Biology subjects

La Rosa, S. L.

Publications and source records attributed to La Rosa, S. L..

16 recordsLinked to original sources

bioRxiv2026

Biodegradation of components from an oxidized polyethylene by a Rhodococcus strain isolated from the gut of Atlantic Salmon

Polyethylene (PE) is the most produced synthetic polymer and as a result, a major source of microplastic waste accumulating globally. Exposure to photo- and thermo-oxidative conditions in the environment can cause PE to degrade into carbonyl-containing compounds, hydrocarbons, and low molecular weight PE (LMWPE). In both marine and freshwater ecosystems, fish, including Atlantic salmon, can ingest PE and its derivatives, creating opportunities for interactions with their gut microbes. Here, we investigated the ability of a bacterial isolate from the gut of salmon, Rhodococcus sp002259485 strain ASF-10, to grow on an LMWPE model substrate for partially depolymerized and oxidized PE. Comparative genomic analyses showed that ASF-10 has a smaller genome than other Rhodococcus species yet retaining conserved functions including those related to utilization of medium- and long-chain hydrocarbons. In-depth characterization of the substrate following growth with ASF-10 confirmed depletion of alkanes and 2-ketones deriving from LMWPE, while the polymeric component remained unchanged. Proteomic analysis identified multiple enzymes that were likely to be involved in the degradation of LMWPE-derivatives, including an alkane 1-monooxygenase, cytochrome P450 hydroxylases and Baeyer-Villiger monooxygenases, as well as proteins for production of biofilm and a surfactant that may enhance accessibility to the substrate. Collectively, our findings advance the understanding of the ecology and enzymatic mechanisms underlying utilization of medium- to long-chain alkanes and oxidized variants thereof, that resemble molecules that can occur from abiotic PE degradation, by a fish gut-associated microbe. This metabolic capacity could be harnessed to develop sustainable strategies for bioremediation of oxidized, LMWPE-derivatives. ImportanceThe widespread presence of plastics in marine and freshwater environments has raised concerns due to their toxicity when ingested by fish. Microbial mechanisms driving breakdown of microplastic components, such as LMWPE and derivatives, in gut systems remain poorly understood. This study reveals how a bacterium isolated from the gut of salmon, Rhodococcus sp002259485 strain ASF-10, metabolizes alkanes and oxidized variants thereof, that can result from abiotic PE decomposition. We identified key enzymes that are potentially involved in this process as well as in the production of biofilm and surfactants that may facilitate access to the substrate. Besides extending the knowledge of the enzymatic basis for degradation of PE-derivatives in gut-associated microbes from aquatic organisms, our results provide a framework that couples advanced compositional characterization of the substrate with omics techniques, offering valuable insight to support future studies aimed at unequivocally identifying microbes and their enzymes implicated in transformation of PE-derivatives.

microbiology↗

bioRxiv2026

Community Curation of Microbial Metabolites Enables Biological Insights of Metabolomics Data

Microbial metabolites play a critical role in regulating ecosystems, including the human body and its microbiota. However, understanding the physiologically relevant role of these molecules, especially through liquid chromatography tandem mass spectrometry (LC-MS/MS)-based untargeted metabolomics, poses significant challenges and often requires manual parsing of a large amount of literature, databases, and webpages. To address this gap, we established the Collaborative Microbial Metabolite Center knowledgebase (CMMC-KB), a platform that fosters collaborative efforts within the scientific community to curate knowledge about microbial metabolites. The CMMC-KB aims to collect comprehensive information about microbial molecules originating from microbial biosynthesis, drug metabolism, exposure-related molecules, food, host-derived molecules, and, whenever available, their known activities. Molecules from other sources, including host-produced, dietary, and pharmaceutical compounds, are also included. By enabling direct integration of this knowledgebase with downstream analytical tools, including molecular networking, we can deepen insights into microbiota and their metabolites, ultimately advancing our understanding of microbial ecosystems.

bioinformatics↗

bioRxiv2026

In vitro model reveals structural and metabolic insights to the porcine caecal microbiota in response to β-mannan exposure

The gastrointestinal microbiota plays a pivotal role in shaping host physiology and health. By selectively promoting bacteria associated with improved host health, microbiota-directed fibres offer a strategy to enhance the beneficial functions of the microbiota. In this work, we developed a pH-controlled in vitro fermentation system (InVitSim) as a model to evaluate the effects of such a fibre - acetylated galactoglucomannan from Norway spruce - on the composition and functionality of porcine caecal microbial communities. We validated the experimental outcomes by comparing the response of the in vitro model to a previous in vivo feeding trial utilising the same {beta}-mannan fibres. Long-read sequencing with Oxford Nanopore, metatranscriptomics, and short-chain fatty acid measurements were undertaken to survey microbial community dynamics and functionality. Microbial communities in pigs and InVitSim responded similarly to {beta}-mannan supplementation, with taxa like Prevotella, Catenibacterium, and Faecalibacterium increasing in abundance. Intriguingly, some taxa were observed to be more affected by {beta}-mannan supplementation in InVitSim than in vivo. These taxa included several bacterial species that were not previously known to utilise {beta}-mannan, yet exhibited upregulated genes encoding carbohydrate-active enzymes involved in the degradation of this substrate. ImportanceIn this study, we establish a fermenter system able to preserve more than 70% of over 300 distinct microbial taxa identified in the porcine caecal gut. The in vitro model and the functional omic data generated from it enabled us to identify relevant microbial populations that responded to the presence of AcGGM by upregulating {beta}-mannan-specific polysaccharide utilisation loci. Our results highlight the value of in vitro approaches as a complementary tool to in vivo trials for learning about the gastrointestinal microbiomes response to dietary interventions on the host level. Description of supplementary filesO_LIIn-depth analyses for in vitro model validation and investigations. C_LIO_LICommon taxa between in vivo and in vitro systems exposed to {beta}-mannans. C_LIO_LIDifferential abundance analysis result visualisations. C_LIO_LIShort-chain fatty acid concentrations and correlation with microbial abundances. C_LI

microbiology↗

bioRxiv2025

Deacetylation of β-Mannans by Two Complementary Carbohydrate Esterases from the Human Gut Microbe Bacteroides cellulosilyticus

{beta}-Mannans are widespread in the human diet as components of plant-derived foods and as food additives. Several classes of {beta}-mannans are decorated with acetylations, which are key for their physicochemical properties and protection against enzymatic degradation. While the process for depolymerization of acetylated {beta}-mannans has been described in depth for members of the phylum Bacillota, there is limited mechanistic knowledge on how Bacteroidota utilize these glycans. Here, we combined proteomics and biochemical analyses to functionally characterize a pair of carbohydrate esterases (CEs) from Bacteroides cellulosilyticus that, together, deacetylate complex {beta}-mannans. We demonstrate that the newly identified BcCExxx enzyme, representing a novel carbohydrate esterase (CE) family, exhibits high specificity by selectively removing axially oriented 2-O-acetyl groups from mannose residues. In contrast, BcCE7 functions as a broad-spectrum esterase, capable of deacetylating oligosaccharides derived from structurally diverse substrates, including {beta}-mannans, xylans, and acetylated cellulose. In transesterification reactions, BcCExxx showed activity on both mannooligosaccharides and polymeric glucomannan. Overall, our findings provide new insight into the strategies that beneficial Bacteroides have evolved to deacetylate complex {beta}-mannans in the human gut. Significance Statement{beta}-Mannans, commonly found in various plant-based foods and used as food additives, can be metabolized by gut microbes, potentially impacting host health. Acetylation of {beta}-mannans enhances their resistance to enzymatic breakdown, making carbohydrate esterases crucial for gut bacteria to utilize these carbohydrates. This study explores the roles of two carbohydrate esterases (CEs) from a human commensal Bacteroides species in deacetylating complex {beta}-mannans. The two esterases together remove acetylations at different positions on mannose units. BcCE7 is a versatile esterase that deacetylates a variety of oligosaccharides, while the newly discovered BcCExxx is highly active towards 2-O-acetylations on mannose units in both oligosaccharides and polymeric {beta}-mannan. This research enhances our understanding of how Bacteroidota species deacetylate {beta}-mannans.

biochemistry↗

bioRxiv2025

Discovery and characterization of bacterial unspecific peroxygenase-like heme-thiolate enzymes

Unspecific peroxygenases (UPOs, EC. 1.11.2.1) are promising biocatalysts for the oxyfunctionalization of organic molecules and the synthesis of industrially relevant compounds due to their vast repertoire of catalyzed reactions. To date, thousands of putative UPO genes have been identified in eukaryotic genomes, most of them in the Ascomycota and Basidiomycota phyla, and several UPOs have been characterized. Remarkably, no related enzymes have ever been reported in prokaryotic organisms. Here, we describe the discovery of a novel family of diverse bacterial heme-thiolate peroxygenases through structure database mining, followed by functional characterization of selected representatives. The bacterial UPO-like proteins (BUPOs) are structurally analogous to family I ("short") fungal UPOs, despite having sequence similarity below 20%. Expression of one of these proteins (HydBUPO) in its native host (Hydrogenophaga sp. A37) was confirmed by proteomics. Several BUPOs were cloned and expressed in Escherichia coli. In biochemical assays, the BUPOs were able to catalyze one-electron oxidation (peroxidase activity) of ABTS and 2,6-dimethoxyphenol, and two-electron oxidation (peroxygenase activity) of naphthalene, indole, 3-phenyl-1-propanol and 16-hydroxypalmitic acid, using hydrogen peroxide as co-substrate. These enzymes thus represent a new family of bacterial heme-thiolate peroxygenases that share structural and functional features with eukaryotic UPOs, offering new potential candidates for developing industrially relevant biocatalysts.

biochemistry↗

bioRxiv2025

Microbial degradation of a widely used model polyethylene is restricted to medium- and long-chain alkanes and their oxidized derivatives

Plastics are widely used materials, yet their chemical stability hinders biodegradation, exacerbating pollution on a global scale. Soils contaminated with plastic may foster microbes adapted to degrade plastics or plastic derivatives, and these organisms and their enzymes offer promising avenues for the development of biotechnological recycling strategies. Here, two microbial communities originating from soil collected at a plastic-contaminated landfill in Norway were enriched to select for bacteria involved in the decomposition of a commonly used, model polyethylene (PE; weight average molecular weight (Mw) [~]4000 g/mol). We leveraged genome-resolved metatranscriptomics to identify active population affiliated with Acinetobacter guillouiae and Pseudomonas sp., showing a suite of upregulated genes (including those encoding alkane 1-monooxygenases, flavin-containing monooxygenases FMOs, cytochrome P450 monooxygenases) with functions compatible with degradation of oxidized products as well as medium- and long-chain hydrocarbons. Strikingly, spectroscopic, spectrometric and chromatographic analyses revealed the unexpected presence of medium- and long-chain alkanes and 2-ketones in the model PE substrate, preventing the erroneous conclusion that the community was interacting with the polymeric component. Consistently, only alkanes and 2-ketones with chain length of 10-35 were selectively degraded by an A. guillouiae isolate, as confirmed by proteomics analyses and substrate characterization following bacterial growth. Besides extending the knowledge on the enzymatic basis for degradation of PE-derivatives in soil-associated microbial systems, our results provide an advanced compositional characterization of a widely used model "PE" material, while offering valuable insight to support future studies aimed at unequivocally identifying organisms and their enzymes implicated in PE transformation.

microbiology↗

bioRxiv2025

Mechanistic Insights into Keratin Degradation by Onygena corvina

Keratin-rich byproducts from the poultry, textile, and leather industries pose a significant challenge for sustainable waste management due to their highly recalcitrant nature. While microbial degradation may offer a viable solution, the mechanisms underlying keratin breakdown remain largely unexplored. In this study, we employed a high-resolution proteogenomic approach to characterize the keratinolytic machinery of Onygena corvina, a non-pathogenic saprophytic fungus. Using a membrane agar plate method with insoluble substrates, we obtained secretomes enriched in secreted and substrate-bound proteins during growth on - and {beta}-keratin-rich substrates, specifically wool and feather meal. Our findings reveal that O. corvina has a richer proteolytic machinery than previously reported, including enzymes that are used across keratin types, as well as enzymes that are specifically targeted to either - or {beta}-keratin. In addition to proteases, the secretomes contain numerous other proteins, including cell wall-modifying enzymes, oxidoreductases, esterases, phosphatases, and sialidases that are involved in the deconstruction of keratin. We propose that these additional enzymes destabilize keratin through a combination of mechanical keratinolysis, removal of post-translational modifications, reduction of disulfide bonds, and cleavage of isopeptide bonds, thereby enhancing proteolytic accessibility. Interestingly, keratin degradation by O. corvina was most efficient when using mixed substrates containing both feather and wool meal. These novel insights into the keratinolytic system of O. corvina underscore the importance of considering synergistic enzyme interactions when developing biotechnological approaches for valorization of keratin-rich by-products.

molecular biology↗

bioRxiv2025

OmniCorr: An R-package for visualizing putative host-microbiota interactions using multi-omics data

Holo-omics leverages omics datasets to explore the interactions between hosts and their associated microbiomes. Although the generation of omics data from matching host and microbiome samples is steadily increasing, there remains a scarcity of computational tools capable of integrating and visualizing this data to facilitate the interpretation and prediction of host-microbiota interactions. We present OmniCorr, an R package designed to: (1) manage the complexity of omics data by clustering similar observations into modules, (2) visualize correlations of these modules across different omics layers, host-microbiota interfaces, and meta-data, and (3) identify statistically significant associations indicative of putative host-microbiota interactions. OmniCorrs utility is demonstrated using datasets from two systems: (i) Atlantic salmon, integrating host transcriptomics with metagenomics and metatranscriptomics to explore dietary impacts, and (ii) cattle, combining host proteomics with metaproteomics and metabolomics to investigate methane emission variability. Availability and ImplementationOmniCorr is freely available at: https://github.com/shashank-KU/OmniCorr.

bioinformatics↗

bioRxiv2025

Improved Genome Assembly of Onygena corvina, a Keratin-Degrading Fungus

ObjectiveOnygena corvina is a non-pathogenic, saprophytic fungus that colonizes feathers, hooves, and hair, and represents a valuable source of keratin-degrading enzymes. Previously, the genome of O. corvina has been assembled based on Illumina short-read sequencing, yielding a reference genome composed of 521 contigs with a contig N50 of 0.229 Mb. ResultsHere, we report an improved O. corvina genome assembly generated using a high-quality hybrid approach that combines Illumina short-read and Oxford Nanopore long-read sequencing. The new assembly consists of only 13 contigs totaling 21.8 Mb, with an N50 of 4.4 Mb, and has a completeness of 98.97%. A total of 7,232 protein-coding genes were identified using an integrative approach that combines de novo predictions, homology-based inferences, and RNA-sequencing-guided evidence. Notably, 158 putative protease-coding genes were identified representing a substantial increase from the 73 predicted proteases in the previous annotation. Our improved genome assembly and associated gene annotations will facilitate comparative genomics, and high-resolution mapping of transcriptomic and proteomic data, to advance research on fungal physiology and fungal abilities to degrade recalcitrant substrates such as keratin.

microbiology↗

bioRxiv2025

Whole genome assembly and annotation of the Bumblebee Wax Moth, Aphomia sociella

The bumble bee wax moth, Apshomia sociella, is an important lepidopteran pest impacting bee colonies essential for pollination and apiculture. Despite its relevance, sequence efforts aimed at understanding the genetic makeup of this species have not yet been undertaken. In this work, we successfully achieved a high-quality de novo genome assembly of A. sociella and comprehensive gene annotations generated from long-read DNA and RNA sequencing with Oxford Nanopore technology. The haploid assembly includes 347 contigs, with an N50 of 4.96 Mb, and contains 27 242 protein-coding genes. Benchmarking Universal Single Copy Orthologs (BUSCO) analyses indicates that the assembly has a high level of completeness (98.3%) and low level of fragmentation (0.6%) and duplication (3.9%). Phylogenomic analyses with other members of the Lepidoptera order placed A. sociella in the same clade as Corcyra cephalonica and indicates close evolutionary relationships with the other two species in the subfamily Galleriinae, namely Achroia grisella and Galleria mellonella. This new high-quality genome assembly represents a valuable resource for investigating the genomic basis of ecological specialization of this species and offers critical support for research aimed at developing sustainable and effective pest management strategies.

genomics↗

bioRxiv2024

The need for high-resolution gut microbiome characterization to design efficient strategies for sustainable aquaculture production

Microbiome-directed dietary interventions such as microbiota-directed fibers (MDFs) have a proven track record in eliciting responses in beneficial gut microbes and are increasingly being promoted as an effective strategy to improve animal production systems. Here we used initial metataxonomic data on fish gut microbiomes as well as a wealth of a priori mammalian microbiome knowledge on -MOS and {beta}-mannan-derived MDFs to study effects of such feed supplements in Atlantic salmon (Salmo salar) and their hitherto poorly characterized gut microbiomes. Our multi-omic analysis revealed that the investigated MDFs (two -mannans and an acetylated {beta}-galactoglucomannan), at a dose of 0.2%, had negligible effects on both host gene expression, and gut microbiome structure and function under studied conditions. While a subsequent trial using a higher (4%) dietary inclusion of {beta}-mannan significantly shifted the gut microbiome composition, there were still no biologically relevant effects on salmon metabolism and physiology. Only a single Burkholderia-Caballeronia-Paraburkholderia (BCP) population demonstrated consistent and significant abundance shifts across both feeding trials, although with no evidence of {beta}-mannan utilization capabilities or changes in gene transcripts for producing metabolites beneficial to the host. In light of these findings, we revisited our omics data to predict and outline novel and potentially beneficial endogenous lactic acid bacteria that should be targeted with future, conceivably more suitable, MDF strategies for salmon. IMPORTANCEThis study focuses on the potential of MDFs to improve aquaculture production. Despite preliminary 16S rRNA amplicon data suggested that populations in the salmon gut microbiome could utilize structurally complex mannans, our findings indicates that endogenous microbes could not metabolize it, nor the host responds to its dietary inclusion, at least not under the trial conditions investigated in this study. We highlight that high-resolution and host-specific microbiome characterization can greatly improve trial design and selection of candidate MDFs for future nutritional interventions. Understanding the intricate interplay between host and its gut microbiome is paramount in studies seeking to leverage endogenous microbial communities to benefit the host. While each new condition, whether it is a disease onset or a nutritional stressor, has the potential to profoundly reshape the microbial diversity, composition and outputs, the functional microbiome information gained under healthy conditions represent a pivotal step towards designing more effective trials involving microbiome-reprogramming feed additives. Overall, we envisage that these results will lead to improved focus on coupling fundamental microbiome characterization to the design of next-generation feeds for salmon aquaculture.

microbiology↗

bioRxiv2023

The Salmon Microbial Genome Atlas enables novel insights into bacteria-host interactions via functional mapping

The essential role of the gut microbiota for host health and nutrition is well established for many terrestrial animals, while its importance for fish and particularly Atlantic salmon is unclear. Here, we present the Salmon Microbial Genome Atlas (SMGA) originating from wild and farmed fish both in freshwater and seawater, and consisting of 211 high-quality bacterial genomes, recovered by cultivation (n=131) and gut metagenomics (n=80). Bacterial genomes were taxonomically assigned into 14 different orders, including 28 distinctive genera and 31 potentially novel species. Benchmarking the SMGA, we functionally characterized key populations in the salmon gut that were detected in vivo. This included the ability to degrade diet-derived fibers and release vitamins and other exo-metabolites with known beneficial effects, which were validated by in vitro cultivation and untargeted metabolomics. Together, the SMGA enables high resolution functional insight into salmon gut microbiota with relevance for salmon nutrition and health.

microbiology↗

bioRxiv2023

Protein Language Models Uncover Carbohydrate-Active Enzyme Function in Metagenomic

In metagenomics, the pool of uncharacterized microbial enzymes presents a challenge for functional annotation. Among these, carbohydrate-active enzymes (CAZymes) stand out due to their pivotal roles in various biological processes related to host health and nutrition. Here, we present CAZyLingua, the first tool that harnesses protein language model embeddings to build a deep learning framework that facilitates the annotation of CAZymes in metagenomic datasets. Our benchmarking results showed on average a higher F1 score (reflecting an average of precision and recall) on the annotated genomes of Bacteroides thetaiotaomicron, Eggerthella lenta and Ruminococcus gnavus compared to the traditional sequence homology-based method in dbCAN2. We applied our tool to a paired mother/infant longitudinal dataset and revealed unannotated CAZymes linked to microbial development during infancy. When applied to metagenomic datasets derived from patients affected by fibrosis-prone diseases such as Crohns disease and IgG4-related disease, CAZyLingua uncovered CAZymes associated with disease and healthy states. In each of these metagenomic catalogs, CAZyLingua discovered new annotations that were previously overlooked by traditional sequence homology tools. Overall, the deep learning model CAZyLingua can be applied in combination with existing tools to unravel intricate CAZyme evolutionary profiles and patterns, contributing to a more comprehensive understanding of microbial metabolic dynamics.

bioinformatics↗

bioRxiv2021

A technical pipeline for screening microbial communities as a function of substrate specificity through single cell fluorescent imaging

The study of specific glycan uptake and metabolism has been shown to be an effective tool in aiding with the continued unravelling of the complexities in the human gut microbiome. To this aim fluorescent labelling of glycans may provide a powerful route towards target. In this study, we successfully used the fluorescent label 2-aminobenzamide (2-AB), most commonly employed for enhancing the detection of protein anchored glycans, to monitor and study microbial degradation of labelled glycans. Both single strain and co-cultured fermentations of microbes from the common human-gut derived Bacteroides genus, were able to grow when supplemented with 2-AB labelled glycans of different monosaccharide composition, degrees of acetylation and polymerization. Utilizing a multifaceted approach that combines chromatography, mass spectrometry, microscopy and flow cytometry techniques, it was possible to comprehensively track the metabolism of the labelled glycans in both supernatants and at a single cell level. We envisage this combination of complimentary techniques will help further the understanding of substrate specificity and the role it plays within microbial communities. IMPORTANCEInformation on how bacterial consortia utilize polysaccharides at strain level, whilst progressing rapidly in recent years still lacks a suitable way to study the vast range of ornamentations and structural motifs found in the natural glycans we consume in everyday life. As multi-omic approaches commonly require complex and costly analysis, a screening platform, as described in our work, could be seen as both a complementary and essential new tool in the understanding of microbial polysaccharide metabolism. Our study demonstrates a fast and efficient glycan labelling technique composed of several integrated procedures and advanced analytical methodologies. Chromatography and mass spectrometry are applied in the tracking of metabolized labelled glycans whilst microscopy and flow cytometry are used in the visualization of labelled bacteria at a single cell level.

biochemistry↗

bioRxiv2020

Human gut Faecalibacterium prausnitzii deploy a highly efficient conserved system to cross-feed on β-mannan-derived oligosaccharides

{beta}-Mannans are hemicelluloses that are abundant in modern diets as components in seed endosperms and common additives in processed food. Currently, the collective understanding of {beta}-mannan saccharification in the human colon is limited to a few keystone species, which presumably liberate low-molecular-weight mannooligosaccharide fragments that become directly available to the surrounding microbial community. Here we show that a dominant butyrate-producer in the human gut, Faecalibacterium prausnitzii, is able to acquire and degrade various {beta}-mannooligosaccharides ({beta}-MOS), which are derived by the primary mannanolytic activity of neighboring gut microbiota. Detailed biochemical analyses of selected protein components from their two {beta}-mannooligosaccharides ({beta}-MOS) utilization loci (FpMULs) supported a concerted model whereby the imported {beta}-MOS are stepwise disassembled intracellularly by highly adapted enzymes. Coculturing experiments of F. prausnitzii with the primary degrader Bacteroides ovatus on polymeric {beta}-mannan resulted in syntrophic growth and production of butyrate, thus confirming the high efficiency of the FpMULs uptake system. Genomic comparison with human F. prausnitzii strains and analyses of 2441 public human metagenomes revealed that FpMULs are highly conserved and distributed worldwide. Together, our results provide a significant advance in the knowledge of {beta}-mannans metabolism and the degree to which its degradation is mediated by cross-feeding interactions between prominent beneficial microbes in the human gut. ImportanceCommensal butyrate-producing bacteria belonging to the Firmicutes phylum are abundant in the human gut and are crucial for maintaining health. Currently, insight is lacking into how they target otherwise indigestible dietary fibers and into the trophic interactions they establish with other glycan degraders in the competitive gut environment. By combining cultivation, genomic and detailed biochemical analyses this work reveals the mechanism enabling F. prausnitzii, as a model clostridial cluster IV Firmicute, to cross-feed and access {beta}-mannan-derived oligosaccharides released in the gut ecosystem by the action of primary degraders. A comprehensive survey of human gut metagenomes shows that FpMULs are ubiquitous in human populations globally, highlighting the importance of microbial metabolism of {beta}-mannans/{beta}-MOS as a common dietary component. Our findings provide a mechanistic understanding of the {beta}-MOS utilization capability by F. prausnitzii that may be exploited to select dietary formulations specifically boosting this beneficial symbiont, thus butyrate production, in the gut.

microbiology↗

bioRxiv2019

Engineered fibre enables targeted activation of butyrate producing microbiota in the distal gut

Beneficial modulation of the gut microbiome has high-impact implications not only in humans, but also in livestock that sustain our current societal needs. In this context, we have tailored an acetylated galactoglucomannan (AcGGM) fibre to match unique enzymatic capabilities of Roseburia and Faecalibacterium species, both renowned butyrate-producing gut commensals. The accuracy of AcGGM was tested within the complex endogenous gut microbiome of pigs, wherein we resolved 355 metagenome-assembled genomes together with quantitative metaproteomes. In AcGGM-fed pigs, both target populations differentially expressed AcGGM-specific polysaccharide utilization loci, including novel, mannan-specific esterases that are critical to its deconstruction. However, AcGGM-inclusion also manifested a "butterfly effect", whereby numerous metabolic changes and interdependent cross-feeding pathways were detected in neighboring non-mannolytic populations that produce short-chain fatty acids. Our findings show that intricate structural features and acetylation patterns of dietary fibre can be customized to specific bacterial populations, with potential to create greater modulatory effects at large.

microbiology↗