Biology subjects

Licona-Cassani, C.

Publications and source records attributed to Licona-Cassani, C..

8 recordsLinked to original sources

bioRxiv2025

Uncharacterized Acetilactobacillus-like genera represent the most abundant microorganisms in honeys produced by native stingless bee

Pot honey, the honey produced by stingless bees, is valued for its antimicrobial capacity, which may be influenced by its microbial content. While Lactobacillaceae species are commonly associated with honeybees and honey microbiomes, most studies have focused on Apis mellifera, leaving pot honey microbial diversity largely unexplored. We present the first pot honey shotgun metagenomic analysis from bee species Melipona beecheii and Scaptotrigona mexicana. We reconstructed 24 metagenome-assembled genomes (MAGs), 15 of which lacked close matches to any described species, showing[≤] 81% Average Nucleotide Identity (ANI) to available reference genomes. Phylogenetic analyses resolved these MAGs into four well-defined clades (intraclade ANI > 99%, interclade ANI[≤] 81%), consistent with four novel species within the family Lactobacillaceae. GTDB-Tk classification placed MAG clades 1 and 2 closest to Nicoliella, and clades 3 and 4 closest to Acetilactobacillus. We validated the presence of these lineages in honey by sequencing three isolates that clustered within MAG clade 2. Aminoacid similarity (AAI/cAAI) indicates the presence of two genus-level lineages: one occupying a transitional genomic space near Nicoliella, and a second representing an undescribed genus. The genomic similarity of our MAGs and isolates to those from pot honey or larval food in Malaysia, Brazil, and Australia suggests these taxa are closely associated with stingless bees and may contribute to honey properties. By reducing the genomic underrepresentation of evolutionarily divergent sister clades related to Nicoliella and Acetilactobacillus, our genome-resolved analyses reveal a globally distributed, phylogenetically cohesive Lactobacillaceae species complex dominating pot honey.

ecology↗

bioRxiv2025

Maternal obesity alters human milk oligosaccharides content and correlates with early acquisition of late colonizers in the neonatal gut microbiome

The infant gastrointestinal tract is critical for metabolic and immune development, shaped by early gut microbiome colonization. Maternal obesity may disrupt this process by altering human milk oligosaccharides (HMOs), influencing microbial succession and infant health. This longitudinal study examines maternal BMI-associated variations in HMOs and infant fecal microbiota. Human milk samples from 97 mothers (stratified by BMI) were collected at 48h, one month, and three months postpartum, with HMOs quantified via UPLC-MS/MS. In a subsample of this population, infant fecal microbiome composition was analyzed using metagenomics tools. Mothers with obesity exhibited reduced 2-FL, LNnT, 3-SL, 6-SL, LNFPI concentration at 48 h postpartum. Infants born to these mothers showed diminished early colonizers such as Gammaproteobacteria at 48h, alongside lower antigen and polyamine biosynthesis pathways. Conversely, late colonizers like Lachnospiraceae species were more abundant at one and three months postpartum. Sialylated and neutral HMOs negatively correlated with these late colonizers, which metabolize such oligosaccharides. These findings suggest maternal obesity alters HMO profiles, potentially disrupts pioneer microbial establishment and accelerating late-colonizer dominance. Reduced keystone bacteria and shifted metabolic pathways may impair immune priming, with long-term health implications. This highlights the interplay between maternal BMI, HMO composition, and infant microbiome succession, underscoring the need to address maternal metabolic health to optimize early microbial colonization and immune programming.

microbiology↗

bioRxiv2025

Analysis of human colostrum reveals differential co-occurrence networks of metabolites, microbiota, and cytokines in maternal obesity

Breastmilk is essential for neonatal development, particularly in seeding the gut microbiota and modulating the maturing immune system. This proof-of-concept study explores the systemic nature of colostrum and the influence of maternal obesity on co-occurrences of colostrum bioactives. Using 16S-rRNA sequencing, untargeted metabolomics, and cytokines quantification, we analyzed co-occurring elements in the colostrum of mothers with normal weight (18.5 < BMI < 25) or obesity (BMI > 30). We identified 5 different co-occurrence networks, characterized by positive correlations of taxonomically related bacteria. Our integrative analysis reveals that Aeromonadaceae, Xanthomonadaceae and Staphylococcaceae negatively correlate with proinflammatory cytokines TNF-, IL-6, and IL-12p70 in the colostrum of mothers with obesity (WO). Additionally, lipid mediators, including 15-HEDE and LysoPC(16:00), were associated with cytokines IL-10 and IL-8, and microbiota taxa Burkholderiaceae, Beijerinckiaceae and Planococcaceae-firstly reported in colostrum from mothers WO. Our findings suggest a pervasive regulation of bioactives in the colostrum of mothers WO. This may have implications for a distinctive neonatal intestine development.

microbiology↗

bioRxiv2023

Draft Genomes of Four Kluyveromyces marxianus Isolates Retrieved from the Elaboration Process of Henequen (Agave fourcroydes) Mezcal.

We report the draft genomes of four Kluyveromyces marxianus isolates obtained from the elaboration process of henequen (Agave fourcroydes) mezcal, a Mexican alcoholic beverage. The average nucleotide identity (ANI) analysis revealed that isolates derived from agave plants are distinct from those from other environments, including agave fermentations.

microbiology↗

bioRxiv2023

A precision overview of genomic resistance screening in isolates of Mycobacterium tuberculosis using web-based bioinformatics tools.

Tuberculosis (TB) is among the most deadly diseases that affect worldwide, its impact is mainly due to the continuous emergence of resistant isolates during treatment due to the laborious process of resistance diagnosis, non-adherence to treatment and circulation of previously resistant isolates of Mycobacterium tuberculosis. The aim in this study was evaluate the performance and functionalities of web-based tools: Mykrobe, TB-profiler, PhyReSse, KvarQ, and SAM-TB for detecting resistance in isolate of Mycobacterium tuberculosis in comparison with conventional drug susceptibility tests. We used 88 M. tuberculosis isolates which were drug susceptibility tested and subsequently fully sequenced and web-based tools analysed. Statistical analysis was performed to determine the correlation between genomic and phenotypic analysis. Our data show that the main sub-lineage was LAM (44.3%) followed by X-type (23.0%) within isolates evaluated. Mykrobe has a higher correlation with DST (98% of agreement and 0.941Cohens Kappa) for global resistance detection, but SAM-TB, PhyReSse and Mykrobe had a better correlation with DST for first-line drug analysis individually. We have identified that 50% of mutations characterised by all web-based tools were canonical in rpoB, katG, embB, pncA, gyrA and rrs regions. Our findings suggest that SAM-TB, PhyReSse and Mykrobe were the web-based tools more efficient to determine canonical resistance-related mutations, however more analysis should be performed to improve second-line detection. The improvement of surveillance programs for the TB isolates applying WGS tools against first line drugs, MDR-TB and XDR-TB are priorities to discern the molecular epidemiology of this disease in the country. ImportanceTuberculosis, an infectious disease caused by Mycobacterium tuberculosis, which most commonly affects the lungs and is often spread through the air when infected people cough, sneeze, or spit. However, despite the existence of effective drug treatment, the patient adherence, long duration of treatment, and late diagnosis, have reduced the effectiveness of therapy and raised the drug resistance. The increase in resistant cases, added to the impact of the COVID-19 pandemic, have highlighted the importance of implementing efficient and timely diagnostic methodologies worldwide. The significance of our research is in evaluating and identifying the more efficient and friendly web-based tool to characterise the resistance in Mycobacterium tuberculosis by whole genome sequencing, which will allow apply it more routinely to improve TB strain surveillance programs locally.

microbiology↗

bioRxiv2022

Genomics epidemiology analysis reveals hidden signatures of drug resistance in Mycobacterium tuberculosis

Mycobacterium tuberculosis (Mtb) causes the majority of reported cases of human tuberculosis (TB), one of the deadliest infectious diseases worldwide. New diagnostic tools and approaches to detect drug-resistance must be introduced by 2025 to achieve the End-TB Strategy goals set for 2030 by the WHO. Genomic epidemiology of TB has allowed the expansion of catalogs listing genetic signatures of Mtb drug-resistance. However, very few Mtb strains from Latin America have participate in previous genomic epidemiologic efforts. Here we present the first functional genomic epidemiology study of drug-resistant Mtb strains in Mexico, incorporating the genomic characterization of 133 genomes, including 53 newly sequenced isolates, to provide a comprehensive phylogeographic analysis of drug resistant Mtb in Mexico. The study evidences the prevalence of Euro-American Lineage L4 (96.2%), featuring a uniform distribution of the sublineages X-type (33.08%), LAM (22.56%), and Haarlem (21.05%). Our results demonstrate low levels of agreement with traditional drug sensitivity tests (DST), raising concerns for drug-resistant isolates lacking any previously reported genetic signatures of resistance. Finally, we propose a novel functional networking tool (FuN-TB) to explore metabolic and cellular signatures of drug resistance. Applying functional genomics approaches to Latin American Mtb genomes will provide new drug-resistance screening targets that can contribute to bed side decision-making and advise local public policy. Abstract importanceWe presented the first phylogeographic analysis of Mycobacterium tuberculosis (Mtb) of Mexico. Our analysis integrates 133 genome sequences and is focused on the identification of genetic signatures associated to drug-resistance. The results show the geographic distribution of sublineages and drug-resistance phenotypic classes. Additionally, we propose a novel functional networking tool (FuN-TB) to explore metabolic and cellular signatures of drug resistance associated. We show for the first time that Mtb isolates from Mexico encode for region-specific genetic signarures of antimicrobial resistance. Applying functional genomics approaches to Latin American Mtb genomes will provide new drug-resistance screening targets that can contribute to bed side decision-making and advise local public policy.

genomics↗

bioRxiv2021

Insights into the trafficking of human leukocytes to colostrum evidences a modulation of the B lymphocyte compartment in obesity

Breastmilk is a dynamic fluid which initial goal is to provide the most adapted nutrition to the neonate. Additional functions have been recently attributed to breastmilk, with the evidence of a specific microbiota and the presence of a variety of components of the immune system, such as cytokines and leukocytes. The composition of breastmilk varies through time, according to the health status of mother and child, and altogether contributes to future health of the infant. Obesity is a rising condition worldwide, that creates a state of systemic, chronic inflammation including leukocytosis. Here, we asked whether colostrum, the milk produced within the first 48 h post-partum, would contain a distinct leukocyte composition depending on the body mass index (BMI) of the mother. We applied a panel of 6 antibodies plus viability marker to the peripheral blood and colostrum obtained from obese (BMI > 30) and lean (BMI < 25) mothers to characterize 10 major leukocyte subpopulations using flow cytometry. While lymphoid cells were otherwise unaffected by their tissue of origin, the phenotypes of granulocyte and monocyte populations significantly contrasted between blood and colostrum, including variations in morphology and surface expression of CD45 and CD16. These differences recapitulated across groups, which suggests a generalized cell-specific phenotype alteration caused by trafficking to colostrum. The B lymphocyte compartment was significantly reduced in obese colostrum and these cells did not exhibit enhanced CD16 shedding in this tissue, unlike B lymphocytes from lean mothers colostrum. This is the first exhaustive characterization of major leukocyte subsets in obese mothers colostrum, and the first report of leukocyte subpopulations from Latin-American womens colostrum. This pioneering study is a steppingstone to further investigate active immunity in human breastmilk.

immunology↗

bioRxiv2020

Convergent evolution of Streptomyces protease inhibitors involving a tRNA-mediated condensation-minus NRPS

Small peptide aldehydes (SPAs) with protease inhibitory activity are natural products typically synthesized by nonribosomal peptide synthetases (NRPS). SPAs are widely used in biotechnology, as therapeutic agents, they are physiologically relevant and regulate development of the natural hosts. During genome evolutionary analysis of Streptomyces lividans 66 we identified an NRPS-like biosynthetic gene cluster (BGC) that lacked a condensation (C) domain but included a tRNA-Utilizing Enzyme (tRUE) belonging to the leucyl/phenylalanyl (L/F) transferase family. This system was predicted to direct the synthesis of a novel SPA with protease inhibitory activity, called livipeptin. Following genome mining and phylogenomic analyses we confirmed the presence of tRUEs within diverse Streptomyces genomes, including fusions with a C-minus NRPS-like protein. We further demonstrate functional cooperation between these enzymes and provide the biosynthetic rules for the synthesis of livipeptin, expanding the known universe of acetyl-leu/phe-arginal SPAs. The L/F-transferase C-minus NRPS productive interaction was shown to be tRNA-dependent after semisynthetic assays in the presence of RNAse, which contrasts with leupeptin, an acetyl-leu-arginal SPA that we show to be produced by Streptomyces roseous ATCC 31245 via a tRUE-minus BGC with multiple complete NRPSs. Thus, livipeptin and leupeptin are the result of convergent evolution, which has driven the appearance of unprecedented biosynthetic logics directing the synthesis of protease inhibitors thought to be at the core of Streptomyces colony biology. Our results pave the way for understanding this Streptomyces trait, as well as for the discovery of novel natural products following evolutionary genome mining approaches. Abstract importanceConvergent evolution in microbiology is believed to be highly recurrent yet examples that have been comprehensively characterized are scarce. Proteases inhibition by small peptide aldehydes is at the core of many microbiological processes, both within the cell and during colony development, and in microbial ecology. Here we report the biosynthetic foundations of leupeptin, the main Streptomyces protease inhibitor, and of livipeptin, a protease inhibitor produced by Streptomyces lividans. Although these peptides belong to the same chemical class, here we show that their biosynthetic routes result from convergent evolution, as they involve unrelated biosynthetic mechanisms, including the recruitment of a tRNA-utilizing enzyme that functionally replaces the condensation domain of a nonribosomal peptide synthetase during livipeptin biosynthesis. Thus, these results pave the way for understanding Streptomyces protease inhibitors as a trait and provide unprecedented knowledge for genome mining of natural products and synthetic biology where proteases inhibition is desirable.

microbiology↗