Small amounts of misassembly can have disproportionate effects on pangenome-based metagenomic analyses

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 13, 2024

Abstract Individual genes from microbiomes can drive host-level phenotypes. To help identify such candidate genes, several recent tools estimate microbial gene copy numbers directly metagenomes. These rely on alignments to pangenomes, which in turn are derived the set of all individual genomes one species. While large-scale metagenomic assembly efforts have made pangenome estimates more complete, mixed communities also introduce contamination into assemblies, and it is unknown how robust pangenome-based analyses these errors. gain insight this problem, we re-analyzed a case-control study gut microbiome cirrhosis, focusing commensal Clostridia previously implicated disease. We tested for differentially prevalent Lachnospiraceae , then investigated were likely be contaminants using sequence similarity searches. Out 86 found that 33 (38%) probably originating taxa as Veillonella Haemophilus unrelated genera independently correlated with disease status. Our results demonstrate even small amounts metagenome below typical quality thresholds, threaten overwhelm gene-level analyses. However, show accurately identified method based gene-to-species correlation. After removing contaminants, observe flagellar motility clusters Lachnospira eligens associated cirrhosis integrated our an analysis visualization pipeline, PanSweep, automatically cases where may bias gene-resolved Importance Metagenome-assembled genomes, or MAGs, constructed without pure cultures microbes. Large scale build MAGs yielded complete pangenomes (i.e., sets species). Pangenomes allow us measure strain variation content, strongly affect phenotype. because come communities, they contaminate DNA, much impacts downstream has not been studied. Using microbes test case, investigate affects content. Surprisingly, small, MAG (<5%) result disproportionately high levels false positive associations (38%). Fortunately, most flagged, provide simple doing so. Furthermore, applying reveals new association between motility.

Language: Английский

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Structures of the multi-domain oxygen sensor DosP: remote control of a c-di-GMP phosphodiesterase by a regulatory PAS domain

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: Nov. 7, 2024

The heme-based direct oxygen sensor DosP degrades c-di-GMP, a second messenger nearly unique to bacteria. In stationary phase Escherichia coli, is the most abundant c-di-GMP phosphodiesterase. Ligation of O2 heme-binding PAS domain (hPAS) protein enhances phosphodiesterase through an allosteric mechanism that has remained elusive. We determine six structures full-length in its aerobic or anaerobic conformations, with without c-di-GMP. elongated dimer regulatory heme containing and separated by 180 Å. absence substrate, regardless status, presents equilibrium two distinct conformations. Binding substrate induces adopt single, ON-state OFF-state conformation depending on status. Structural biochemical studies this multi-domain mutants provide insights into signal regulation second-messenger levels. bacterial uses sensing gas control levels cyclic di-GMP. Here, authors structural basis signal.

Language: Английский

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The Campylobacter jejuni BumS sensor phosphatase detects the branched short-chain fatty acids isobutyrate and isovalerate as direct cues for signal transduction

mBio, Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 13, 2024

ABSTRACT Two-component signal transduction systems (TCSs) are nearly ubiquitous across bacterial species and enable bacteria to sense respond specific cues for environmental adaptation. The Campylobacter jejuni BumSR TCS is unusual in that the BumS sensor exclusively functions as a phosphatase rather than kinase control phosphorylated levels of its cognate BumR response regulator (P-BumR). We previously found directs short-chain fatty acid butyrate generated by resident microbiota so C. identifies ideal lower intestinal niches avian human hosts colonization. However, an indirect cue did not inhibit vitro activity P-BumR. In this work, we expanded repertoire metabolites sensed modulate expression genes required colonization include branched acids isobutyrate isovalerate. Unlike butyrate, isovalerate inhibited P-BumR, indicating these direct BumS. Isobutyrate reduced thermostability caused reorganization protein structure suggest how sensing inhibits activity. also identified residues sensory domain detect isobutyrate, isovalerate, optimal reveal gut can recognize metabolites. Our work reveals senses alter influence hosts. IMPORTANCE TCSs prevalent many bacteria, but each actually known systems. Microbiota-generated detected bacterium only indirectly dephosphorylation regulator. Here, branched-short chain abundant intestines. Both potent, BumS, whereas cue. Leveraging cues, altered upon detection provide understanding mechanics mode executed other phosphatase-driven TCSs.

Language: Английский

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Ubiquitous purine sensor modulates diverse signal transduction pathways in bacteria

Research Square (Research Square), Journal Year: 2023, Volume and Issue: unknown

Published: Nov. 16, 2023

Purines and their derivatives are key molecules for controlling intracellular energy homeostasis nucleotide synthesis. In eukaryotes, including humans, purines also act as signaling that mediate extracellular communication control cellular processes, such proliferation, migration, differentiation, apoptosis. However, the role of in bacteria is largely unknown. Here, by combining structural sequence information, we define a purine-binding motif, which present sensor domains thousands bacterial receptors modulate motility, gene expression, metabolism second messenger turnover. The screening compound libraries microcalorimetric titrations selected validated ability to specifically bind purine derivatives. physiological relevance sensing was demonstrated system modulates c-di-GMP levels.

Language: Английский

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