao Zeng – bioRxiv

Water microbiome

A difficult coexistence: resolving the iron-induced nitrification delay in groundwater filters – Francesc Corbera-Rubio – bioRxiv

Human virome

Discovering and exploring the hidden diversity of human gut viruses using highly enriched virome samples – Moreno Zolfo – bioRxiv

January 8, 2024

Posted on by

The microbiome digest team, Juan Pablo Cardenas Astudillo, Axel Künstner and Svetlana Ugarcina Perovic (it’s me), wishes you happy and healthy 2024! Also, we wish to have more members in our team in order to cover all daily microbiome science news: if you are interested in reviewing microbiome papers at your convenience (with our support!) and digest them for the community, feel free to contact us. We are happy to welcome you!

And, yes, see you at MVIF #25!

Vaginal microbiome

Vaginal Lactobacillus fatty acid response mechanisms reveal a novel strategy for bacterial vaginosis treatment – Meilin Zhu – bioRxiv

Gut microbiome

BilR is a gut microbial enzyme that reduces bilirubin to urobilinogen – Brantley Hall – Nature Microbiology

Influence of feeding practices in the composition and functionality of infant gut microbiota and its relationship with health – Misael Martínez-Martínez – PlosOne

Mucin-degrading gut bacteria promote anti-parasitic immunity – Mathis Wolter – bioRxiv

Host genetic regulation of human gut microbial structural variation – Daria V. Zhernakova – Nature

Animal microbiome

Deciphering the gut microbiome of grass carp through multi-omics approach – Ming Li – Microbiome

Spotting disease disrupts the microbiome of infected purple sea urchins, Strongylocentrotus purpuratus – Chloe G. Shaw – BMC Microbiology

Animal experiments

Desulfovibrio vulgaris interacts with novel gut epithelial immune receptor LRRC19 and exacerbates colitis – Runxiang Xie – Microbiome

Individualized microbiotas dictate the impact of dietary fiber on colitis sensitivity – Erica Bonazzi – Microbiome

A consortia of clinical E. coli strains with distinct in vitro adherent/invasive properties establish their own co-colonization niche and shape the intestinal microbiota in inflammation-susceptible mice – Rachel M. Bleich – Microbiome

Environmental microbiome

A unified compendium of prokaryotic and viral genomes from over 300 anaerobic digestion microbiomes – Victor Borin Centurion – Environmental Microbiome

Plant, root, soil microbiome

Unraveling the interplay between root exudates, microbiota, and rhizosheath formation in pearl millet – Abdelrahman Alahmad – Microbiome

Methods

mEnrich-seq: methylation-guided enrichment sequencing of bacterial taxa of interest from microbiome – Lei Cao – Nature Methods

Bioinformatics

A catalogue of small proteins from the global microbiome – Yiqian Duan – bioRxiv

December 6, 2023

Posted on by

Human salivary microbiome

Salivary microbiome changes distinguish response to chemoradiotherapy in patients with oral cancer – de Medeiros et al. – Microbiome

Human skin microbiome

[PREPRINT]Commensal skin bacteria exacerbate inflammation and delay skin healing – Khadka et al. – bioRxiv

Human vaginal microbiome

Integrating compositional and functional content to describe vaginal microbiomes in health and disease – Holm et al. – Microbiome

Comparison of vaginal microbiota between women with inflammatory bowel disease and healthy controls – Bar et al. – PLOS One

Human gut microbiome

Engraftment of essential functions through multiple fecal microbiota transplants in chronic antibiotic-resistant pouchitis—a case study using metatranscriptomics – Deng et al. – Microbiome

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

Vitamin D modulation of brain-gut-virome disorder caused by polystyrene nanoplastics exposure in zebrafish (Danio rerio) – Teng et al – Microbiome

Animal microbiome (for animals in the wild)

Diversity of gut microbiome in Rocky Mountainsnail across its native range – Chalifour, Elder & Li – PLOS One

[PREPRINT]Testing the effectiveness of a commercially sold probiotic on restoring the gut microbiota of honey bees: a field study – Damico et al. – bioRxiv

Core gut microbes Cloacibacterium and Aeromonas associated with different gastropod species could be persistently transmitted across multiple generations – Lin et al. – Microbiome

Plant, root, and soil microbiome

Effects of multiple N, P, and K fertilizer combinations on strawberry growth and the microbial community – Bai et al. – PLOS One

Comparison of microbial community assemblages in the rhizosphere of three Amaranthus spp. – Chee-Sanford & Connor – PLOS One

Bioinformatics

Phantom oscillations in principal component analysis – Shinn – PNAS
This phenomenon is not new (e.g. know as horseshoe effect) but Shinn gives a very understandable explanation.

The MAGMA pipeline for comprehensive genomic analyses of clinical Mycobacterium tuberculosis samples – Heupink et al. – PLOS Computational Biology

[PREPRINT]metaExpertPro: a computational workflow for metaproteomics spectral library construction and data-independent acquisition mass spectrometry data analysis – Sun et al. – bioRxiv

[PREPRINT]MolPad: An R-Shiny Package for Cluster Co-Expression Analysis in Longitudinal Microbiomics – Ma, Thairu & Sankaran

November 10, 2023

Posted on by

Read about new species discovered in the female genitourinary tract Lactobacillus isalae, Gardnerella pickettii and Gardnerella greenwoodii, and important UTI and other latest microbiome science news.
Happy Friday! And see you next week at MVIF!

Urinary microbiome

A human urothelial microtissue model reveals shared colonization and survival strategies between uropathogens and commensals – Carlos Flores – Science Advances

Gardnerella pickettii sp. nov. (formerly Gardnerella genomic species 3) and Gardnerella greenwoodii sp. nov. (formerly Gardnerella genomic species 8) isolated from female urinary microbiome – Márcia Sousa – International Journal of Systematic and Evolutionary Microbiology

Vaginal microbiome

Lactobacillus isalae sp. nov., isolated from the female reproductive tract – Tom Eilers – International Journal of Systematic and Evolutionary Microbiology

Identification of a DNA-cytosine methyltransferase that impacts global transcription to promote group B streptococcal vaginal colonization – Haider S. Manzer – mBio

Gut microbiome

Aggression: A gut reaction? The effects of the gut microbiome on aggression – Atara Uzan-Yulzari – bioRxiv

Oral microbiome

Establishment of tongue microbiota by 18 months of age and determinants of its microbial profile – Shinya Kageyama – mBio

Animal microbiome

Pet cats may shape the antibiotic resistome of their owner’s gut and living environment – Yiwen Yang – Microbiome

The impact of kit, environment and sampling contamination on the observed microbiome of bovine milk – Christopher J Dean – bioRxiv

Animal experiments

Early life exposure to broccoli sprouts confers stronger protection against enterocolitis development in an immunological mouse model of inflammatory bowel disease – Lola Holcomb – mSystems

Daily fluctuation of colonic microbiome in response to nutrient substrates in a pig model – Hongyu Wang – npj Biofilms and Microbiomes

Water microbiome

Assessing the impact of anti-microbial showerheads on the prevalence and abundance of opportunistic pathogens in shower water and shower water-associated aerosols – Sarah Pitell, Sarah-Jane Haig – Frontiers in Microbiomes

Global abundance patterns, diversity, and ecology of Patescibacteria in wastewater treatment plants – Huifeng Hu – bioRxiv

Technique

A high-throughput and low-waste viability assay for microbes – Christian T. Meyer – Nature Microbiology

Bioinformatics

Comparison of gene clustering criteria reveals intrinsic uncertainty in pangenome analyses – Saioa Manzano-Morales – Genome Biology

ACR: metagenome-assembled prokaryotic and eukaryotic genome refinement tool – Hoon Je Seong – Briefings in Bioinformatics


September 15, 2023

Posted on by

Today’s digest features the BugSigDB, AMPSphere and more. Also, you can check out my tips for online conferencing and how to do it better. See you at #MVIF next week!

Respiratory microbiome

The landscape of antibiotic resistance genes in the nasopharynx of preterm infants: Prolonged signature of hospitalization and effects by antibiotics – Achal Dhariwal – bioRxiv

Breast cancer microbiome

Integrating current analyses of the breast cancer microbiome – Sidra Sohail and Michael B. Burns – Plos One

Vaginal microbiome

Diet influences community dynamics following vaginal group B Streptococcus colonization – Christina J. Megli – bioRxiv

Gut microbiome

Gut microbes exacerbate systemic inflammation and behavior disorders in neurologic disease CADASIL – Sheng Liu – Microbiome

Water microbiome

Exploring novel alkane-degradation pathways in uncultured bacteria from the North Atlantic Ocean – Mirna Vázquez Rosas Landa – mSystems

Insect microbiome

Plastics shape the black soldier fly larvae gut microbiome and select for biodegrading functions – Francesca De Filippis – Microbiome

Animal experiment

Enhancing Recovery from Gut Microbiome Dysbiosis and Alleviating DSS-Induced Colitis in Mice with a Consortium of Rare Short-Chain Fatty Acid-Producing Bacteria – Achuthan Ambat – bioRxiv

Bioinformatics

BugSigDB captures patterns of differential abundance across a broad range of host-associated microbial signatures – Ludwig Geistlinger – Nature Biotechnology

Computational exploration of the global microbiome for antibiotic discovery – Célio Dias Santos-Júnior – bioRxiv