Biology subjects

Hallberg, Z.

Publications and source records attributed to Hallberg, Z..

4 recordsLinked to original sources

bioRxiv2026

Phage-based microbiome manipulation reveals ecological interactions within gut communities

Mechanistic understanding of gut ecology is limited by the availability of tools for precise manipulation of microbiome composition. Here, we isolate lytic phages to enable targeted removal of gut commensal Escherichia fergusonii (Ef) from complex, undefined stool-derived in vitro communities. A single phage drove resistance without fitness cost in monoculture, but resistant Ef exhibited reduced fitness in communities, enabling expansion of closely related Proteobacteria. Resistance arose via reversible promoter inversion linked to outer-membrane function. A phage cocktail overcame resistance to achieve Ef knockout across communities with minimal collateral effects. Using knockout communities, we show that Ef is necessary and sufficient for preventing Salmonella invasion. Replacement with an Ef transposon-mutant library revealed that community-specific fitness defects are enriched in genes involved in outer-membrane assembly. Disruption of these genes sensitized Ef to antagonistic community members, highlighting interspecies warfare as a key driver of microbiome ecology. These results establish phage-mediated perturbation as a framework for linking species to community-level function and for enabling precision microbiome engineering.

microbiology↗

bioRxiv2024

Laboratory evolution of E. coli with a natural vitamin B12 analog reveals roles for cobamide uptake and adenosylation in methionine synthase-dependent growth

Bacteria encounter chemically similar nutrients in their environment that impact their growth in distinct ways. Among such nutrients are cobamides, the structurally diverse family of cofactors related to vitamin B12 (cobalamin), which function as cofactors for diverse metabolic processes. Given that different environments contain varying abundances of different cobamides, bacteria are likely to encounter cobamides that enable them to grow robustly as well as those that do not function efficiently for their metabolism. Here, we performed a laboratory evolution of a cobamide-dependent strain of Escherichia coli with pseudocobalamin (pCbl), a cobamide that E. coli uses less effectively than cobalamin for MetH-dependent methionine synthesis, to identify genetic adaptations that lead to improved growth with less-preferred cobamides. After propagating and sequencing nine independent lines and validating the results by constructing targeted mutations, we found that mutations that increase expression of the outer membrane cobamide transporter BtuB are beneficial during growth under cobamide-limiting conditions. Unexpectedly, we also found that overexpression of the cobamide adenosyltransferase BtuR confers a specific growth advantage in pCbl. Characterization of the latter phenotype revealed that BtuR and adenosylated cobamides contribute to optimal MetH-dependent growth. Together, these findings improve our understanding of how bacteria expand their cobamide-dependent metabolic potential. ImportanceIn nature, bacteria commonly experience fluctuations in the availability of required nutrients. Thus, their environment often contains nutrients that are insufficient in quantity or that function poorly in their metabolism. Cobamides, the vitamin B12 family of cofactors, are ideal for investigating the influence of nutrient quality on bacterial growth. We performed a laboratory evolution experiment in E. coli with a less-preferred cobamide to examine whether and how bacteria can improve their growth with less ideal nutrients. We found that overexpression of genes for cobamide uptake and modification are genetic adaptations that improve growth under these conditions. Given that cobamides are key shared metabolites in microbial communities, our results reveal insights into bacterial interactions and competition for nutrients.

microbiology↗

bioRxiv2020

Identification of a novel cobamide remodeling enzyme in the beneficial human gut bacterium Akkermansia muciniphila

The beneficial human gut bacterium Akkermansia muciniphila provides metabolites to other members of the gut microbiota by breaking down host mucin, but most of its other metabolic functions have not been investigated. A. muciniphila is known to use cobamides, the vitamin B12 family of cofactors with structural diversity in the lower ligand, though the specific cobamides it can use have not been examined. We found that growth of A. muciniphila strain MucT was nearly identical with each of seven cobamides tested, in contrast to nearly all bacteria that have been studied. Unexpectedly, this promiscuity is due to cobamide remodeling - the removal and replacement of the lower ligand - despite the absence of the canonical remodeling enzyme CbiZ in A. muciniphila. We identified a novel enzyme, CbiR, that is capable of initiating the remodeling process by hydrolyzing the phosphoribosyl bond in the nucleotide loop of cobamides. CbiR does not share homology with other cobamide remodeling enzymes or B12-binding domains, and instead is a member of the AP endonuclease 2 enzyme superfamily. We speculate that CbiR enables bacteria to repurpose cobamides they otherwise cannot use in order to grow under a cobamide-requiring condition; this function was confirmed by heterologous expression of cbiR in E. coli. Homologs of CbiR are found in over 200 microbial taxa across 22 phyla, suggesting that many bacteria may use CbiR to gain access to the diverse cobamides present in their environment. ImportanceCobamides, the vitamin B12 family of cobalt-containing cofactors, are required for metabolism in all domains of life, including most bacteria. Cobamides have structural variability in the lower ligand, and selectivity for particular cobamides has been observed in most organisms studied to date. Here, we discover that the beneficial human gut bacterium Akkermansia muciniphila can use a diverse range of cobamides due to its ability to change the cobamide structure via "cobamide remodeling". We identify and characterize the novel enzyme CbiR that is necessary for initiating the cobamide remodeling process. The discovery of this enzyme has implications not only for understanding the ecological role of A. muciniphila in the gut, but for other bacteria that carry this enzyme as well.

microbiology↗

bioRxiv2019

Accurate prediction of bacterial two-component signaling with a deep recurrent neural network ORAKLE

Two-component systems (2CS) are a primary method that bacteria use to detect and respond to environmental stimuli. Receptor histidine kinases (HK) detect an environmental signal, activating the appropriate response regulator (RR). Genes for such cognate HK-RR pairs are often located proximally on the chromosome, allowing easier identification of the target for a particular signal. However, almost half of all HK and RR proteins are orphans, with no nearby partner, complicating identification of the proteins that respond to a particular signal. To address this problem, we trained a neural network on the amino acid sequences of known 2CS pairs. Next, we developed a recommender algorithm that ranks a set of HKs for an arbitrary fixed RR and arbitrary species whose amino acid sequences are known. The recommender strongly favors known 2CS pairs, and correctly selects orphan pairs in Escherichia coli. We expect that use of these results will permit rapid discovery of orphan HK-RR pairs.

bioinformatics↗