Article
Biotechnology & Applied Microbiology
Zhishan Wang, Ni Li, Weiping Wang, Yongqiang Zhu, Yang Liu
Summary: The study found that the community structures and diversity of endophytic bacteria in hybrid rice seeds are affected by genotype, genetic relationship, and rice blast resistance. This is important for understanding the interaction between endophytic bacteria and the host.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2023)
Review
Food Science & Technology
Gilberto V. de Melo Pereira, Dao Pedro de Carvalho Neto, Bruna L. Maske, Juliano De Dea Lindner, Alexander S. Vale, Gabriel R. Favero, Jessica Viesser, Julio C. de Carvalho, Aristoteles Goes-Neto, Carlos R. Soccol
Summary: This review explores the application of next-generation sequencing (NGS) technologies in analyzing the microbial composition of traditional fermented milk products worldwide. The study reveals a more complex bacterial diversity in these products, including uncultivable microorganisms, sub-dominant populations, and late-growing species. These discoveries are vital in improving the monitoring, manipulation, and safety of fermented foods.
CRITICAL REVIEWS IN FOOD SCIENCE AND NUTRITION
(2022)
Article
Agronomy
Xinjian Zhang, Chunli Ling, Xiaoqing Wu, Susu Fan, Qingxia Liang, Fangyuan Zhou
Summary: This study investigated the differences in bacterial communities surrounding strawberry roots grown in two artificial substrates and greenhouse soil. The results provide basic information on root bacterial diversity of strawberries grown in different substrates and help to explore beneficial root microorganisms for sustainable strawberry production.
Article
Environmental Sciences
Emine Gozde Ozbayram, Reyhan Akcaalan, Melek Isinibilir, Meric Albay
Summary: This study explored the bacterial diversity of marine mucilage in the Marmara Sea and the North Aegean Sea using the metabarcoding approach. The results showed a diverse bacterial community dominated by Proteobacteria and Bacteroidetes species. The study also identified correlations between pH levels and the abundances of certain bacterial orders, as well as a positive correlation between total phosphorus and one bacterial order.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2022)
Article
Immunology
Zhendong Huang, Peng Wang, Zhanxu Pu, Lianming Lu, Guoqing Chen, Xiurong Hu, Amna Fayyaz, Yunpeng Gai
Summary: The repeated application of fungicide may have detrimental effects on the rhizosphere bacterial community of citrus. However, the usage of mancozeb did not significantly impact the chemical properties and richness and diversity of rhizosphere bacterial community in citrus-cultivated soil.
MICROBIAL PATHOGENESIS
(2021)
Article
Biochemistry & Molecular Biology
Lei Zhao, Rasmus Nielsen, Thorfinn Sand Korneliussen
Summary: Commonly used methods for inferring phylogenies are not well-suited for handling challenges associated with noisy, diploid sequencing data. To address this problem, we introduce two new probabilistic approaches, distAngsd-geno and distAngsd-nuc, that account for uncertainty in genotype calling and are specifically designed for next-generation sequencing data.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Cell Biology
Hanna Goelz, Simon Wetzel, Negin Mehrbarzin, Stefan Utzolino, Georg Haecker, Mohamed Tarek Badr
Summary: NGS-based methods show higher sensitivity in identifying clinically relevant pathogens in ascitic fluid infections, especially in detecting hard-to-culture anaerobic bacteria. Clinical data analysis demonstrates a correlation between sequencing results and various clinical parameters.
Article
Environmental Sciences
Li Zhao, Sonia Brugel, Kesava Priyan Ramasamy, Agneta Andersson
Summary: Bacteria are important consumers of dissolved organic matter in aquatic systems. The response of bacterial communities to changing DOM types and inputs from climate change is not well understood.
FRONTIERS IN MARINE SCIENCE
(2023)
Article
Food Science & Technology
Hiran Castagnino Kunert-Filho, Thales Quedi Furian, Renata Sesterhenn, Gabriela Zottis Chitolina, Daiane Elisa Willsmann, Karen Apellanis Borges, Carlos Tadeu Pippi Salle, Hamilton Luiz de Souza Moraes, Vladimir Pinheiro do Nascimento
Summary: Poultry products are prone to contamination by microorganisms during the slaughtering process. High-throughput next generation sequencing (HT-NGS) allows for precise and culture-independent assessment of the microbiome in poultry carcasses. Differences in microbiome composition were observed among slaughterhouses, with some unique microorganisms detected in specific establishments. Significant reductions in microbial sequences were found as the slaughtering process progressed, and stricter control procedures were associated with lower contamination. These findings provide valuable insights for ensuring food safety in slaughterhouses.
INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY
(2022)
Article
Microbiology
Priti Gawas, Savita Kerkar
Summary: In Goa's salt pans, diverse halophilic microbes with biotechnological applications were found. Detecting the presence of these microbes is important for harnessing their potential. Using metabarcoding, the bacterial community and function of three salt pans in Goa were examined. It was found that different salt pans have unique microbial communities, and adjacent estuaries play a critical role in determining bacterial diversity.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Microbiology
Boxue Si, Kaizhen Liu, Guoxin Huang, Meiqing Chen, Jiyong Yang, Xufang Wu, Ning Li, Wenhao Tang, Shengguo Zhao, Nan Zheng, Yangdong Zhang, Jiaqi Wang
Summary: The variation of milk fat is closely related to rumen bacteria, and certain rumen bacteria have a potential impact on the deposition of specific fatty acids in raw milk.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Agriculture, Multidisciplinary
Mahesh Adhikari, Sang Woo Kim, Hyun Seung Kim, Ki Young Kim, Hyo Bin Park, Ki Jung Kim, Youn Su Lee
Summary: This study investigated the bacterial structures, including the Acidovorax species community, in watermelon cultivated soils across different regions of South Korea. The results from next generation sequencing revealed a similar trend in bacterial community and diversity among the soil samples, highlighting the importance of environmental factors in shaping microbial communities. Further correlation analysis between soil parameters and dominant bacterial communities will be conducted to better understand their interactions.
PLANT PATHOLOGY JOURNAL
(2021)
Article
Microbiology
Bashir Hussain, Jung-Sheng Chen, Bing-Mu Hsu, I-Tseng Chu, Suprokash Koner, Tsung-Hsien Chen, Jagat Rathod, Michael W. Y. Chan
Summary: This study utilized high-throughput sequencing to analyze the bacterial composition in fermented fruit products, identifying low abundance potential opportunistic pathogens and validating major pathogenic species. The results indicated that fermentation is a reliable and safe process, as pathogenic bacteria were not detected in the fermentation products.
Article
Microbiology
Tijana Martinovic, Petr Kohout, Ruben Lopez-Mondejar, Camelia Algora Gallardo, Robert Starke, Michal Tomsovsky, Petr Baldrian
Summary: Clearcutting has significant consequences for temperate forests, particularly on bacterial community composition, which responds less significantly compared to fungal communities. It indicates independent development of the two microbial domains.
FEMS MICROBIOLOGY ECOLOGY
(2022)
Article
Microbiology
Michele Bertoni Mann, Janira Prichula, Icaro Maia Santos de Castro, Juliana Mello Severo, Michelle Abadie, Thayna Mendes De Freitas Lima, Valentina Caorsi, Marcio Borges-Martins, Jeverson Frazzon, Ana Paula Guedes Frazzon
Summary: The study characterized the oral bacterial community of the critically endangered species Melanophryniscus admirabilis in southern Brazil, identifying Proteobacteria as the dominant phylum and highlighting the potential impact of low dietary diversity on bacterial composition. Additionally, the detection of important pathways related to pesticide degradation and other compounds suggests that the bacterial communities play a crucial role in the health and survival of M. admirabilis in anthropogenic environments.
Article
Biochemistry & Molecular Biology
Abraham Loera-Muro, Maria Goretty Caamal-Chan, Thelma Castellanos, Angelica Luna-Camargo, Trinidad Aguilar-Diaz, Aaron Barraza
Summary: Bacteria can establish beneficial interactions with plants by acting as growth promoters and enhancing stress tolerance, but interactions may not always be positive or synergistic. When bacteria form a consortium, neutral or antagonistic interactions may occur.
CANADIAN JOURNAL OF MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Keren Martinez-Aguilar, Jose Luis Hernandez-Chavez, Raul Alvarez-Venegas
Summary: Priming is a defense mechanism in plants that prepares the immune system for faster and/or stronger activation of cellular defenses against future stress. Treating seeds with compounds like INA can induce resistance to pathogens, with the resistance being potentially inherited by offspring.
Article
Fisheries
Ruth Escamilla-Montes, Aaron Barraza, Antonio Luna-Gonzalez, Carlos Angulo, Jesus Arturo Fierro-Coronado, Genaro Diarte-Plata, Ma del Carmen Flores-Miranda
Summary: The study evaluated the effect of dietary inulin on the intestinal bacterial communities of Penaeus vannamei through 16S metagenomic analysis. The results showed differences in the composition of bacterial communities between the inulin treatment and control groups, but no significant differences in microbial diversity. Most bacterial organisms in all samples exhibited genes related to carbohydrate and amino acid metabolism, while fewer genes related to energy, lipid, and cofactors and vitamin metabolism were observed.
LATIN AMERICAN JOURNAL OF AQUATIC RESEARCH
(2021)
Article
Microbiology
Aaron Barraza, Juan J. Montes-Sanchez, M. Goretty Caamal-Chan, Abraham Loera-Muro
Summary: The study found that lactating creole goats grazing in arid plant communities in the Sonoran Desert have different diet preferences, but exhibit some similarities in microbial communities in the rumen and large intestine, with low presence of archaea.
Article
Fisheries
Ruth Escamilla-Montes, Genaro Diarte-Plata, Gabriela B. Mendoza-Maldonado, Aaron Barraza, Carlos Angulo, Seyed Hossein Hoseinifar, Jesus A. Fierro-Coronado, Antonio Luna-Gonzalez
Summary: Invertebrates' immune defense mechanisms have a critical role in pathogen recognition and elimination. This study focused on the transcriptome analysis of Argopecten ventricosus to identify immune-related genes. The results showed that probiotic bacilli can significantly increase the expression of certain immune-related genes.
LATIN AMERICAN JOURNAL OF AQUATIC RESEARCH
(2022)
Article
Plant Sciences
Marco Catoni, Raul Alvarez-Venegas, Dawn Worrall, Geoff Holroyd, Aaron Barraza, Estrella Luna, Jurriaan Ton, Michael R. Roberts
Summary: This research focuses on the epigenetic changes in tomato plants primed for pathogen resistance, showing that treatment with beta-aminobutyric acid (BABA) results in a significant reduction in global cytosine methylation, particularly in CHH sequence contexts. The differentially methylated regions (DMRs) identified mainly consist of hypomethylated CHH DMRs, which are enriched in gene promoters and DNA transposons. Genes overlapping with CHH DMRs are enriched for stress response-related gene ontology terms and promoters of genes differentially expressed in response to infection with Botrytis cinerea. However, the majority of primed genes do not contain DMRs and the overall distribution of methylated cytosines in primed genes is not affected by BABA treatment. Therefore, it is suggested that methylation may confer priming via in-trans regulation and/or by targeting a smaller group of regulatory genes controlling stress responses.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Multidisciplinary Sciences
Barbara Gonzalez-Acosta, Aaron Barraza, Cesar Guadarrama-Analco, Claudia J. Hernandez-Guerrero, Sergio Francisco Martinez-Diaz, Cesar Salvador Cardona-Felix, Ruth Noemi Aguila-Ramirez
Summary: This study investigated the microbial communities associated with two marine sponges and found that depth was a stronger factor than host in structuring the microbiome.
Article
Agronomy
Aaron Barraza, Rosalia Nunez-Pastrana, Abraham Loera-Muro, Thelma Castellanos, Carlos Julian Aguilar-Martinez, Isaac Salvador Sanchez-Sotelo, Maria Goretty Caamal-Chan
Summary: This study investigated the molecular mechanisms underlying the interaction between Phytophthora capsici and Capsicum chinense, a susceptible cultivar. Three elicitors were used to induce early defense in the plants, and the expression of defense-related genes was analyzed. The results showed that MeJA and BABA elicitors reduced disease symptoms and up-regulated genes related to the JA/ET signaling pathway. This suggests that JA signaling plays an important role in the early defense against P. capsici.
Article
Plant Sciences
Chainika Gupta, Romesh Kumar Salgotra, Raul Alvarez Venegas, Reetika Mahajan, Umang Koul
Summary: The study analyzed the genetic architecture of common bean agronomic traits in India, identifying significant marker-trait associations that could be utilized in marker-assisted breeding to improve yield. Population structure analysis divided the accessions into three subpopulations, with ten major MTAs contributing to phenotypic variation.
PLANT GENETIC RESOURCES-CHARACTERIZATION AND UTILIZATION
(2022)
Article
Biochemistry & Molecular Biology
Eliana Valencia-Lozano, Lisset Herrera-Isidron, Jorge Abraham Flores-Lopez, Osiel Salvador Recoder-Melendez, Aaron Barraza, Jose Luis Cabrera-Ponce
Summary: This study used transcriptome-wide analysis to reveal the molecular mechanisms involved in potato microtuber development. The analysis identified several up- and down-regulated genes, as well as protein-protein interaction networks related to life growth and development, cell cycle, and transcription factors.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Marine & Freshwater Biology
Lina Angelica Zermeno-Cervantes, Aaron Barraza, Herson Antonio Gonzalez-Ponce, Sergio Francisco Martinez-Diaz, Cesar Salvador Cardona-Felix
Summary: White shrimp farming is a significant aquaculture activity globally, but the intensification process can have negative impacts on shrimp health, leading to dysbiosis. This study examines the bacterial load and microbial population changes in the hepatopancreas of Penaeus vannamei infected with pathogenic Vibrio parahaemolyticus strain associated with acute hepatopancreatic necrosis disease (AHPND). The results reveal a significant shift in the microbial community structure, with an increase in Vibrio genus dominance before the visible manifestation of the disease.
Article
Biochemistry & Molecular Biology
Leonardo Garcia-Murillo, Eliana Valencia-Lozano, Nicolas Alberto Priego-Ranero, Jose Luis Cabrera-Ponce, Fatima Patricia Duarte-Ake, Juan Carlos Vizuet-de-Rueda, Diana Marcela Rivera-Toro, Humberto Herrera-Ubaldo, Stefan de Folter, Raill Alvarez-Venegas
Summary: With the continual degradation of arable land caused by a growing population, improving crops and crop protection plays a crucial role in maintaining and increasing crop productivity. Alternatives to pesticide use include biological control agents, the creation of resistant crop varieties, the application of plant activator agrochemicals, and the utilization of gene editing techniques such as CRISPR-Cas. In this study, it was demonstrated that editing tomato plants using CRISPR activation (CRISPRa) can activate defense genes and enhance resistance against pathogen infection.
Editorial Material
Plant Sciences
Alexandre Berr, Raul Alvarez-Venegas
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Horticulture
Abraham Loera-Muro, Enrique Troyo-Dieguez, Bernardo Murillo-Amador, Aaron Barraza, Goretty Caamal-Chan, Gregorio Lucero-Vega, Alejandra Nieto-Garibay
Summary: This study compared the morphologies of M. spicata and R. officinalis plants, and found that the use of vermicompost leachate in a closed hydroponic system can increase the growth of mint plants without altering the quality of the product or microbial communities.