Hugo G. Castelán‐Sánchez

Western University

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Sonia Dávila‐Ramos

Universidad Autónoma del Estado de Morelos

Marina Escalera‐Zamudio

University of Oxford

Bernardo Gutiérrez

University of Oxford

Oliver G. Pybus

University of Oxford

Luis Delaye

Instituto Tecnológico Superior de Irapuato

Ramón Alberto Batista‐García

Universidad Autónoma del Estado de Morelos

Rhys P. D. Inward

University of Oxford

Natalia Martínez de la Viña

University of Oxford

Selene Zárate

Universidad Autónoma de la Ciudad de México

Andreu Comas‐García

Autonomous University of San Luis Potosí

Cooperative Institutions

Universidad Nacional Autónoma de México

Instituto Politécnico Nacional

Universidad Autónoma del Estado de Morelos

Center for Research and Advanced Studies of the National Polytechnic Institute

Asociación Mexicana de Psicología y Desarrollo Comunitario

Secretaria de Salud

Mexican Social Security Institute

Universidad Autónoma de la Ciudad de México

University of Oxford

Departamento de Salud

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Genetic Insights into the Microevolutionary Dynamics and Early Introductions of Human Monkeypox Virus in Mexico

medRxiv (Cold Spring Harbor Laboratory) (2023)

Israel Gómez-Sánchez Hugo G. Castelán‐Sánchez León P. Martínez-Castilla Juan Manuel Hurtado-Ramírez Gamaliel López-Leal

ABSTRACT The recent global outbreak of Monkeypox, caused by the Monkeypox virus (MPVX) emerged in Europe in 2022 and rapidly spread to over 40 countries. The Americas are currently facing the highest impact, reporting over 50,000 cases by early 2023. Here, we analyze 880 MPXV isolates worldwide to gain insights into the evolutionary patterns and initial introduction events of the virus in Mexico. We found that MPXV entered Mexico on multiple occasions, from the United Kingdom, Portugal, and Canada, and subsequently spread locally in different regions of Mexico. Additionally, we show that MPXV has an open pangenome, highlighting the role of gene turnover in shaping its genomic diversity, rather than SNPs variations, which do not contribute significantly to genome diversity. Although the genome presents multiple SNP sites in coding regions, these remain under purifying selection, suggesting their evolutionary conservation. One notable exception is the amino acid site 63 of the protein encoded by the Cop-A4L gene, intricately related to viral maturity, for which we picked up a strong signal of positive selection. Ancestral state reconstruction deduced that the ancestral state at site 63 corresponds to the amino acid valine, present only in isolates of clade I. However, the isolates of the current outbreak evolved for threonine at site 63. Finally, our findings contribute to the knowledge of the evolutionary processes of the Monkeypox virus.

Monkeypox

10.1101/2023.08.26.23294674

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Gut Microbiota: Association with Fiber Intake, Ultra-Processed Food Consumption, Sex, Body Mass Index, and Socioeconomic Status in Medical Students

Nutrients (2024)

Laura Moreno-Altamirano Karina Robles-Rivera Hugo G. Castelán‐Sánchez Felipe Vaca‐Paniagua María del Carmen Iñárritu Pérez

The gut microbiota plays a vital role in various physical and physiological processes, including immune system regulation, neurotransmitter production, inflammatory response modulation, and the inhibition of pathogenic organisms. An imbalance in the microbial community, known as dysbiosis, has been associated with numerous health issues. Biological influences, health behaviors, socioeconomic determinants, and nutritional status can disrupt this balance.

Consumption

10.3390/nu16234241

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Inoculation withPseudomonas fluorescensUM270 alters the maize root-associated endobiome and interacting networks in a milpa model

bioRxiv (Cold Spring Harbor Laboratory) (2023)

Blanca Rojas-Sánchez Hugo G. Castelán‐Sánchez Gustavo Santoyo

Abstract The traditional milpa system is a polyculture originating in Mesoamerica, whose core is maize ( Zea mays L.), associated with squash ( Cucurbita spp.) and beans ( Phaseolus vulgaris L.). In recent years, milpa-type crops have decreased owing to climate change, rapid population growth, and the excessive use of agrochemicals; therefore, the application of plant growth-promoting rhizobacteria (PGPR) to counteract these negative effects has been little explored. In this study, a maize crop in a milpa system was fertilized with the PGPR Pseudomonas fluorescens UM270, and the endophytic root microbiome (endobiome) of maize was assessed by 16S rRNA and internal transcribed spacer regions (ITS) sequencing. The results showed that UM270 the rhizosphere inoculation of P. fluorescens UM270 did not increase alpha diversity in either monoculture or the milpa, but it did alter the endophytic microbiome of maize plant roots by stimulating the presence of bacterial operational taxonomic units (OTUs) of the genera Burkholderia and Pseudomonas (in a monoculture), whereas in the milpa system, the PGPR stimulated a greater endophytic diversity and the presence of genera such as Burkholderia, Variovorax , and N-fixing rhizobia genera, including Rhizobium, Mesorhizobium and Bradyrhizobium . No clear association was found between fungal diversity and the presence of strain UM270, but beneficial fungi such as Rizophagus irregularis and Exophiala pisciphila were detected in the milpa system. In addition, network analysis revealed unique interactions with species like Stenotrophomonas sp., Burkholderia xenovorans , and Sphingobium yanoikuyae , which would potentially be playing a beneficial role with the plant. To the best of our knowledge, this is the first study in which the root microbiome of maize growing under a milpa model was assessed by bio-inoculation with PGPRs.

Stenotrophomonas

Pseudomonas fluorescens

Monoculture

Amaranthus hypochondriacus

10.1101/2023.05.15.540877

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Genomic characterization of two bacteriophages (vB_EcoS-phiEc3 and vB_EcoS-phiEc4) belonging to the genus Kagunavirus with lytic activity against uropathogenic Escherichia coli

Microbial Pathogenesis (2022)

Gerardo E. Rodea Edgar González-Villalobos Óscar Medina‐Contreras Hugo G. Castelán‐Sánchez Pamela Aguilar-Rodea

Lytic cycle

Subfamily

10.1016/j.micpath.2022.105494

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Emergence and widespread circulation of a recombinant SARS-CoV-2 lineage in North America

medRxiv (Cold Spring Harbor Laboratory) (2021)

Bernardo Gutiérrez Hugo G. Castelán‐Sánchez Darlan da Silva Cândido Ben Jackson Shay Fleishon

Abstract Genetic recombination is an important driving force of coronavirus evolution. While some degree of virus recombination has been reported during the COVID-19 pandemic, previously detected recombinant lineages of SARS-CoV-2 have shown limited circulation and been observed only in restricted areas. Prompted by reports of unusual genetic similarities among several Pango lineages detected mainly in North and Central America, we present a detailed phylogenetic analysis of four SARS-CoV-2 lineages (B.1.627, B.1.628, B.1.631 and B.1.634) in order to investigate the possibility of virus recombination among them. Two of these lineages, B.1.628 and B.1.631, are split into two distinct clusters (here named major and minor ). Our phylogenetic and recombination analyses of these lineages find well-supported phylogenetic differences between the Orf1ab region and the rest of the genome (S protein and remaining reading frames). The lineages also contain several deletions in the NSP6, Orf3a and S proteins that can augment reconstruction of reliable evolutionary histories. By reconciling the deletions and phylogenetic data, we conclude that the B.1.628 major cluster originated from a recombination event between a B.1.631 major virus and a lineage B.1.634 virus. This scenario inferred from genetic data is supported by the spatial and temporal distribution of the three lineages, which all co-circulated in the USA and Mexico during 2021, suggesting this region is where the recombination event took place. We therefore support the designation of the B.1.628 major cluster as recombinant lineage XB in the Pango nomenclature. The widespread circulation of lineage XB across multiple countries over a longer timespan than the previously designated recombinant XA lineage raises important questions regarding the role and potential effects of recombination on the evolution of SARS-CoV-2 during the ongoing COVID-19 pandemic.

Lineage (genetic)

10.1101/2021.11.19.21266601

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Citations (10)

Diversity of the Maize Root Endosphere and Rhizosphere Microbiomes Modulated by the Inoculation with Pseudomonas fluorescens UM270 in a Milpa System

Plants (2024)

Blanca Rojas-Sánchez Hugo G. Castelán‐Sánchez Esmeralda Y. Garfias-Zamora Gustavo Santoyo

Milpa is an agroecological production system based on the polyculture of plant species, with corn featuring as a central component. Traditionally, the milpa system does not require the application of chemicals, and so pest attacks and poor growth in poor soils can have adverse effects on its production. Therefore, the application of bioinoculants could be a strategy for improving crop growth and health; however, the effect of external inoculant agents on the endemic microbiota associated with corn has not been extensively studied. Here, the objective of this work was to fertilize a maize crop under a milpa agrosystem with the PGPR Pseudomonas fluorescens UM270, evaluating its impact on the diversity of the rhizosphere (rhizobiome) and root endophytic (root endobiome) microbiomes of maize plants. The endobiome of maize roots was evaluated by 16S rRNA and internal transcribed spacer region (ITS) sequencing, and the rhizobiome was assessed by metagenomic sequencing upon inoculation with the strain UM270. The results showed that UM270 inoculation of the rhizosphere of P. fluorescens UM270 did not increase alpha diversity in either the monoculture or milpa, but it did alter the endophytic microbiome of maize plant roots by stimulating the presence of bacterial operational taxonomic units (OTUs) of the genera Burkholderia and Pseudomonas (in a monoculture), whereas, in the milpa system, the PGPR stimulated greater endophytic diversity and the presence of genera such as Burkholderia, Variovorax, and N-fixing rhizobia genera, including Rhizobium, Mesorhizobium, and Bradyrhizobium. No clear association was found between fungal diversity and the presence of strain UM270, but beneficial fungi, such as Rizophagus irregularis and Exophiala pisciphila, were detected in the Milpa system. In addition, network analysis revealed unique interactions with species such as Stenotrophomonas sp., Burkholderia xenovorans, and Sphingobium yanoikuyae, which could potentially play beneficial roles in the plant. Finally, the UM270 strain does not seem to have a strong impact on the microbial diversity of the rhizosphere, but it does have a strong impact on some functions, such as trehalose synthesis, ammonium assimilation, and polyamine metabolism. The inoculation of UM270 biofertilizer in maize plants modifies the rhizo- and endophytic microbiomes with a high potential for stimulating plant growth and health in agroecological crop models.

Pseudomonas fluorescens

Monoculture

Lupinus

Polyculture

10.3390/plants13070954

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Campylobacter prophage diversity reveals pervasive recombination between prophages from different Campylobacter species

Microbiology Spectrum (2023)

Adán Manuel Piña-González Hugo G. Castelán‐Sánchez Juan Manuel Hurtado-Ramírez Gamaliel López-Leal

ABSTRACT Prophages, bacteriophages integrated into bacterial genomes, play a critical role in the genetic diversity and evolution of bacterial species. In this study, we investigated the prophage population harbored in Campylobacter species. A total of 446 high-quality and complete genomes of Campylobacter isolated from different sources revealed 431 prophages. We analyzed the phylogenomic relationships between 490 phages and prophages, unveiling a wide diversity of undescribed prophages. Bacteriophage pangenomes revealed shared genetic repertoires among different phage genera. In addition, we found recombination events between prophages from different phage genera, mainly in prophages infecting Campylobacter jejuni and Campylobacter coli , showing distinct evolutionary histories in specific regions of the prophage genomes. Specifically, these regions showed variations in gene content, enrichment in structural genes and others in hypothetical proteins, genes involved in transcription, DNA-associated factors, and genes associated with lysis. Finally, Campylobacter prophages alter the host genetic repertoire by carrying virulence factors and antibiotic-resistance genes. IMPORTANCE Prophages play an important role in shaping the genetic diversity and evolution of their hosts. Acquisition or loss of prophages can lead to genomic variations, including changes in the bacterial phenotype promoted by recombination events, genetic repertoire exchanges and dissemination of virulence factors, and antibiotic resistance. By studying prophages in Campylobacter species, scientists can gain insights into the evolutionary patterns, pathogenicity mechanisms, epidemiology, and population dynamics of these species. This has implications for public health, antibiotic resistance surveillance, and the development of targeted therapeutic approaches.

Prophage

Bacterial genome size

10.1128/spectrum.02795-23

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Genome Sequence of Actinobacillus seminis Strain ATCC 15768, a Reference Strain of Ovine Pathogens That Causes Infections in Reproductive Organs

Genome Announcements (2018)

Erasmo Negrete‐Abascal Juan Fernando Montes-García Sergio Vaca-Pacheco Abraham M. Leyto-Gil Edgar Fragoso-Garcia

The draft genome sequence of Actinobacillus seminis strain ATCC 15768 is reported here. The genome comprises 22 contigs corresponding to 2.36 Mb with 40.7% G+C content and contains several genes related to virulence, including a putative RTX protein.

Strain (injury)

10.1128/genomea.01453-17

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Citations (3)

Genome evolution and early introductions of the SARS-CoV-2 Omicron Variant in Mexico

medRxiv (Cold Spring Harbor Laboratory) (2022)

Hugo G. Castelán‐Sánchez León P. Martínez-Castilla Gustavo Sganzerla Martinez Jesús Torres-Flores Gamaliel López-Leal

ABSTRACT A new variant of SARS-CoV-2 Omicron (Pango lineage designation B.1.1.529), was first reported to the World Health Organization (WHO) by South African health authorities on November 24, 2021. The Omicron variant possesses numerous mutations associated with increased transmissibility and immune escape properties. In November 2021, Mexican authorities reported Omicron’s presence in the country. In this study, we infer the first introductory events of Omicron and the impact that human mobility can have on the spread of the virus. We also evaluated the adaptive evolutionary processes in Mexican SARS-CoV-2 genomes during the first month of circulation of Omicron. We infer 173 introduction events of Omicron in Mexico in the first two months of detection; subsequently, of the introductions, there was an increase in the prevalence for January. This higher prevalence of the novel variant results in a peak of cases reported, on average, six weeks after a higher mobility trend was reported. The peak of cases reported is due to the BA.1.1 Omicron sub-lineage dominated, followed by BA.1 and BA.15 sub-lineages in the country from January to February 2022. Additionally, we identified the presence of diversifying natural selection in the genomes of Omicron and found mainly five non-synonymous mutations in the RDB domain of the Spike protein, all of them related to evasion of the immune response. In contrast, the other proteins in the genome are highly conserved—however, there are homoplasies mutations in non-structural proteins, indicating a parallel evolution.

Lineage (genetic)

Positive selection

10.1101/2022.07.13.22277603

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Importance of Microbiome of Fecal Samples Obtained from Adolescents with Different Weight Conditions on Resistance Gene Transfer

Microorganisms (2022)

Armando Navarro Gerardo E. Rodea Hugo G. Castelán‐Sánchez Héctor Armando Saucedo-Pastrana Delia Licona-Moreno

Antimicrobial resistance (AMR) is a relevant public health problem worldwide, and microbiome bacteria may contribute to the horizontal gene transfer associated with antimicrobial resistance. The microbiome of fecal samples from Mexican adolescents were analyzed and correlated with eating habits, and the presence of AMR genes on bacteria in the microbiome was evaluated. Fecal samples from adolescents were collected and processed to extract genomic DNA. An Illumina HiSeq 1500 system was used to determine resistance genes and the microbiome of adolescents through the amplification of gene resistance and the V3–V4 regions of RNA, respectively. Analysis of the microbiome from fecal samples taken from 18 obese, overweight, and normal-weight adolescents revealed that the Firmicutes was the most frequent phylum, followed by Bacteroidetes, Actinobacteria, Proteobacteria and Verrucomicrobia. The following species were detected as the most frequent in the samples: F. prausnitzii, P. cori, B. adolescentis, E. coli and A. muciniphila. The presence of Bacteroides, Prevotella and Ruminococcus was used to establish the enterotype; enterotype 1 was more common in women and enterotype 2 was more common in men. Twenty-nine AMR genes were found for β-lactamases, fluoroquinolones, aminoglycosides, macrolide, lincosamides, streptogramin (MLS), tetracyclines and sulfonamides. The presence of microorganisms in fecal samples that harbor AMR genes that work against antimicrobials frequently used for the treatment of microbial infections such as b-lactams, macrolides, aminoglycosides, MLS, and tetracyclines is of great concern, as these organisms may be an important reservoir for horizontal AMR gene transfer.

10.3390/microorganisms10101995

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