Author Archives: Axel Künstner

February 21, 2024

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Human nasal microbiome

[PREPRINT]Nasal commensals reduce Staphylococcus aureus proliferation by restricting siderophore availability – Zhao et al. – bioRxiv

Human oral microbiome

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

Human gut microbiome

Horizontal gene transfer after faecal microbiota transplantation in adolescents with obesity – Behling et al. – Microbiome

Animal microbiome

Psychological stress-induced microbial metabolite indole-3-acetate disrupts intestinal cell lineage commitment – Wei et al. – Cell Metabolism

Gut microbiota contributes to bisphenol A-induced maternal intestinal and placental apoptosis, oxidative stress, and fetal growth restriction in pregnant ewe model by regulating gut-placental axis – Zhang et al. – Microbiome

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

Novel insights into the rhizosphere and seawater microbiome of Zostera marina in diverse mariculture zones – Sun et al. – Microbiome

Alteration of bacterial community composition in the sediments of an urban artificial river caused by sewage discharge – Li et al. – PeerJ

The exometabolome of microbial communities inhabiting bare ice surfaces on the southern Greenland Ice Sheet – Doting et al. – Environmental Microbiology

Searching for microbial contribution to micritization of shallow marine sediments – Garuglieri et al. – Environmental Microbiology

Food microbiology

Unveiling the microbial communities and metabolic pathways of Keem, a traditional starter culture, through whole-genome sequencing – Rana et al. – Scientific Reports

Phages and viruses

[PREPRINT]Fecal Virome Transplantation (FVT) from healthy humans remodels the gut bacteriome and virome and reduces metabolic syndrome in mice – Cervantes-Echeverría et al. – bioRxiv

[PREPRINT]Discovering and exploring the hidden diversity of human gut viruses using highly enriched virome samples – Zolfo et al. – bioRxiv

Microbes in the news (popular press, EurekAlert, ScienceDaily, Youtube, NPR, etc)

Why addressing how our brain and our gut talk to each other matter for IBS – Gut microbiota for health

February 13, 2024

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General microbiome

Model-free prediction of microbiome compositions – Asher & Bashan – Microbiome

Pregnancy and early life

Divergent maturational patterns of the infant bacterial and fungal gut microbiome in the first year of life are associated with inter-kingdom community dynamics and infant nutrition – Mercer et al. – Microbiome

Human airway microbiome

Genomic attributes of airway commensal bacteria and mucosa – Cuthbertson et al. – Communications Biology

Human skin microbiome

[REVIEW]Triggers for the onset and recurrence of psoriasis: a review and update – Liu et al. – Cell Communication and Signaling

Human vaginal microbiome

Uterine fibroids and longitudinal profiles of the vaginal microbiota in a cohort presenting for transvaginal ultrasound – Robbins – PLOS One

Human gut microbiome

Microbial-derived imidazole propionate links the heart failure-associated microbiome alterations to disease severity – Raju et al. – Genome Medicine

Horizontal gene transfer after faecal microbiota transplantation in adolescents with obesity – Behling et al. – Microbiome

Differential effects of antiretroviral treatment on immunity and gut microbiome composition in people living with HIV in rural versus urban Zimbabwe – Colorado et al. – Microbiome

Gut microbiome signature of metabolically healthy obese individuals according to anthropometric, metabolic and inflammatory parameters – Lee et al. – Scientific Reports

Animal microbiome

Metagenome-assembled genome reveals species and functional composition of Jianghan chicken gut microbiota and isolation of Pediococcus acidilactic with probiotic properties – Shen et al. – Microbiome

Falcon gut microbiota is shaped by diet and enriched in Salmonella – Ahmad et al. – PLOS One

Sex differences in colonic gene expression and fecal microbiota composition in a mouse model of obesity-associated colorectal cancer – Chang et al. – Scientific Reports

Cadaver decomposition microbiome

A conserved interdomain microbial network underpins cadaver decomposition despite environmental variables – Burcham et al. – Nature Microbiology

Bioinformatics

YACHT: an ANI-based statistical test to detect microbial presence/absence in a metagenomic sample – Koslicki et al. – Bioinformatics

Gut microbiome-metabolome interactions predict host condition – Shtossel et al. – Microbiome

Techniques

Fecal microbiome composition and diversity of cryopreserved canine stool at different duration and storage conditions – Barko et al. – PLOS One

January 31, 2024

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General microbiome

Finding Candida auris in public metagenomic repositories – Mario-Vasquez et al. – PLOS One

Pregnancy and early life

A pilot study of fecal pH and redox as functional markers in the premature infant gut microbiome – Letourneau et al. – PLOS One

[PREPRINT]Assembly, stability, and dynamics of the infant gut microbiome are linked to bacterial strains and functions in mother’s milk – Allert et al. – bioRxiv

Human nasal microbiome

A genome-wide association study reveals the relationship between human genetic variation and the nasal microbiome – Liu et al. – Communications Biology

Human gut microbiome

Differential peripheral immune signatures elicited by vegan versus ketogenic diets in humans – Link et al. – Nature Medicine

Metagenomic analyses of 7000 to 5500 years old coprolites excavated from the Torihama shell-mound site in the Japanese archipelago – Nishimura et al. – PLOS One

[PREPRINT]Unravelling the ancient fungal DNA from the Iceman’s gut – Oskolkov et al. – bioRxiv

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

Streptococcus anginosus promotes gastric inflammation, atrophy, and tumorigenesis in mice – Fu et al. – Cell

Gut complement induced by the microbiota combats pathogens and spares commensals – Wu et al. – Cell

Complement in breast milk modifies offspring gut microbiota to promote infant health – Xu et al. – Cell

Antidiabetic effects and mechanism of γ-polyglutamic acid on type II diabetes mice – Li et al. – International Journal of Biological Macromolecules

Bacterial microbiome associated with cigarette beetle Lasioderma serricorne (F.) and its microbial plasticity in relation to diet sources – Srinivasan et al. – PLOS One

Animal microbiome (for animals in the wild)

Metagenomics reveals the temporal dynamics of the rumen resistome and microbiome in goat kids – Chai et al. – Microbiome

[PREPRINT]Thermal fluctuations independently modulate physiological plasticity and the dynamics of the gut microbiome in a tropical rocky shore oyster – Arromrak et al. – bioRxiv

[PREPRINT]Diversity and structure of the deep-sea sponge microbiome in the equatorial Atlantic Ocean – Williams et al. – bioRxiv

Plant, root, and soil microbiome

[PREPRINT]Temporal and spatial dynamics within the fungal microbiome of grape fermentation – Onetto et al. – bioRxiv

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

Autotrophic biofilms sustained by deeply sourced groundwater host diverse bacteria implicated in sulfur and hydrogen metabolism – Valentin-Alvarado et al. – Microbiome

Phages and viruses

[PREPRINT]Viroid-like colonists of human microbiomes – Zheludev et al. – bioRxiv

Bioinformatics

[PREPRINT]DeepGOMeta: Predicting functions for microbes – Hoehndorf et al. – bioRxiv

[PREPRINT]Predicting microbial genome-scale metabolic networks directly from 16S rRNA gene sequences – Øyås et al. – bioRxiv

Techniques

[REVIEW]Unraveling metagenomics through long-read sequencing: a comprehensive review – Kim et al. – Journal of Translational Medicine

Microbes in the news

Non-prescription therapeutics for IBS: where are we? – Costantino – Gut Microbiota for Health by ESNM

January 24, 2024

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Human gut microbiome

[REVIEW]Crosstalk between gut microbiome and neuroinflammation in pathogenesis of HIV-associated neurocognitive disorder – Chen et al. – Journal of the Neurological Sciences

Purified diet affects intestinal epithelial proliferation and barrier functions through gut microbial alterations – Shiratori et al. – International Immunology

[PREPRINT]Gut environmental factors explain variations in the gut microbiome composition and metabolism within and between healthy adults – Prochazkova et al. – bioRxiv

Causal relationship between gut microbiota and gastrointestinal diseases: a mendelian randomization study – Wu et al. – Journal of Translational Medicine

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

Psychological stress-induced microbial metabolite indole-3-acetate disrupts intestinal cell lineage commitment – Wei et al. – Cell Metabolism

Animal microbiome (for animals in the wild)

[PREPRINT]Effect of composting and storage on the microbiome and resistome of cattle manure from a commercial dairy farm in Poland – Zalewska et al. – bioRxiv

Assessing the microbiota of the snail intermediate host of trematodes, Galba truncatula – McCann et al. – Parasites & Vectors

Plant, root, and soil microbiome

Host genotype, soil composition, and geo-climatic factors shape the fonio seed microbiome – Tabassum et al. – Microbiome

A tripartite bacterial-fungal-plant symbiosis in the mycorrhiza-shaped microbiome drives plant growth and mycorrhization – Zhang et al. – Microbiome

Built environment (subways, indoor surfaces)

[PREPRINT]Identification and classification of the genomes of novel Microviruses in a poultry slaughterhouse – Xie et al. – bioRxiv

Bioinformatics

[PREPRINT]iVirP: An integrative, efficient, and user-friendly pipeline to annotate viral contigs from raw reads of metagenome or VLP sequencing – Li, Jiao and liang – bioRxiv

[PREPRINT]Microbiome-based correction for random errors in nutrient profiles derived from self-reported dietary assessments – Wang et al. – bioRxiv

Techniques

[PREPRINT]MicroFisher: Fungal taxonomic classification for metatranscriptomic and metagenomic data using multiple short hypervariable markers – Wang et al. – bioRxiv

Microbes in the news

How does chronic stress harm the gut? New clues emerge – Kozlov – Nature

January 17, 2024

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Pregnancy and early life

Human milk cream alters intestinal microbiome of preterm infants: a prospective cohort study – Adeniyi-Ipadeola et al. – Pediatric Research

A bacterial sialidase mediates early-life colonization by a pioneering gut commensal – Buzun et al. – Cell Host & Microbe

Multi-site human microbiome

[DATA]Multi-cohort shotgun metagenomic analysis of oral and gut microbiota overlap in healthy adults – Rashidi et al. – Scientific Data

Human respiratory microbiome

[REVIEW]Positioning the preventive potential of microbiome treatments for cystic fibrosis in the context of current therapies – Cauwenberghs et al. – Cell Reports Medicine

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

The gut microbiota modulate locomotion via vagus-dependent glucagon-like peptide-1 signaling – Lai et al. – npj Biofilms and Microbiomes volume

Nonylphenol induces depressive behavior in rats and affects gut microbiota: A dose–dependent effect – Pan et al. – Environmental Pollution

Animal microbiome (for animals in the wild)

Ocular mucosal homeostasis of teleost fish provides insight into the coevolution between microbiome and mucosal immunity – Kong et al. – Microbiome

Plant, root, and soil microbiome

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

Biogeographic survey of soil bacterial communities across Antarctica – Varliero et al. – Microbiome

Microbes in space

[PREPRINT]Testing microbial biomining from asteroidal material onboard the International Space Station – Santomartino et al. – bioRxiv

Bioinformatics

[PREPRINT]AnnoView enables large-scale analysis, comparison, and visualization of microbial gene neighborhoods – Wei et al. – bioRxiv

Techniques

Comparison of the DNBSEQ platform and Illumina HiSeq 2000 for bacterial genome assembly – Hu et al. – Scientific Reports

December 6, 2023

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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 28, 2023

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Pregnancy and early life

[PREPRINT]Delivery mode impacts gut bacteriophage colonization during infancy – Subramanian et al. – medRxiv

Human oral microbiome

Oral microbiota analyses of paediatric Saudi population reveals signatures of dental caries – Alyousef et al. – BMC Oral Health

Human gut microbiome

Gastric coinfection with thiopeptide-positive Cutibacterium acnes decreases FOXM1 and pro-inflammatory biomarker expression in a murine model of Helicobacter pylori-induced gastric cancer – Lunger et al. – Microbiology Spectrum

[REVIEW]Butterflies in the gut: the interplay between intestinal microbiota and stress – Lai et al. – Journal of Biomedical Science

[REVIEW]Genetics, Nutrition, and Health: A New Frontier in Disease Prevention – Agrawal et al. – Journal of the American Nutrition Association

Age-dependent changes in the gut microbiota and serum metabolome correlate with renal function and human aging – Sun et al. – Aging Cell

The changes of gut microbiota and metabolites in different drug-induced liver injuries – Zhu et al. – Journal of Medical Microbiology

[PREPRINT]The differing prevalences of propionate and butyrate producing bacteria in the human gut microbiota – Christensen et al. – bioRxiv

[PREPRINT]The Parkinson’s drug entacapone disrupts gut microbiome homeostasis via iron sequestration – Pereira et al. – bioRxiv

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

Mutual modulation of gut microbiota and the immune system in type 1 diabetes models – Rosell-Mases et al. – Nature Communications

[PREPRINT]Microbiota-dependent early life programming of gastrointestinal motility – Frith et al. – bioRxiv

Horizontal transmission of gut microbiota attenuates mortality in lung fibrosis – Gurczynski et al. – JCI insight

High-altitude and low-altitude adapted chicken gut-microbes have different functional diversity – Bhagat et al. – Scientific Reports

Animal microbiome (for animals in the wild)

Introducing an environmental microbiome to axenic Aedes aegypti mosquitoes documents bacterial responses to a blood meal – LaReau et al. – Applied and Environmental Microbiology

Altered microbiota, antimicrobial resistance genes, and functional enzyme profiles in the rumen of yak calves fed with milk replacer – Zhuang et al. – Microbiology Spectrum

Plant, root, and soil microbiome

[PREPRINT]Global patterns in gene content of soil microbiomes emerge from microbial interactions – Crocker et al. – bioRxiv

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

Metagenomic analysis reveals diverse microbial community and potential functional roles in Baner rivulet, India – Brar et al. – Journal of Genetic Engineering and Biotechnology

Bioinformatics

mb-PHENIX: Diffusion and Supervised Uniform Manifold Approximation for denoising microbiota data – Padron-Manrique et al. – Bioinformatics

Facilitating bioinformatics reproducibility with QIIME 2 provenance Replay – Keefe et al. – PLOS Computational Biology

Techniques

High-throughput identification and quantification of bacterial cells in the microbiota based on 16S rRNA sequencing with single-base accuracy using BarBIQ – Jin, Yamamoto & Shiroguchi

October 18, 2023

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Human gut microbiome

Association between gut microbiota and influenza: a bidirectional two-sample mendelian randomization study – Xu et al. – BMC Infectious Diseases

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

LACC1 regulates changes in the intestinal flora in a mouse model of inflammatory bowel disease – Xu & Wang – BMC Gastroenterology

Animal microbiome (for animals in the wild)

[PREPRINT]Sex-specific gut bacteria manipulation impacts offspring production in the honeybee parasite small hive beetle, Aethina tumida Murray – Biswas et al. – bioRxiv

Selective enrichment of founding reproductive microbiomes allows extensive vertical transmission in a fungus-farming termite – Sinotte et al. – Proc. R. Soc. B

Microbiome variations among age classes and diets of captive Asian elephants (Elephas maximus) in Thailand using full-length 16S rRNA nanopore sequencing – Klinsawat et al. – Scientific Reports

Temporal and spatial variations in body mass and thermogenic capacity associated with alterations in the gut microbiota and host transcriptome in mammalian herbivores – Ren et al. – Science of The Total Environment

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

Metagenome sequencing and recovery of 444 metagenome-assembled genomes from the biofloc aquaculture system – Rajeev et al. – Scientific Data

Net-spinning caddisflies create denitrifier-enriched niches in the stream microbiome – Bertagnolli et al. – ISME Communications

Parasites, Phages and viruses

Effects of heat tolerance on the gut microbiota of Sarcophaga peregrina (Diptera: Sarcophagidae) and impacts on the life history traits – Ren et al. – Parasites & Vectors

Bioinformatics / Techniques

[PREPRINT]Comprehensive Identification of Pathogenic Microbes and Antimicrobial Resistance Genes in Food Products Using Nanopore Sequencing-Based Metagenomics – Wing-Tung et al. – bioRxiv

Causal inference on microbiome-metabolome relations in observational host-microbiome data via in silico in vivo association pattern analyses – Hertel et al. – Cell Reports Methods

Rank selection for non-negative matrix factorization – Cai, Gu & Kenney

October 11, 2023

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General microbiome

Major data analysis errors invalidate cancer microbiome findings – Gihawi et al. – mBio

Relative abundance data can misrepresent heritability of the microbiome – Bruihning et al. – Microbiome

Human gut microbiome

Discrimination exposure impacts unhealthy processing of food cues: crosstalk between the brain and gut – Zhang et al. – Nature Mental Health

[REVIEW]The impact of acute and chronic stress on gastrointestinal physiology and function: a microbiota–gut–brain axis perspective – Leigh et al. – The Journal of Physiology

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

Vertical transmission of gut bacteria in commercial chickens is limited – Shterzer et al. – Animal Microbiome

Animal microbiome (for animals in the wild)

[PREPRINT]The role of family and environment in determining the skin microbiome of captive aquatic frogs, Xenopus laevis – Chapman et al. – bioRxiv

Vertical transmission of gut bacteria in commercial chickens is limited – Shterzer et al. – Animal Microbiome

Bioinformatics/Techiques

[PREPRINT]MetaQuad: Shared Informative Variants Discovery in Metagenomic Samples – Xu et al. – bioRxiv

[PREPRINT]Insertion sequence driven evolution of the microbiota revealed by a novel metagenomics pipeline – Kirsch, Hryckowian & Duerkop

[PREPRINT]A comparison of short-read, HiFi long-read, and hybrid strategies for genome-resolved metagenomics – Eisenhofer et al. – bioRxiv

The newest Oxford Nanopore R10.4.1 full-length 16S rRNA sequencing enables the accurate resolution of species-level microbial community profiling – Zhang et al. – Applied and Environmental Microbiology

[PERSPECTIVE]Challenges and opportunities in sharing microbiome data and analyses – Huttenhower, Finn & McHardy – Nature Microbiology

October 4, 2023

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General microbiome

[OPINION]Toward an integrative framework for microbial community coalescence – Custer, Bresciani & Dini-Andreote – Trends in Microbiology

Statistically learning the functional landscape of microbial communities – Skwara et al. – Nature Ecology & Evolution

Human skin microbiome

Skin microbiota secretomes modulate cutaneous innate immunity against Borrelia burgdorferi s.s – Baquer et al. – Scientific Reports

Human gut microbiome

Temporal changes in fecal microbiota of patients infected with COVID-19: a longitudinal cohort – Galperine et al. – BMC Infectious Diseases

Association Between Bowel-Movement Pattern and Cognitive Function: Prospective Cohort Study and a Metagenomic Analysis of the Gut Microbiome – Ma et al. – Neurology

[REVIEW]The gut microbiome tango in the progression of chronic kidney disease and potential therapeutic strategies – Tang, Yu & Pan – Journal of Translational Medicine

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

Microbiota-gut-brain axis drives overeating disorder – Fan et al. – Cell Metabolism

Animal microbiome (for animals in the wild)

Exploring gut microbiota in adult Atlantic salmon (Salmo salar L.): Associations with gut health and dietary prebiotics – Wang et al. – Animal Microbiome

Plant, root, and soil microbiome

Using wasps as a tool to restore a functioning vine grape mycobiota and preserve the mycobial “terroir” – Di Paola et al. – Scientific Reports

Soil microbes mediate the effects of resource variability on plant invasion – Zhang et al. – Ecology

Bioinformatics

[PREPRINT]Deepurify: a multi-modal deep language model to remove contamination from metagenome-assembled genomes – Zou et al. – bioRxiv

[PREPRINT]BATTER: Accurate Prediction of Rho-dependent and Rho-independent Transcription Terminators in Metagenomes – Jin et al. – bioRxiv

[PREPRINT]Gut Microbiome Wellness Index 2 for Enhanced Health Status Prediction from Gut Microbiome Taxonomic Profiles – Chang et al. – bioRxiv

Techniques

INVADEseq to identify cell-adherent or invasive bacteria and the associated host transcriptome at single-cell-level resolution – Nino et al. – Nature Protocols