Manuel Kleiner

The paper examines how climate influences osmotic stress tolerance in Luteibacter populations, finding distinct genomic strategies in semi-arid and humid strains.

This study shows bloom-forming bacteria, like GSB-TRL01, invest heavily in anti-phage defense systems, which reduces lysis and allows blooms to persist.

This study investigates the formation and persistence of a near-clonal green sulfur bacteria bloom using multi-omics approaches, revealing metabolic strategies that support high cell density and environmental stability.

The paper identifies conserved inhibitory mechanisms in root-associated bacteria that affect both Arabidopsis thaliana and Chlamydomonas reinhardtii, using a scalable algal model to study cryptic inhibition.

TrIdent automates transductomics analysis by identifying DNA mobilized by virus-like particles, showing high agreement with manual classifications and revealing enriched bacterial families in murine gut transductomes.

This study uses differential proteomics to compare bacterial growth in vitro and in planta, identifying species-specific strategies for root colonization.

The paper identifies two putative CI effectors from Cardinium hertigii that function similarly to known Wolbachia CI effectors despite lacking homology to cif genes.

The paper compares AUC and SpC quantification methods in metaproteomics, finding AUC outperforms SpC in accuracy and dynamic range, but MBR harms AUC results.

This study shows that dietary protein source affects gastrointestinal health, with animal-based protein causing more GI symptoms and intestinal permeability than plant-based protein.

The paper introduces TriMic, a wheat root-associated bacterial culture collection and synthetic community to study wheat-microbe interactions, providing genomes and tools for mechanistic research.

The paper analyzes the murine gut transductome before and after perturbations to identify bacterial families and mobile genetic elements involved in horizontal gene transfer.

This paper introduces an anion exchange chromatography method for purifying virus-like particles (VLPs) that outperforms CsCl in throughput and reproducibility while maintaining similar purity levels.

The paper evaluates statistical methods for differential metaproteomics, finding that several approaches effectively identify differentially abundant proteins despite data challenges.

The paper uses genome-scale metabolic modeling to study interactions in a maize root-associated synthetic community, showing root exudates enhance metabolic diversity and interspecies interactions.

The paper investigates how co-inoculation with AMF and PSB affects tomato rhizosphere dynamics across growth stages using metagenome-informed metaproteomics.

This study develops and tests CRISPR-based sex transformation systems in Lucilia cuprina, finding that dCas9 causes lethality while Cas9 is well-tolerated.

ZeaMiC provides a culture collection of maize root-associated bacteria to study plant-microbe and microbe-microbe interactions.

The paper develops a minimal growth medium for a maize root-associated microbial community to study plant-microbe interactions in controlled settings.

This study identifies metabolic adaptations in sulfate-reducing bacteria (SRB) that enable their persistence in symbiosis with gutless marine worms, revealing a conserved core metabolism distinct from free-living relatives.

The paper analyzes microbial proteins in fermented foods using metaproteomics, finding they contribute up to 11% of total protein content and 60% of identified proteins.

This study compares Scribe and database search engines in metaproteomic analysis of a ground-truth microbiome dataset, finding Scribe detects more proteins and quantifies microbial composition more accurately.

This study identifies a methanotroph-specific bacteriohemerythrin homolog in Methylomonas denitrificans FJG1 that likely facilitates oxygen delivery to methane monooxygenase under low oxygen conditions.

This study investigates how interactions between soil microbes and abiotic factors influence heterosis in maize, finding that microbial effects are context-dependent and abiotic factors may be a larger driver.

The paper presents a metaproteomic dataset to evaluate the performance of ddaPASEF and diaPASEF in terms of detection, coverage, and strain-level resolution.

This study identifies phase variation of capsular polysaccharides and other resistance mechanisms as key strategies enabling stable coexistence between gut Bacteroidales and their lytic bacteriophages.

This study compares DIA-MS and DDA-MS for metaproteomics, finding DIA-MS provides more reproducible and accurate protein and peptide identifications across laboratories.

This study shows dietary protein source affects host physiology through both direct and microbiota-mediated mechanisms in mice and humans.

This study shows that different dietary protein sources alter gut microbiota composition and function in mice, affecting amino acid and mucus degradation processes.

The paper quantifies dietary protein digestion and microbial processing in mice, showing some proteins escape host digestion and are modified by gut microbiota, with health-relevant proteins differentially enriched.

This paper uses stable isotope fingerprinting to link gut microbiota to their carbon sources and shows diet-induced substrate switching in vivo.