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Article: Human Gut Microbiome Across Different Lifestyles: From Hunter-Gatherers to Urban Populations.

Rosas-Plaza, Santiago / Hernández-Terán, Alejandra / Navarro-Díaz, Marcelo / Escalante, Ana E / Morales-Espinosa, Rosario / Cerritos, René

Frontiers in microbiology

2022 Volume 13, Page(s) 843170

Abstract: Human lifestyle and its relationship with the human microbiome has been a line of research widely studied. This is because, throughout human history, civilizations have experienced different environments and lifestyles that could have promoted changes in ...

Abstract	Human lifestyle and its relationship with the human microbiome has been a line of research widely studied. This is because, throughout human history, civilizations have experienced different environments and lifestyles that could have promoted changes in the human microbiome. The comparison between industrialized and non-industrialized human populations in several studies has allowed to observe variation in the microbiome structure due to the population lifestyle. Nevertheless, the lifestyle of human populations is a gradient where several subcategories can be described. Yet, it is not known how these different lifestyles of human populations affect the microbiome structure on a large scale. Therefore, the main goal of this work was the collection and comparison of 16S data from the gut microbiome of populations that have different lifestyles around the world. With the data obtained from 14 studies, it was possible to compare the gut microbiome of 568 individuals that represent populations of hunter-gatherers, agricultural, agropastoral, pastoral, and urban populations. Results showed that industrialized populations present less diversity than those from non-industrialized populations, as has been described before. However, by separating traditional populations into different categories, we were able to observe patterns that cannot be appreciated by encompassing the different traditional lifestyles in a single category. In this sense, we could confirm that different lifestyles exhibit distinct alpha and beta diversity. In particular, the gut microbiome of pastoral and agropastoral populations seems to be more similar to those of urban populations according to beta diversity analysis. Beyond that, beta diversity analyses revealed that bacterial composition reflects the different lifestyles, representing a transition from hunters-gatherers to industrialized populations. Also, we found that certain groups such as
Language	English
Publishing date	2022-04-26
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2587354-4
ISSN	1664-302X
ISSN	1664-302X
DOI	10.3389/fmicb.2022.843170
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Article ; Online: Laboratory biases hinder Eco-Evo-Devo integration: Hints from the microbial world.

Rivera-Yoshida, Natsuko / Hernández-Terán, Alejandra / Escalante, Ana E / Benítez, Mariana

Journal of experimental zoology. Part B, Molecular and developmental evolution

2019 Volume 334, Issue 1, Page(s) 14–24

Abstract: How specific environmental contexts contribute to the robustness and variation of developmental trajectories and evolutionary transitions is a central point in Ecological Evolutionary Developmental Biology ("Eco-Evo-Devo"). However, the articulation of ... ...

Abstract	How specific environmental contexts contribute to the robustness and variation of developmental trajectories and evolutionary transitions is a central point in Ecological Evolutionary Developmental Biology ("Eco-Evo-Devo"). However, the articulation of ecological, evolutionary and developmental processes into integrative frameworks has been elusive, partly because standard experimental designs neglect or oversimplify ecologically meaningful contexts. Microbial models are useful to expose and discuss two possible sources of bias associated with conventional gene-centered experimental designs: the use of laboratory strains and standard laboratory environmental conditions. We illustrate our point by showing how contrasting developmental phenotypes in Myxococcus xanthus depend on the joint variation of temperature and substrate stiffness. Microorganismal development can provide key information for better understanding the role of environmental conditions in the evolution of developmental variation, and to overcome some of the limitations associated with current experimental approaches.
MeSH term(s)	Bias ; Biological Evolution ; Ecosystem ; Models, Biological ; Myxococcus xanthus/genetics ; Myxococcus xanthus/growth & development ; Research Design
Language	English
Publishing date	2019-11-14
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2103823-5
ISSN	1552-5015 ; 0022-104X ; 1552-5007
ISSN (online)	1552-5015
ISSN	0022-104X ; 1552-5007
DOI	10.1002/jez.b.22917
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Article ; Online: Microbiota composition in the lower respiratory tract is associated with severity in patients with acute respiratory distress by influenza

Hernández-Terán, Alejandra / Vega-Sánchez, Angel E. / Mejía-Nepomuceno, Fidencio / Serna-Muñoz, Ricardo / Rodríguez-Llamazares, Sebastián / Salido-Guadarrama, Iván / Romero-Espinoza, Jose A. / Guadarrama-Pérez, Cristobal / Sandoval-Gutierrez, Jose L. / Campos, Fernando / Mondragón-Rivero, Erika N. / Ramírez-Venegas, Alejandra / Castillejos-López, Manuel / Téllez-Navarrete, Norma A. / Pérez Padilla, Rogelio / Vázquez-Pérez, Joel A.

Virol J. 2023 Dec., v. 20, no. 1 p.19-19

2023

Abstract: Several factors are associated with the severity of the respiratory disease caused by the influenza virus. Although viral factors are one of the most studied, in recent years the role of the microbiota and co-infections in severe and fatal outcomes has ... ...

Abstract	Several factors are associated with the severity of the respiratory disease caused by the influenza virus. Although viral factors are one of the most studied, in recent years the role of the microbiota and co-infections in severe and fatal outcomes has been recognized. However, most of the work has focused on the microbiota of the upper respiratory tract (URT), hindering potential insights from the lower respiratory tract (LRT) that may help to understand the role of the microbiota in Influenza disease. In this work, we characterized the microbiota of the LRT of patients with Influenza A using 16S rRNA sequencing. We tested if patients with different outcomes (deceased/recovered) and use of antibiotics differ in their microbial community composition. We found important differences in the diversity and composition of the microbiota between deceased and recovered patients. In particular, we detected a high abundance of opportunistic pathogens such as Granulicatella, in patients either deceased or with antibiotic treatment. Also, we found antibiotic treatment correlated with lower diversity of microbial communities and with lower probability of survival in Influenza A patients. Altogether, the loss of microbial diversity could generate a disequilibrium in the community, potentially compromising the immune response increasing viral infectivity, promoting the growth of potentially pathogenic bacteria that, together with altered biochemical parameters, can be leading to severe forms of the disease. Overall, the present study gives one of the first characterizations of the diversity and composition of microbial communities in the LRT of Influenza patients and its relationship with clinical variables and disease severity.
Keywords	Granulicatella ; Orthomyxoviridae ; antibiotics ; community structure ; disease severity ; distress ; immune response ; influenza ; microbial communities ; microorganisms ; pathogenicity ; probability ; respiratory system
Language	English
Dates of publication	2023-12
Size	p. 19.
Publishing place	BioMed Central
Document type	Article ; Online
ZDB-ID	2160640-7
ISSN	1743-422X
ISSN	1743-422X
DOI	10.1186/s12985-023-01979-3
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Article ; Online: Microbiota composition in the lower respiratory tract is associated with severity in patients with acute respiratory distress by influenza.

Hernández-Terán, Alejandra / Vega-Sánchez, Angel E / Mejía-Nepomuceno, Fidencio / Serna-Muñoz, Ricardo / Rodríguez-Llamazares, Sebastián / Salido-Guadarrama, Iván / Romero-Espinoza, Jose A / Guadarrama-Pérez, Cristobal / Sandoval-Gutierrez, Jose L / Campos, Fernando / Mondragón-Rivero, Erika N / Ramírez-Venegas, Alejandra / Castillejos-López, Manuel / Téllez-Navarrete, Norma A / Pérez-Padilla, Rogelio / Vázquez-Pérez, Joel A

Virology journal

2023 Volume 20, Issue 1, Page(s) 19

Abstract	Several factors are associated with the severity of the respiratory disease caused by the influenza virus. Although viral factors are one of the most studied, in recent years the role of the microbiota and co-infections in severe and fatal outcomes has been recognized. However, most of the work has focused on the microbiota of the upper respiratory tract (URT), hindering potential insights from the lower respiratory tract (LRT) that may help to understand the role of the microbiota in Influenza disease. In this work, we characterized the microbiota of the LRT of patients with Influenza A using 16S rRNA sequencing. We tested if patients with different outcomes (deceased/recovered) and use of antibiotics differ in their microbial community composition. We found important differences in the diversity and composition of the microbiota between deceased and recovered patients. In particular, we detected a high abundance of opportunistic pathogens such as Granulicatella, in patients either deceased or with antibiotic treatment. Also, we found antibiotic treatment correlated with lower diversity of microbial communities and with lower probability of survival in Influenza A patients. Altogether, the loss of microbial diversity could generate a disequilibrium in the community, potentially compromising the immune response increasing viral infectivity, promoting the growth of potentially pathogenic bacteria that, together with altered biochemical parameters, can be leading to severe forms of the disease. Overall, the present study gives one of the first characterizations of the diversity and composition of microbial communities in the LRT of Influenza patients and its relationship with clinical variables and disease severity.
MeSH term(s)	Humans ; Influenza, Human/genetics ; Influenza, Human/microbiology ; Influenza, Human/virology ; Microbiota/genetics ; Nose ; Respiratory Distress Syndrome ; Respiratory System/microbiology ; RNA, Ribosomal, 16S/genetics
Chemical Substances	RNA, Ribosomal, 16S
Language	English
Publishing date	2023-02-01
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2160640-7
ISSN	1743-422X ; 1743-422X
ISSN (online)	1743-422X
ISSN	1743-422X
DOI	10.1186/s12985-023-01979-3
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Article ; Online: Host genotype explains rhizospheric microbial community composition: the case of wild cotton metapopulations (Gossypium hirsutum L.) in Mexico.

Hernández-Terán, Alejandra / Navarro-Díaz, Marcelo / Benítez, Mariana / Lira, Rafael / Wegier, Ana / Escalante, Ana E

FEMS microbiology ecology

2020 Volume 96, Issue 8

Abstract: The rhizosphere provides several benefits to the plant host being a strong determinant for its health, growth and productivity. Nonetheless, the factors behind the assembly of the microbial communities associated with the rhizosphere such as the role of ... ...

Abstract	The rhizosphere provides several benefits to the plant host being a strong determinant for its health, growth and productivity. Nonetheless, the factors behind the assembly of the microbial communities associated with the rhizosphere such as the role of plant genotypes are not completely understood. In this study, we tested the role that intraspecific genetic variation has in rhizospheric microbial community assemblages, using genetically distinct wild cotton populations as a model of study. We followed a common garden experiment including five wild cotton populations, controlling for plant genotypes, environmental conditions and soil microbial community inoculum, to test for microbial differences associated with genetic variation of the plant hosts. Microbial communities of the treatments were characterized by culture-independent 16S rRNA gene amplicon sequencing with Illumina MiSeq platform. We analyzed microbial community diversity (alpha and beta), and diversity structure of such communities, determined by co-occurrence networks. Results show that different plant genotypes select for different and specific microbial communities from a common inoculum. Although we found common amplicon sequence variants (ASVs) to all plant populations (235), we also found unique ASVs for different populations that could be related to potential functional role of such ASVs in the rhizosphere.
MeSH term(s)	Bacteria/genetics ; Genotype ; Gossypium ; Mexico ; Microbiota ; Plant Roots ; RNA, Ribosomal, 16S/genetics ; Rhizosphere ; Soil ; Soil Microbiology
Chemical Substances	RNA, Ribosomal, 16S ; Soil
Language	English
Publishing date	2020-06-03
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	283722-5
ISSN	1574-6941 ; 0168-6496
ISSN (online)	1574-6941
ISSN	0168-6496
DOI	10.1093/femsec/fiaa109
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Article: In vitro

Hernández-Terán, Alejandra / Wegier, Ana / Benítez, Mariana / Lira, Rafael / Sosa Fuentes, Tania Gabriela / Escalante, Ana E

PeerJ

2019 Volume 7, Page(s) e7017

Abstract: One of the ... ...

Abstract	One of the best
Language	English
Publishing date	2019-06-10
Publishing country	United States
Document type	Journal Article
ZDB-ID	2703241-3
ISSN	2167-8359
ISSN	2167-8359
DOI	10.7717/peerj.7017
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Article ; Online: Bioconversion of Lignocellulosic Biomass into Value Added Products under Anaerobic Conditions: Insight into Proteomic Studies.

Vélez-Mercado, Martha Inés / Talavera-Caro, Alicia Guadalupe / Escobedo-Uribe, Karla María / Sánchez-Muñoz, Salvador / Luévanos-Escareño, Miriam Paulina / Hernández-Terán, Fernando / Alvarado, Alejandra / Balagurusamy, Nagamani

International journal of molecular sciences

2021 Volume 22, Issue 22

Abstract: Production of biofuels and other value-added products from lignocellulose breakdown requires the coordinated metabolic activity of varied microorganisms. The increasing global demand for biofuels encourages the development and optimization of production ... ...

Abstract	Production of biofuels and other value-added products from lignocellulose breakdown requires the coordinated metabolic activity of varied microorganisms. The increasing global demand for biofuels encourages the development and optimization of production strategies. Optimization in turn requires a thorough understanding of the microbial mechanisms and metabolic pathways behind the formation of each product of interest. Hydrolysis of lignocellulosic biomass is a bottleneck in its industrial use and often affects yield efficiency. The accessibility of the biomass to the microorganisms is the key to the release of sugars that are then taken up as substrates and subsequently transformed into the desired products. While the effects of different metabolic intermediates in the overall production of biofuel and other relevant products have been studied, the role of proteins and their activity under anaerobic conditions has not been widely explored. Shifts in enzyme production may inform the state of the microorganisms involved; thus, acquiring insights into the protein production and enzyme activity could be an effective resource to optimize production strategies. The application of proteomic analysis is currently a promising strategy in this area. This review deals on the aspects of enzymes and proteomics of bioprocesses of biofuels production using lignocellulosic biomass as substrate.
MeSH term(s)	Anaerobiosis ; Bacteria, Anaerobic/classification ; Bacteria, Anaerobic/enzymology ; Bacteria, Anaerobic/metabolism ; Biofuels/microbiology ; Biomass ; Cellulases/metabolism ; Hydrolysis ; Lignin/metabolism ; Oxygenases/metabolism ; Proteome/metabolism ; Proteomics/methods
Chemical Substances	Biofuels ; Proteome ; lignocellulose (11132-73-3) ; Lignin (9005-53-2) ; Oxygenases (EC 1.13.-) ; ligninase (EC 1.14.99.-) ; Cellulases (EC 3.2.1.-)
Language	English
Publishing date	2021-11-12
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms222212249
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Article ; Online: Soil microbial composition and carbon mineralization are associated with vegetation type and temperature regime in mesocosms of a semiarid ecosystem.

Avitia, Morena / Barrón-Sandoval, Alberto / Hernández-Terán, Alejandra / Benítez, Mariana / Barron-Gafford, Greg A / Dontsova, Katerina / Pavao-Zuckerman, Mitchell A / Escalante, Ana E

FEMS microbiology letters

2021 Volume 368, Issue 4

Abstract: Transition from historic grasslands to woody plants in semiarid regions has led to questions about impacts on soil functioning, where microorganisms play a primary role. Understanding the relationship between microbes, plant diversity and soil ... ...

Abstract	Transition from historic grasslands to woody plants in semiarid regions has led to questions about impacts on soil functioning, where microorganisms play a primary role. Understanding the relationship between microbes, plant diversity and soil functioning is relevant to assess such impacts. We evaluate the effect that plant type change in semiarid ecosystems has for microbial diversity and composition, and how this is related to carbon mineralization (CMIN) as a proxy for soil functioning. We followed a mesocosm experiment during 2 years within the Biosphere 2 facility in Oracle, AZ, USA. Two temperature regimes were established with two types of plants (grass or mesquite). Soil samples were analyzed for physicochemical and functional parameters, as well as microbial community composition using 16S rRNA amplicon metagenomics (Illumina MiSeq). Our results show the combined role of plant type and temperature regime in CMIN, where CMIN in grass has lower values at elevated temperatures compared with the opposite trend in mesquite. We also found a strong correlation of microbial composition with plant type but not with temperature regime. Overall, we provide evidence of the major effect of plant type in the specific composition of microbial communities as a potential result of the shrub encroachment.
MeSH term(s)	Carbon/analysis ; Carbon/metabolism ; Ecosystem ; Microbiota ; Plants/classification ; Plants/metabolism ; Plants/microbiology ; Soil/chemistry ; Soil Microbiology ; Temperature
Chemical Substances	Soil ; Carbon (7440-44-0)
Language	English
Publishing date	2021-02-05
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	752343-9
ISSN	1574-6968 ; 0378-1097
ISSN (online)	1574-6968
ISSN	0378-1097
DOI	10.1093/femsle/fnab012
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Article: Domesticated, Genetically Engineered, and Wild Plant Relatives Exhibit Unintended Phenotypic Differences: A Comparative Meta-Analysis Profiling Rice, Canola, Maize, Sunflower, and Pumpkin.

Hernández-Terán, Alejandra / Wegier, Ana / Benítez, Mariana / Lira, Rafael / Escalante, Ana E

Frontiers in plant science

2017 Volume 8, Page(s) 2030

Abstract: Agronomic management of plants is a powerful evolutionary force acting on their populations. The management of cultivated plants is carried out by the traditional process of human selection or plant breeding and, more recently, by the technologies used ... ...

Abstract	Agronomic management of plants is a powerful evolutionary force acting on their populations. The management of cultivated plants is carried out by the traditional process of human selection or plant breeding and, more recently, by the technologies used in genetic engineering (GE). Even though crop modification through GE is aimed at specific traits, it is possible that other non-target traits can be affected by genetic modification due to the complex regulatory processes of plant metabolism and development. In this study, we conducted a meta-analysis profiling the phenotypic consequences of plant breeding and GE, and compared modified cultivars with wild relatives in five crops of global economic and cultural importance: rice, maize, canola, sunflower, and pumpkin. For these five species, we analyzed the literature with documentation of phenotypic traits that are potentially related to fitness for the same species in comparable conditions. The information was analyzed to evaluate whether the different processes of modification had influenced the phenotype in such a way as to cause statistical differences in the state of specific phenotypic traits or grouping of the organisms depending on their genetic origin [wild, domesticated with genetic engineering (domGE), and domesticated without genetic engineering (domNGE)]. In addition, we tested the hypothesis that, given that transgenic plants are a construct designed to impact, in many cases, a single trait of the plant (e.g., lepidopteran resistance), the phenotypic differences between domGE and domNGE would be either less (or inexistent) than between the wild and domesticated relatives (either domGE or domNGE). We conclude that (1) genetic modification (either by selective breeding or GE) can be traced phenotypically when comparing wild relatives with their domesticated relatives (domGE and domNGE) and (2) the existence and the magnitude of the phenotypic differences between domGE and domNGE of the same crop suggest consequences of genetic modification beyond the target trait(s).
Language	English
Publishing date	2017-12-05
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2613694-6
ISSN	1664-462X
ISSN	1664-462X
DOI	10.3389/fpls.2017.02030
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Article: Longitudinal Characterization of a Neutralizing and Total Antibody Response in Patients with Severe COVID-19 and Fatal Outcomes.

Serna-Muñoz, Ricardo / Hernández-Terán, Alejandra / Soto-Nava, Maribel / Tapia-Trejo, Daniela / Ávila-Ríos, Santiago / Mejía-Nepomuceno, Fidencio / García, Emma / Castillejos-López, Manuel / Higuera-Iglesias, Anjarath Lorena / Aquino-Gálvez, Arnoldo / Thirion-Romero, Ireri / Pérez-Padilla, Rogelio / Aguilar-Faisal, José Leopoldo / Vázquez-Pérez, Joel Armando

Vaccines

2022 Volume 10, Issue 12

Abstract: The host immune response to SARS-CoV-2 appears to play a critical role in disease pathogenesis and clinical manifestations in severe COVID-19 cases. Until now, the importance of developing a neutralizing antibody response in the acute phase and its ... ...

Abstract	The host immune response to SARS-CoV-2 appears to play a critical role in disease pathogenesis and clinical manifestations in severe COVID-19 cases. Until now, the importance of developing a neutralizing antibody response in the acute phase and its relationship with progression to severe disease or fatal outcome among hospitalized patients remains unclear. In this study, we aim to characterize and compare longitudinally the primary humoral immune host response in the early stages of the disease, looking for an association between neutralization, antibody titers, infective viral lineage, and the clinical outcome in hospitalized and non-hospitalized patients. A total of 111 patients admitted at INER from November 2021 to June 2022 were included. We found that patients with negative or low neutralization showed a significant reduction in survival probability compared to patients with medium or high neutralization. We observed a significant decrease in the median of neutralization in patients infected with viral variants with changes in RBD of the spike protein. Our results suggest that developing an early and robust neutralizing response against SARS-CoV-2 may increase survival probability in critical patients.
Language	English
Publishing date	2022-12-01
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2703319-3
ISSN	2076-393X
ISSN	2076-393X
DOI	10.3390/vaccines10122063
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