Biology subjects

Flores, G. E.

Publications and source records attributed to Flores, G. E..

5 recordsLinked to original sources

bioRxiv2025

Time-resolved growth of diverse human-associated Akkermansia on human milk oligosaccharides

The infant gut microbiota is strongly influenced by human milk oligosaccharides (HMOs), a set of glycans that comprise a large constituent of milk and reach the large intestine intact. During growth on HMOs, bacteria produce beneficial metabolites including short chain fatty acids (SCFAs) that are important for host health. Select gut microorganisms have unique sets of enzymes capable of catabolizing distinct HMOs leading to host-specific differences in glycan access, and ultimately differences in SCFA production. Here we cultivated three species of human-associated Akkermansia, an early life commensal that is correlated with a healthy metabolic status in adults, on five individual HMOs in two different media backgrounds. Analysis of growth rates, growth yield, metabolic output, and individual HMO consumption through time revealed differences across species that was influenced by growth media. Most notably, A. biwaensis CSUN-19 has robust growth in both media backgrounds paired with nearly complete degradation of all HMOs. Across all conditions, overall SCFA production was generally commensurate with growth, but most strikingly, A. muciniphila MucT and A. biwaensis CSUN-19 produced succinate only when grown in the presence of N-acetyl glucosamine, but not with mucin. The third organism tested, A. massiliensis CSUN-17 had weaker growth, lower degradation of HMOs, but higher production of propionate in media containing N-acetyl glucosamine. Interactions between Akkermansia and HMOs can influence colonization of other early life commensals, potentially influencing health outcomes throughout life. This study highlights the importance of characterizing growth of individual Akkermansia species on distinct HMO leading to fermentation into organic acids. IMPORTANCEAkkermansia are a widely distributed bacterial genus found in the healthy human gut that are capable of degrading host-produced glycans including human milk oligosaccharides (HMOs). Previous end-point experiments demonstrated varying degradation efficiencies across Akkermansia species with A.biwaensis displaying enhanced growth on multiple HMOs. However, the temporal dynamics and growth preferences when offered substrate choice across the lineage are unknown. Here, we characterized the temporal growth dynamics, HMO catabolism, and metabolic output of three Akkermansia species across five HMOs and two media backgrounds. Specifically, we demonstrate that one species, A. biwaensis CSUN-19, has robust growth independent of media background with nearly complete degradation of all HMOs tested. Overall, the species-, HMO-, and media-specific response of Akkermansia may impact the colonization success of each species, ultimately influencing host-microbe and microbe-microbe interactions in the developing infant gut microbiome.

microbiology↗

bioRxiv2023

Mechanism of 2-Fucosyllactose degradation by Human-Associated Akkermansia

Among the first microorganisms to colonize the human gut of breastfed infants are bacteria capable of fermenting human milk oligosaccharides (HMOs). One of the most abundant HMOs, 2-fucosyllactose (2-FL), may specifically drive bacterial colonization of the intestine. Recently, differential growth has been observed across multiple species of Akkermansia on various HMOs including 2FL. In culture, we found growth of two species, A. muciniphila MucT and A. biwaensis CSUN-19, in HMOS corresponded to a decrease in the levels of 2-FL and an increase in lactose, indicating that the first step in 2-FL catabolism is the cleavage of fucose. Using phylogenetic analysis and transcriptional profiling, we found that the number and expression of fucosidase genes from two glycoside hydrolase (GH) families, GH29 and GH95, varies between these two species. During mid-log phase growth, the expression of several GH29 genes was increased by 2-FL in both species, whereas the GH95 genes were induced only in A. muciniphila. We further show that one putative fucosidase and a {beta}-galactosidase from A. biwaensis are involved in the breakdown of 2-FL. Our findings indicate that that plasticity of GHs of human associated Akkermansia sp. enable access to additional growth substrates present in HMOs, including 2-FL. Our work highlights the potential for Akkermansia to influence the development of the gut microbiota early in life and expands the known metabolic capabilities of this important human symbiont. IMPORTANCEAkkermansia are mucin degrading specialists widely distributed in the human population. Akkermansia biwaensis has recently been observed to have enhanced growth relative to other human associated Akkermansia on multiple human milk oligosaccharides (HMOs). However, the mechanisms for enhanced growth are not understood. Here, we characterized the phylogenetic diversity and function of select genes involved in growth of A. biwaensis on 2-fucosyllactose (2-FL), a dominant HMO. Specifically, we demonstrate that two genes in a genomic locus, a putative {beta}-galactosidase and -fucosidase, are likely responsible for the enhanced growth on 2-FL. The functional characterization of A. biwaensis growth on 2-FL delineates the significance of a single genomic locus that may facilitate enhanced colonization and functional activity of select Akkermansia early in life.

microbiology↗

bioRxiv2023

Interindividual Diversity of Human Gut Mucin-Degrading Microbial Consortia

Mucin is a glycoprotein secreted throughout the mammalian gastrointestinal tract that can support endogenous microorganisms in the absence of complex polysaccharides. While diverse mucin degrading bacteria have been identified, the individual host microbial community differences capable of metabolizing this complex polymer are not well described. To determine whether individuals have taxonomically distinct but functionally similar mucin-degrading communities, we used a ten-day in vitro sequential batch culture fermentation from three human donors with mucin as the sole carbon source. For each donor, 16S rRNA gene amplicon sequencing was used to characterize microbial community succession, and the short-chain fatty acid profile was determined from the final community. Although two of the final communities had genus-level taxonomic differences signified by the presence of Desulfovibrio and Akkermansia, other members, such as Bacteroides, were shared between all three final communities. Metabolic output differences were most notable for one of the donors communities, with significantly less production of acetate and propionate than the other two communities. These findings reinforce the concept of a taxonomically distinct and, at broad levels, a functionally redundant gut microbiome. Furthermore, the mechanisms and efficiencies of mucin degradation across individuals are important for understanding how this community-level process impacts human health.

microbiology↗

bioRxiv2021

Utilization efficiency of human milk oligosaccharides by human-associated Akkermansia is strain-dependent

Akkermansia muciniphila are mucin degrading bacteria found in the human gut and are often associated with positive human health. However, despite being detected as early as one month of age, little is known about the role of Akkermansia in the infant gut. Human milk oligosaccharides (HMOs) are abundant components of human milk and are structurally similar to the oligosaccharides that comprise mucin, the preferred growth substrate of human-associated Akkermansia. A limited subset of intestinal bacteria has been shown to grow well on HMOs and mucin. We therefore examined the ability of genomically diverse strains of Akkermansia to grow on HMOs. First, we screened 85 genomes representing the four known Akkermansia phylogroups to examine their metabolic potential to degrade HMOs. Furthermore, we examined the ability of representative isolates to grow on individual HMOs in a mucin background and analyzed the resulting metabolites. All Akkermansia genomes were equipped with an array of glycoside hydrolases associated with HMO-deconstruction. Representative strains were all able to grow on HMOs with varying efficiency and growth yield. Strain CSUN-19 belonging to the AmIV phylogroup, grew to the highest level in the presence of fucosylated and sialylated HMOs. This activity may be partially related to the increased copy numbers and/or the enzyme activities of the -fucosidases, -sialidases, and {beta}-galactosidases. Utilization of HMOs by strains of Akkermansia suggests that ingestion of HMOs by an infant may enrich for these potentially beneficial bacteria. Further studies are required to realize this opportunity and deliver long-lasting metabolic benefits to the human host. ImportanceHuman milk oligosaccharides (HMOs) are utilized by a limited subset of bacteria in the infant gut. Akkermansia are detected in infants as young as one month of age and are thought to contribute to the HMO deconstruction capacity of the infant. Here, using phylogenomics, we examined the genomic capacity of different Akkermansia phylogroups to potentially deconstruct HMOs. Furthermore, we experimentally showed that strains from all the currently known phylogroups of Akkermansia can deconstruct all the major types of HMOs, albeit with different utilization efficiencies. This study thus examines Akkermansia-HMO interactions that can potentially influence the gut microbial ecology during the first 1,000 days of life - a critical phase for the development of the gut microbiome and infant health. This study will be of interest to a wide range of scientists from microbiologists, glycochemists/glycobiologists, to functional food developers investigating Akkermansia as probiotics or functional foods containing milk oligosaccharides as prebiotics.

microbiology↗

bioRxiv2019

Clustering of the structures by using \"snakes-and-dragons\" approach, or correlation matrix as a signal

Biological, ecological, social, and technological systems are complex structures with multiple interacting parts, often represented by networks. Correlation matrices describing interdependency of the variables in such structures provide key information for comparison and classification of such systems. Classification based on correlation matrices could supplement or improve classification based on variable values, since the former reveals similarities in system structures, while the latter relies on the similarities in system states. Importantly, this approach of clustering correlation matrices is different from clustering elements of the correlation matrices, because our goal is to compare and cluster multiple networks - not the nodes within the networks. A novel approach for clustering correlation matrices, named \"snakes-&-dragons,\" is introduced and illustrated by examples from neuroscience, human microbiome, and macroeconomics.

bioinformatics↗