Luis D. Alcaraz

Luis D. Alcaraz
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Luis D. verified their affiliation via an institutional email.
Verified
Luis D. verified their affiliation via an institutional email.
  • Doctor of Philosophy
  • Professor (Full) at National Autonomous University of Mexico

About

140
Publications
39,456
Reads
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3,624
Citations
Introduction
Professor, working and researching at the Faculty of Sciences, National Autonomous University of Mexico (Universidad Nacional Autónoma de México; UNAM). Research topics are environmental genomics, molecular microbiology, and comparative genomics. Our main research interest is microbe-host interactions. We have funded research in plant-associated microbiomes and metagenomics.
Current institution
National Autonomous University of Mexico
Current position
  • Professor (Full)
Additional affiliations
August 2017 - present
National Autonomous University of Mexico
Position
  • Professor (Full)
September 2012 - August 2017
National Autonomous University of Mexico
Position
  • Professor (Associate)
January 2012 - October 2012
Wilfrid Laurier University
Position
  • PostDoc Position
Education
September 2004 - October 2009
September 1998 - December 2004

Publications

Publications (140)
Article
Full-text available
Studies have suggested that reduced nutrient availability enhances microbial diversity around plant roots, positively impacting plant productivity. However, the specific contributions of rhizosphere microbiomes in nutrient-poor environments still need to be better understood. This study investigates tomato (Solanum lycopersicum L.) root microbiome...
Article
Full-text available
Solirubrobacter , though widespread in soils and rhizospheres, has been relatively unexplored despite its ubiquity. Previously acknowledged as a common soil bacterium, our research explores its phylogenomics, pangenomics, environmental diversity, and interactions within bacterial communities. By analysing seven genomic sequences, we have identified...
Article
Full-text available
Arid zones contain a diverse set of microbes capable of survival under dry conditions, some of which can form relationships with plants under drought stress conditions to improve plant health. We studied squash (Cucurbita pepo L.) root microbiome under historically arid and humid sites, both in situ and performing a common garden experiment. Plants...
Article
Full-text available
Mining operations often generate tailing dams that contain toxic residues and are a source of contamination when left unconfined. The establishment of a plant community over the tailings has been proposed as a containment strategy known as phytostabilization. Previously, we described naturally occurring mine tailing colonizing plants such as Acacia...
Article
Full-text available
The two-step model for plant root microbiomes considers soil as the primary microbial source. Active selection of the plant’s bacterial inhabitants results in a biodiversity decrease toward roots. We collected sixteen samples of in situ ruderal plant roots and their soils and used these soils as the main microbial input for single genotype tomatoes...
Article
Full-text available
The production of traditional agave spirits in Mexico, such as mezcal, involves a process that uses environmental microorganisms to ferment the cooked must from agave plants. By analysing these microorganisms, researchers can understand the dynamics of microbial communities at the interface of natural and human‐associated environments. This study i...
Article
Full-text available
La microbiología ambiental no es nueva, inició desde finales del siglo XIX, la novedad es la secuenciación masiva a principios del siglo XXI en el campo, revelándonos la vasta diversidad bacteriana que aún desconocemos. Enfatizamos la importancia de estudiar los microbiomas en estados de salud y cómo podemos explorar aspectos cruciales de la intera...
Preprint
Full-text available
Studies have shown that reduced nutrient availability enhances microbial diversity around plant roots, positively impacting plant productivity. However, the specific contributions of rhizosphere microbiomes in nutrient-poor environments still need to be better understood. This study investigates the role of Plant Growth-Promoting Rhizobacteria (PGP...
Article
Full-text available
The mosquito Aedes spp. holds important relevance for human and animal health, as it serves as a vector for transmitting multiple diseases, including dengue and Zika virus. The microbiome’s impact on its host’s health and fitness is well known. However, most studies on mosquito microbiomes have been conducted in laboratory settings. We explored the...
Preprint
Full-text available
The production of traditional agave spirits in Mexico is a deeply rooted traditional process that relies on environmental microorganisms to ferment the cooked must from agave plants. Analysis of these microorganisms provides the opportunity to understand the dynamics of the microbial communities in the interface of natural and human-associated envi...
Article
Full-text available
Due to the enormous diversity of non-culturable viruses, new viruses must be characterized using culture-independent techniques. The associated host is an important phenotypic feature that can be inferred from metagenomic viral contigs thanks to the development of several bioinformatic tools. Here, we compare the performance of recently developed v...
Preprint
Full-text available
Solirubrobacter , a genus within the Actinobacteriota phylum, is commonly found in soils and rhizospheres yet remains unexplored despite its widespread presence and diversity, as revealed through metagenomic studies. Previously recognized as a prevalent soil bacterium, our study delved into phylogenomics, pangenomics, environmental diversity, and b...
Preprint
Full-text available
The sheer diversity of unculturable viruses has prompted the need to describe new viruses through culture-independent techniques. The associated host is one important phenotypic feature that can be inferred from metagenomic viral contigs -- thanks to the development of various bioinformatic tools. Here we compare the performance of recently develop...
Article
Full-text available
Biofertilizers supply living microorganisms to help plants grow and keep their health. This study examines the microbiome composition of a commercial biofertilizer known for its plant growth-promoting activity. Using ITS and 16S rRNA gene sequence analyses, we describe the microbial communities of a biofertilizer, with 163 fungal species and 485 ba...
Article
Full-text available
Social cheating is the exploitation of public goods that are costly metabolites, like exoproteases. Exoprotease exploitation in Pseudomonas aeruginosa has been studied in reference strains. Experimental evolution with reference strains during continuous growth in casein has demonstrated that non-exoprotease producers that are lasR mutants are selec...
Article
Full-text available
Buffelgrass (Pennisetum ciliare) is an invasive plant introduced into Mexico’s Sonoran desert for cattle grazing and has converted large areas of native thorn scrub. One of the invasion mechanisms buffelgrass uses to invade is allelopathy, which consists of the production and secretion of allelochemicals that exert adverse effects on other plants’...
Preprint
Full-text available
Biofertilizers supply living microorganisms to help plants grow and maintain their health. In this study, we examine the microbiome composition of a commercial biofertilizer that has been proven to promote plant growth. Using ITS and 16S rRNA gene sequence analyses, we describe the microbial communities of the biofertilizer, with 182 fungal species...
Article
Full-text available
Introduction Recent studies have revealed the presence of N-acyl-homoserine lactones (AHLs) quorum sensing (QS) signals in the oral environment. Yet, their role in oral biofilm development remains scarcely investigated. The use of quorum quenching (QQ) strategies targeting AHLs has been described as efficient for the control of pathogenic biofilms....
Data
Table S1. Yeasts isolated from extreme environmental conditions. Table S2. Isolation of yeasts that inhabit extreme environments using different media and parameters.
Article
Full-text available
Yeasts are microscopic fungi inhabiting all Earth environments, including those inhospitable for most life forms, considered extreme environments. According to their habitats, yeasts could be extremotolerant or extremophiles. Some are polyextremophiles, depending on their growth capacity, tolerance, and survival in the face of their habitat’s physi...
Article
Full-text available
Subways are urban transport systems with high capacity. Every day around the world, there are more than 150 million subway passengers. Since 2013, thousands of microbiome samples from various subways worldwide have been sequenced. Skin bacteria and environmental organisms dominate the subway microbiomes. The literature has revealed common bacterial...
Article
Full-text available
Buffelgrass (Pennisetum ciliare) is an invasive plant introduced into Mexico’s Sonoran desert for cattle grazing and has converted large areas of native thorn scrub. One of the invasion mechanisms buffelgrass uses to invade is allelopathy, which consists of the production and secretion of allelochemicals that exert adverse effects on other plants’...
Preprint
Full-text available
Arid zones contain a diverse set of microbes capable of survival under dry conditions, some of which can form relationships with plants under drought stress conditions to improve plant health. We studied squash (Cucurbita pepo L.) root microbiome under historically arid and humid sites, both in situ and performing a common garden experiment. Plants...
Article
Full-text available
Metagenomic and traditional paleolimnological approaches are suitable to infer past biological and environmental changes, however, they are often applied independently, especially in tropical regions. We combined both approaches to investigate Holocene Prokaryote and Eukaryote diversity and microbial metabolic pathways in ancient Lake Chalco, Mexic...
Preprint
Full-text available
Neobuxbaumia tetetzo , commonly known as tetecho, is a columnar cactus endemic to Mexico. In the last 15 years, damage has been observed in young and adult plants of N. tetetzo , ranging from chlorotic spots with a wet appearance in early stages to tissue necrosis in advanced stages and finally the death of the plant; Pectobacterium brasiliense is...
Article
The biggest non-tree perennial plant species endemic to Mexico were called metl in the Nahua culture; during colonial times, renamed with the Antillean word maguey. Carl von Linné finally renamed them as Agave, a Greek-Latin root word meaning admirable. Since pre-Columbian times, one of the major products obtained from some Agave species is the fer...
Article
Full-text available
Interaction between hands and the environment permits the interchange of microorganisms. The Mexico City subway is used daily by millions of passengers that get in contact with its surfaces. In this study, we used 16S rRNA gene sequencing to characterize the microbiomes of frequently touched surfaces and compare regular and women-only wagons. We al...
Article
Full-text available
The vaginal microbiota of healthy women typically has low diversity, which increases after perturbations. Among these, lifestyle associated with certain sexual and antimicrobial practices may be associated with higher diversity. To test this hypothesis, we characterized the vaginal microbiota in the cervicovaginal and introital sites in sexually ac...
Article
Full-text available
The metro is one of the more representative urban transportation systems of Mexico City, and it transports approximately 4.5 million commuters every day. Large crowds promote the exchange of microbes between humans. In this study, we determined the bacterial diversity profile of the Mexico City metro by massive sequencing of the 16S rRNA gene. We i...
Preprint
Full-text available
Interaction between hands and the environment permits the interchange of microorganisms. The Mexico City subway is used daily by millions of passengers that get in contact with its surfaces. In this study, we used 16S rRNA gene sequencing to characterize the microbiomes of frequently touched surfaces, also comparing regular and women-only wagons. W...
Article
Full-text available
Irritable bowel syndrome (IBS) is the most frequent functional gastrointestinal disorder, worldwide, with a high prevalence among Mestizo Latin Americans. Because several inflammatory disorders appear to affect this population, a further understanding of host genomic background variants, in conjunction with colonic mucosa dysbiosis, is necessary to...
Preprint
Full-text available
The two-step model for plant root microbiomes considers soil as the primary microbial source. Active selection of the plant's bacterial inhabitants results in a biodiversity decrease towards roots. We collected in situ ruderal plant roots and their soils and used these soils as the main microbial input for single genotype tomatoes grown in a greenh...
Article
Full-text available
Several universal genomic traits affect trade-offs in the capacity, cost, and efficiency of the biochemical information processing that underpins metabolism and reproduction. We analyzed the role of these traits in mediating the responses of a planktonic microbial community to nutrient enrichment in an oligotrophic, phosphorus-deficient pond in Cua...
Preprint
Full-text available
The metro is one of the more representative urban systems of Mexico City, and it transports approximately 4.5 million commuters every day. Large crowds promote the constant exchange of human and environmental microbes. In this study, we determined the bacterial diversity profile of the Mexico City subway by massive sequencing of the 16S rRNA gene....
Preprint
Full-text available
Several universal genomic traits affect the capacity, cost, and efficiency of biochemical information processing underpinning metabolism and reproduction. We analyzed their role in mediating planktonic microbial community responses to nutrient enrichment in an oligotrophic, phosphorus-deficient pond in Cuatro Cienegas, Mexico - one of the first who...
Preprint
Some of the biggest non-three plants endemic to Mexico were called metl in the Nahua culture. During colonial times they were renamed with the antillan word maguey . This was changed again by Carl von Linné who called them Agave (a greco-latin voice for admirable). For several Mexican prehispanic cultures, Agave species were not only considered as...
Article
Pseudomonas aeruginosa is a metabolically versatile bacterium and also an important opportunistic pathogen. It has a remarkable genomic structure since the genetic information encoding its pathogenicity-related traits belongs to its core-genome while both environmental and clinical isolates are part of the same population with a highly conserved ge...
Preprint
Full-text available
Mine tailings phytostabilization has been proposed as a bioremediation strategy to constrain the contaminants dispersion using plants to limit the effects of erosion. Rhizospheric bacteria impact plant health and facilitate plant establishment through their metabolic functions, which could be relevant in bioremediation strategies. We studied both c...
Article
Full-text available
A weekly conference series paired with lectures entitled "Microbiome-MX: exploring the Microbiota and Microbiome Research in Mexico" was organized to provide a multidisciplinary overview of the most recent research done in Mexico using high-throughput sequencing. Scientists and postgraduate students from several disciplines such as microbiology, bi...
Article
Full-text available
Background The Streptococcus genus is relevant to both public health and food safety because of its ability to cause pathogenic infections. It is well-represented (>100 genomes) in publicly available databases. Streptococci are ubiquitous, with multiple sources of isolation, from human pathogens to dairy products. The Streptococcus genus has tradit...
Article
Full-text available
Barriers to microbial migrations can lead adaptive radiations and increased endemism. We propose that extreme unbalanced nutrient stoichiometry of essential nutrients can be a barrier to microbial immigration over geological timescales. At the oasis in the Cuatro Ciénegas Basin in Mexico, nutrient stoichiometric proportions are skewed given the low...
Chapter
To understand microbial life and get the full picture, we ought to zoom out in order to grasp its magnitud and diversity and zoom in to dissect their genes and functions. We have obtained a significant amount of data on the great diversity of bacteria in the different environments of the Cuatro Ciénegas Basin (CCB), equivalent to obtaining the cens...
Article
Obesity is a metabolic disorder and global health issue. In Mexico 4.4% of children between 5 and 11 years-old are overweight or obese. Here we address this issue studying the gut microbiome in a sample of Mexican children affected by obesity. We performed metagenomic shotgun-sequencing of DNA isolated from fecal samples from a cohort of normal we...
Article
Full-text available
Microbiomes influence plant establishment, development, nutrient acquisition, pathogen defense, and health. Plant microbiomes are shaped by interactions between the microbes and a selection process of host plants that distinguishes between pathogens, commensals, symbionts and transient bacteria. In this work, we explore the microbiomes through mass...
Article
Full-text available
Microbiomes influence plant establishment, development, nutrient acquisition, pathogen defense, and health. Plant microbiomes are shaped by interactions between the microbes and a selection process of host plants that distinguishes between pathogens, commensals, symbionts and transient bacteria. In this work, we explore the microbiomes through mass...
Article
Full-text available
The definition of bacterial essential genes has been widely pursued using different approaches. Their study has impacted several fields of research such as synthetic biology, the construction of bacteria with minimal chromosomes, the search for new antibiotic targets, or the design of strains with biotechnological applications. Bacterial genomes ar...
Preprint
Full-text available
Background. Comparative genomics between closely related bacterial strains can distinguish important features determining pathogenesis, antibiotic resistance, and phylogenetic structure. The Streptococcus genus is relevant to public health and food safety and it is well-represented (>100 genomes) in databases of publicly available databases. Strept...
Preprint
Background. Comparative genomics between closely related bacterial strains can distinguish important features determining pathogenesis, antibiotic resistance, and phylogenetic structure. The Streptococcus genus is relevant to public health and food safety and it is well-represented (>100 genomes) in databases of publicly available databases. Strept...
Article
Full-text available
Human papillomavirus (HPV), an etiological agent of cervical cancer (CC), has infected humans since ancient times. Amerindians are the furthest migrants out of Africa, and they reached the Americas more than 14,000 years ago. Some groups still remain isolated, and some migrate to towns, forming a gradient spanning urbanization. We hypothesized that...
Preprint
Barriers to immigration can lead to localized adaptive radiations and increased endemism. We propose that extreme oligotrophy can be a strong barrier to immigration over geological timescales, and facilitate the evolution of diverse and coevolved microbial communities. We show here that the endangered oasis of Cuatro Cienegas Basin can be a model f...
Article
Full-text available
We assembled the complete genome sequences of Bacillus pumilus strains 145 and 150a from Cuatrociénegas, Mexico. We detected genes codifying for proteins potentially involved in antagonism (bacteriocins) and defense mechanisms (abortive infection bacteriophage proteins and 4-azaleucine resistance). Both strains harbored prophage sequences. Our resu...
Article
Full-text available
The geothermal system of the Araró region, located in the Trans-Mexican Volcanic Belt of México, hosts various hot springs with unique physicochemical characteristics, including temperatures ranging from 45°C to 78°C. The microbial diversity in these hot springs has been explored only by culture-dependent surveys. In this study, we performed metage...
Preprint
Full-text available
Background . Comparative genomics between closely related bacterial strains aids to distinguish important features like pathogenesis, antibiotic resistance, and phylogenetic structure. Streptococcus is relevant because public health and food safety and it are well-represented (>100 genomes ) in databases of publicly available databases. Streptococc...
Article
Full-text available
The milpa is a traditional maize-based polyculture in Mexico that is typically practiced as rainfed agriculture. Because milpa cultivation has been practiced over a vast range of environmental and cultural conditions, this agroecosystem is recognized as an important repository of biological and cultural diversity. As for any agroecosystem, the rela...
Article
Full-text available
Sugarcane is one of the most important crops worldwide and is a key plant for the global production of sucrose. Sugarcane cultivation is severely affected by drought stress and it is considered as the major limiting factor for their productivity. In recent years, this plant has been subjected to intensive research focused on improving its resilienc...
Data
List of sugarcane genes and primers used for the RT-qPCR validation. (PDF)
Data
Pearson's correlation analysis among replicates of each biological sample. (PDF)
Data
Unigenes found against the Kyoto Encyclopedia of Genes and Genomes (KEGG) biochemical pathways. (XLSX)
Data
RT-qPCR analysis of five significatively regulated genes randomly selected into the osmotic stress treatments. (PDF)
Data
Original KEGG map used for depict the starch and sucrose metabolism genes in Fig 3. (PNG)
Article
Full-text available
Four extensively drug-resistant Pseudomonas aeruginosa strains, isolated from patients with pneumonia, were sequenced using PacBio RS-II single-molecule real-time (SMRT) technology. Genome sequence analysis identified great variability among mobile genetic elements, as well as some previously undescribed genomic islands and new variants of class 1...
Article
Full-text available
Two Pseudomonas aeruginosa strains isolated from children with bacteremia in Mexico City were sequenced using PacBio RS-II single-molecule real-time (SMRT) technology. The strains consist of a 7.0- to 7.4-Mb chromosome, with a high content of mobile elements, and variation in the genetic content of class 1 integron In1409.
Article
Full-text available
We sequenced the Bacillus horikoshii 20a genome, isolated from sediment collected in Cuatro Cienegas, Mexico. We identified genes involved in establishing antagonistic interactions in microbial communities (antibiotic resistance and bacteriocins) and genes related to the metabolism of cyanophycin, a reserve compound and spore matrix material potent...
Article
Full-text available
One of the best-studied transcriptional regulatory proteins in bacteria is the Escherichia coli catabolite repressor protein (CRP) that when complexed with 3′-5′-cyclic AMP (cAMP) changes its conformation and interacts with specific DNA-sequences. CRP DNA-binding can result in positive or negative regulation of gene expression depending on the posi...
Article
Full-text available
Phytostabilization is a remediation technology that uses plants for in-situ stabilization of contamination in soils and mine tailings. The objective of this study was to identify native plant species with potential for phytostabilization of the abandoned mine tailings in Nacozari, Sonora in northern Mexico. A flora of 42 species in 16 families of a...
Data
Raw data on the plants from the Nacozari tailings Raw data on the abundance of perennial and annual plant species, physicochemical properties of tailings, growth of Amaranthus watsonii and Prosopis velutina and metal concentration in rhizosphere and leaves of plants growing in the Nacozari tailings.
Article
Full-text available
Las bacterias son clave en el ambiente, comenzando por la importancia de las mismas interacciones entre ellas, hasta el hecho de que sean las responsables de los ciclos biogeoquímicos del planeta. El estudio de la diversidad microbiológica, mediante herramientas genómicas, nos permite identificar genes clave involucrados en interacciones biológicas...
Article
Full-text available
Background Cockatiels ( Nymphicus hollandicus ) were originally endemic to Australia; now, they are popular pets with a global distribution. It is now possible to conduct detailed molecular studies on cultivable and uncultivable bacteria that are part of the intestinal microbiome of healthy animals. These studies show that bacteria are an essential...
Data
CatchAll and breakaway diversity estimations
Data
Multiple ordinations on avian microbiomes
Article
Full-text available
Background. Cockatiels (Nymphicus hollandicus) were originally endemic to Australia, but they are nowadays popular worldwide pet birds. It is now possible to make detailed molecular studies on cultivable and uncultivable bacteria that are part of the intestinal microbiome of healthy animals, these studies showed that bacteria are an essential part...
Article
Full-text available
Background. Cockatiels (Nymphicus hollandicus) were originally endemic to Australia, but they are nowadays popular worldwide pet birds. It is now possible to make detailed molecular studies on cultivable and uncultivable bacteria that are part of the intestinal microbiome of healthy animals, these studies showed that bacteria are an essential part...
Chapter
Full-text available
Recent technological development in high throughput DNA sequencing has opened many venues for biological systems analysis, where the data generation is no longer the bottleneck but its analysis. The sequencing technological advancements are being used in the study of a large and previously unknown microbe world; this unknown world has revealed itse...
Article
Full-text available
The ethylene-responsive element-binding factors AP2/ERF compose one of the largest families of transcription factors in plants. Dreb2-type gene from Carica papaya L. cv. Maradol was found to be a member of the AP2/ERF family and contains a conserved APETALA 2 (AP2) domain located within the group IV of the AP2/ERF superfamily. CpDreb2-type gene is...
Article
Full-text available
The genome and transcriptome sequences of the aquatic, rootless, and carnivorous plant Utricularia gibba L. (Lentibulariaceae), were recently determined. Traps are necessary for U. gibba because they help the plant to survive in nutrient-deprived environments. The U. gibba's traps (Ugt) are specialized structures that have been proposed to selectiv...
Data
The Lowest Common Ancestor profile for the raw Ugt data set, the size of the circle is proportional to the number of sequences assigned. (PDF)
Data
Kegg Ortholog annotation for U. gibba, Ugt, and Ugm. (XLS)
Data
Heat-map showing the 16S rRNA profiles for Ugt, Ugm and the comparative microbiomes. (PDF)
Data
Heat-map showing LCA profiles for Ugt, Ugm and the comparative microbiomes. (PDF)
Data
Pan-genome recruitments for both Ugt and Ugm. It shows the reference pan-genome, its query length, coverage, and average identity of the overall alignment. (XLS)
Data
Taxonomy summary of best hits in the M5RNA DB for Ugt. (XLS)
Data
Structural 16S rRNA profiles for Archaea, Eukarya, and Bacteria for the unfiltered Ugt data set. (PDF)

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