Biology subjects

Ochoa-Leyva, A.

Publications and source records attributed to Ochoa-Leyva, A..

7 recordsLinked to original sources

bioRxiv2025

Extensive Hidden Prophage Diversity in Enterobacter Species Reveals Host Specificity and Local Distribution

Bacteriophages are key drivers of bacterial evolution, particularly through their integration as prophages within host genomes. However, the diversity and host specificity of prophages in clinically relevant pathogens such as Enterobacter species remain poorly characterized. In this study, we revealed the diversity of prophages, mapped their distribution, and explored their relationships with their bacterial hosts. We analyzed 3,661 prophage sequences identified from the genomes of 20 different Enterobacter species. This analysis uncovered an extensive hidden diversity, comprising 1,617 phage genera and 2,423 phage species--nearly 80% of which were singletons--highlighting an exceptionally rich prophage landscape. We found substantial variation in prophage species richness across host species and isolation sources, with E. kobei and environmental isolates exhibiting the highest richness. Prophage populations showed strong host specificity and limited cross-species transmission. Moreover, these prophages exhibited geographic structuring and significant congruence between host and prophage phylogenies, as well as with the ecological lifestyles of their bacterial hosts. Although some interspecies transmission events were detected, they were infrequent. Overall, this study provides new insights into the diversity of Enterobacter prophages and underscores their ecological and clinical relevance in shaping host adaptation and phage-host dynamics. IMPORTANCEEnterobacter species are emerging opportunistic pathogens increasingly implicated in hospital-acquired infections. Although prophages play a pivotal role in bacterial genome evolution and host adaptation, their diversity and distribution across Enterobacter species remain largely uncharacterized. In this study, we performed a large-scale genomic analysis of 3,661 prophages from 20 Enterobacter species and uncovered an extensive and previously hidden prophage diversity. Our analysis revealed significant differences in prophage species richness across both host species and isolation sources, with E. kobei and environmental isolates exhibiting the highest richness. Prophage populations were strongly structured by host species and geography, showing limited cross-species transmission and a high degree of congruence between phage and host phylogenies. These findings highlight the structured and lineage-specific nature of prophage populations in Enterobacter and provide valuable insights into phage-host coevolution, microbial biogeography, and the design of targeted phage therapy strategies.

genomics↗

bioRxiv2024

Host Genome Drives the Diversity, Richness, and Beneficial Microbes in the Shrimp Microbiota: A Hologenome Perspective.

Despite the growing understanding of the factors influencing the shrimp microbiome, the impact of host genetics on modulating the intestinal microbiota still needs to be studied. Moreover, the existing studies were typically conducted using animal models and under laboratory conditions. Here, we investigated the effect of two shrimp genetics, fast-growth (Gen1) and disease-resistant (Gen2), on shaping the microbiota of the hepatopancreas and the intestine in open-pond aquaculture farming conditions. First, we identified significant genomic differences between the two genetic lines using genome-wide SNP analysis. Then, the microbiota analysis confirmed that organs had a more substantial impact, explaining 33.9% of the variability, followed by the genetic line, which explained 17.3%. The microbiota of the hepatopancreas was more significantly affected by the genetic line than the intestine. Gen1 exhibited higher richness, diversity, niche breadth, and abundance of beneficial microbes than Gen2, suggesting that Gen1 had a more generalist microbiota. By comparing the microbiota of another set of healthy and diseased shrimps, we confirmed that a higher presence of beneficial microbes was linked to a healthy shrimp status. Additionally, we genotyped and determined the microbiota of wild-type shrimps, proving that they differ from those observed in both genetic lines. Interestingly, ponds with Gen1 had better productivity than Gen2, suggesting a potential link between higher productivity and the microbiota selected by Gen1. Our study highlights the importance of the holobiome perspective in breeding and management programs. It suggests that a specific genetic line and its associated microbiota could be used to select the larvae to be cultivated, improving shrimp aquaculture production.

genomics↗

bioRxiv2024

Fecal Virome Transplantation (FVT) from healthy humans remodels the gut bacteriome and virome and reduces metabolic syndrome in mice

AbstractThe gut microbiome regulates host processes, including metabolism, and comprises viruses, archaea, fungi, protists, and bacteria. However, previous studies have primarily focused on the bacterial components of the microbiome. This study conducted cross-infection experiments by fecal virome transplantation (FVT) to examine the impact of virus-like particles (VLPs) from normal-weight individuals on bacterial and virome diversity and metabolic changes in mice. We found that FVT significantly restored glucose tolerance in mice, even though they were maintained on a high-fat diet (HFD). Shotgun metagenomics and 16s profiling confirmed that FVT shifted gut bacterial and viral richness and diversity, resulting in several differentially abundant bacteria and phages. The abundance of Akkermansia muciniphila decreased significantly after FVT, remained low until the end of the experiment (week 17), and correlated with a decreased glucose tolerance. On the other hand, there was a significant increase in Allobaculum and Coprococcus at weeks 10 and 17 post-FVT. The abundance of Allobaculum correlated with an increased glucose tolerance, indicating a beneficial hypoglycemic effect on the mice inoculated with VLPs. We also found an increased virome diversity at week 17, while richness was similar to the one before FVT. The study provides a proof of concept for the efficacy of FVT from human donors to mice, improving glucose tolerance by altering the gut microbiota and virome despite maintaining a HFD. Overall, our results suggest that trans-kingdom interactions between the virome and bacteriome from humans could be translated to mice as a study model.

microbiology↗

bioRxiv2022

A loss of crAssphage stability in the human gut virome is associated with obesity and metabolic syndrome

Viral metagenomics studies of the human gut microbiota unravel differences in phage populations between healthy and disease, stimulating interest in the role that phages play in bacterial ecosystem regulation. CrAssphages are not only the most abundant viruses but also are a common component of the gut phageome across human populations. However, the role of crAssphages in obesity (O) and obesity with metabolic syndrome (OMS) remains largely unknown. Therefore, we explored the role that crAssphages have on both diseases in a childrens cohort. We found decreased crAssphage abundance, prevalence, richness, and diversity in O and OMS compared to normal-weight (NW), suggesting a loss of crAssphages stability in the human phageome associated with the disease. Interestingly, when we analyzed the abundance of host crAssphages bacteria, we found that Bacteroidetes, Bacteroidia, and Bacteroidales were significantly decreased in O and OMS, suggesting a possible relation with the loss of crAssphages stability. Regarding crAssphage taxonomy, a significantly decreased abundance of the crAssphage Alpha subfamily and the Alpha_1 and Alpha_4 genus and a significant overabundance of the Delta_8 was found in OMS. A strong taxonomical signature of obesity is the over-abundance of Bacilli, which also were significantly increased in O and OMS. Notably, we found a significant negative correlation between crAssphages and Bacilli abundances, suggesting an association between the decreased abundance of crAssphage and the over-abundance of Bacilli in OMS. Furthermore, we found a loss of crAssphage stability in the human virome associated with the presence of obesity, having a more significant impact on obesity with metabolic syndrome, suggesting that these bacteriophages could play an essential role in inhibiting metabolic syndrome in obese individuals. Our results open a promising treatment for these diseases through fecal crAssphage transplantation.

genomics↗

bioRxiv2020

In silico secretome characterization of clinical Mycobacterium abscessus isolates provides insights into antigenic differences

Mycobacterium abscessus (MAB) is a widely disseminated pathogenic non-tuberculous mycobacterium (NTM). Like with M. tuberculosis complex (MTBC), excreted / secreted (ES) proteins play an essential role for its virulence and survival inside the host. ES proteins contain highly immunogenic proteins, which are of interest for novel diagnostic assays and vaccines. Here, we used a robust bioinformatics pipeline to predict the secretome of the M. abscessus ATCC 19977 reference strain and fifteen clinical isolates belonging to all three MAB subspecies, M. abscessus subsp. abscessus, M. abscessus subsp. bolletii, and M. abscessus subsp. massiliense. We found that ~18% of the proteins encoded in the MAB genomes were predicted as secreted and that the three MAB subspecies shared > 85 % of the predicted secretomes. MAB isolates with a rough (R) colony morphotype showed larger predicted secretomes than isolates with a smooth (S) morphotype. Additionally, proteins exclusive to the secretomes of MAB R variants had higher antigenic densities than those exclusive to S variants, independently of the subspecies. For all investigated isolates, ES proteins had a significantly higher antigenic density than non-ES proteins. We identified 337 MAB ES proteins with homologues in previously investigated M. tuberculosis secretomes. Among these, 222 have previous experimental support of secretion, and some proteins showed homology with protein drug targets reported in the DrugBank database. The predicted MAB secretomes showed a higher abundance of proteins related to quorum-sensing and Mce domains as compared to MTBC indicating the importance of these pathways for MAB pathogenicity and virulence. Comparison of the predicted secretome of M. abscessus ATCC 19977 with the list of essential genes revealed that 99 secreted proteins corresponded to essential proteins required for in vitro growth. All predicted secretomes were deposited in the Secret-AAR web-server (http://microbiomics.ibt.unam.mx/tools/aar/index.php).

bioinformatics↗

bioRxiv2020

Gut Phageome Analysis Reveals Disease-Specific Hallmarks in Childhood Obesity

Changes in the composition of the human gut microbiome are recognized to have a significant association with obesity and metabolic syndrome. Mexico leads worldwide childhood-obesity rankings representing an epidemic problem for public health. To this date, it is still unclear how the gut phageome, the bacteriophage component of the virome, influences childhood obesity and obesity with metabolic syndrome. We characterized the gut phageome of 28 school-age children with healthy normal-weight (NW), obese (O), and obese with metabolic syndrome (OMS) profiles, using metagenomic sequencing of virus-like particles (VLPs) from fecal samples. Viromes derived from VLPs were mainly dominated by Caudovirales, and only Inoviridae family was significantly increased in obesity. The three groups showed a similar number of VLPs, while a significant increase in phage richness and diversity was found in obesity groups compared NW. Few phage contigs dominated the phageome composition in NW, being increased in obesity groups. Interestingly, the majority of the phageome was shared among all individuals, establishing a core and common phageome, which abundances correlated with anthropometric and biochemical traits and bacteria previously associated with obesity and metabolic syndrome. We also established a healthy core phageome shared in >80% of NW samples, with a decreased prevalence in the O and OMS groups. Our data support that changes in the gut phageome may contribute to obesity and metabolic syndrome development via bacterial dysbiosis. We consider the phageome characterization provides the basis for novel diagnostic and therapeutic strategies for managing obesity and preventing metabolic syndrome development in obese children through potential phage manipulation. To the best of our knowledge, this study represents the most in-depth sequenced dataset of human bacteriophages, demonstrating for the first time that alterations of the gut phageome characterize obesity.

genomics↗

bioRxiv2018

Bacterial diversity and population dynamics during the fermentation of palm wine from Guerrero Mexico

Palm wine is obtained by fermentation of palm tree sap. In the Pacific coast of Mexico, palm wine is called Tuba and it is consumed as a traditional fermented beverage. Tuba has empirical applications such as an auxiliary in gastrointestinal diseases and a good source of nutrients. In the present study, a next-generation sequencing of the V3-V4 regions of the 16S rRNA gene was employed to analyze bacterial diversity and population dynamics during the fermentation process of Tuba, both in laboratory controlled conditions and in commercial samples from local vendors. Taxonomic identification showed that Fructobacillus was the main genus in all the samples, following by Leuconostoc, Gluconacetobacter, Sphingomonas, and Vibrio. Alpha diversity analysis demonstrated variability between all the samples. Beta diversity clustered the bacterial population according to the collection origin of the sample. Metabolic functional profile inference showed that the members of the bacterial communities may present the vitamin, antibiotic and antioxidant biosynthesis genes. Additionally, we further investigated the correlation between the predominant genera and some composition parameters of this beverage. This study provides the basis of the bacterial community composition and functionality of the fermented beverage.

microbiology↗