Article
Agronomy
Cesar E. Falconi, Viviana Yanez-Mendizabal, Roberto J. Haro, Darwin R. Claudio
Summary: In this study, a native microbial cocktail was introduced to improve the fermentation process of cocoa beans. The results showed that the cocktail improved the quality and flavor of the beans, and also reduced the fermentation time.
Article
Food Science & Technology
A. K. Carole Sanya, Yann E. Madode, Sijmen E. Schoustra, Eddy J. Smid, Anita R. Linnemann
Summary: This study investigated the different processing technologies and quality characteristics of fermented maize starch from two socio-cultural groups in Benin, the Fon and the Goun. The results showed variations in the microbial composition and metabolic characteristics of the fermented starch samples from different processing technologies. Further research on the individual differences in processing practices is necessary to improve the product quality and shelf life.
FOOD RESEARCH INTERNATIONAL
(2023)
Article
Food Science & Technology
Mohamad Djali, Kimberly Santasa, Rossi Indiarto, Edy Subroto, Fetriyuna Fetriyuna, Elazmanawati Lembong
Summary: Cocoa bean shell (CBS), a by-product from cocoa processing, was studied in several cocoa industries in Indonesia. The research found that roasted Criollo cocoa pods in the Kendeng Lembu cocoa industry had higher ash and protein content, as well as higher concentration of bioactive substances.
Article
Microbiology
Benjamin J. Callahan, Dmitry Grinevich, Siddhartha Thakur, Michael A. Balamotis, Tuval Ben Yehezkel
Summary: LoopSeq is a commercially available synthetic long-read (SLR) sequencing technology that generates highly accurate long reads from standard short reads, enabling direct identification of microbial genes and species in complex samples. Compared to standard Illumina amplicon sequencing, LoopSeq offers an order-of-magnitude improvement in length and accuracy, allowing accurate identification of species and strains from complex to low-biomass microbiome samples.
Article
Multidisciplinary Sciences
Mauricio Moreno-Zambrano, Matthias S. Ullrich, Marc-Thorsten Huett
Summary: This study focused on mathematical modeling of cocoa bean fermentation, revealing the importance of fermentation mechanisms and parameters for quality control. The results supported biochemical mechanisms such as consumption of fructose by lactic acid bacteria and production of acetic acid by yeast, while showing the sensitivity of model parameters to factors like cocoa bean variety, temperature control, and container material. The findings suggest that mathematical modeling could serve as an alternative to traditional chemical fingerprinting for interpreting fermentation data.
ROYAL SOCIETY OPEN SCIENCE
(2022)
Article
Food Science & Technology
Gabriel A. Rivas, Liliana Semorile, Lucrecia Delfederico
Summary: The microbial communities in Malbec vineyards in Argentina were characterized with a predominance of Proteobacteria and Actinobacteria in the soil and rhizosphere. The order Rhizobiales stood out with its plant-growth promotion properties. Ascomycota and Basidiomycota were the most abundant phyla in fungal communities. The wine samples showed low levels of lactic acid bacteria and the presence of acetic acid bacteria throughout fermentation without affecting the wine acidity.
LWT-FOOD SCIENCE AND TECHNOLOGY
(2022)
Article
Food Science & Technology
Marcelina Maria Mendoza Salazar, Pilar Ximena Lizarazo-Medina
Summary: The quality of cocoa seeds is influenced by various factors, with fermentation being a crucial one due to the synthesis of flavor precursors by fungi and bacteria. The diversity of biological variants involved in fermentation processes varies between different regions, with unique variants of certain genera detected at each site. Differences in environmental conditions and indigenous microbiota of cocoa cultivation zones explain the findings of this study, including variations in physicochemical parameters and fermentation duration.
FOOD RESEARCH INTERNATIONAL
(2021)
Article
Agricultural Engineering
Philip M. Roveto, Adwaith Gupta, Andrew J. Schuler
Summary: The study showed that surface skewness has significant impacts on biofilm development, with surfaces with negative skewness promoting nitrite oxidation and biomass growth. Analysis of 16s rRNA gene sequencing revealed differences in bacterial populations, and PCoA analysis indicated divergence between populations on skew and flat surfaces.
BIORESOURCE TECHNOLOGY
(2021)
Article
Microbiology
Wei Cheng, Xuefeng Chen, Wei Lan, Gengdian Liu, Xijia Xue, Ruilong Li, Tianquan Pan, Na Li, Duan Zhou, Xingjie Chen
Summary: In this study, the microbial community and volatile components in fermented grains (FG) during ultra-long fermentation of compound-flavor Baijiu (CFB) were analyzed. The relationships between dominant microbial communities, physicochemical parameters, and volatile components were investigated. The findings provide insights into the fermentation mechanisms and aroma quality control of CFB.
FRONTIERS IN MICROBIOLOGY
(2023)
Review
Genetics & Heredity
Hiral G. Chaudhari, Shobha Prajapati, Zuhour Hussein Wardah, Gopal Raol, Vimalkumar Prajapati, Rajesh Patel, Ali A. Shati, Mohammad Y. Alfaifi, Serag Eldin I. Elbehairi, R. Z. Sayyed
Summary: A large part of the Earth's biological systems consists of microorganisms, most of which have not been cultured. Traditional methods of culturing microbes have limitations, prompting the development of culture-independent molecular methods. Metagenomics has revolutionized research by revealing the diversity and novelty of microbial communities and genomes. This review focuses on the development of this field, sequencing techniques and data analysis, as well as interpretation and representation.
FRONTIERS IN GENETICS
(2023)
Article
Biotechnology & Applied Microbiology
Marcel Suleiman, Francesca Demaria, Cristina Zimmardi, Boris Alexander Kolvenbach, Philippe Francois-Xavier Corvini
Summary: Pharmaceuticals accumulation in the environment is a concern for our planet and health. Little is known about the biodegradation capacity of microbial communities for multiple micropollutants. This study demonstrates the feasibility of cultivating stable microbial communities capable of degrading a mixture of highly concentrated pharmaceuticals.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2023)
Article
Microbiology
Peeter Laas, Kelly Ugarelli, Rafael Travieso, Sandro Stumpf, Evelyn E. Gaiser, John S. Kominoski, Ulrich Stingl
Summary: Planktonic microbial communities in wetland ecosystems play a vital role, yet they are relatively underexplored compared to other aquatic ecosystems. This study conducted a high-resolution analysis of bacterial and eukaryotic microbial communities in the Florida Everglades, revealing significant variations along the salinity gradient.
Article
Food Science & Technology
Rebecca Ghisolfi, Francesca Bandini, Filippo Vaccari, Gabriele Bellotti, Cristian Bortolini, Vania Patrone, Edoardo Puglisi, Lorenzo Morelli
Summary: This study used high-throughput sequencing to assess the impact of box, ground, and jute fermentation methods on bacterial and fungal communities. The results showed noticeable differences between the three methods, with box fermentation having higher bacterial species diversity and ground processing resulting in a wider fungal community. The box method was found to be preferable due to its limited microbial diversity and the presence of microorganisms that ensure good fermentation. The study provided a comprehensive exploration of the microbiota of differently treated cocoa beans and improved understanding of the technological processes for obtaining a standardized end-product.
Article
Soil Science
Antje Bettermann, Jeroen H. T. Zethof, Doreen Babin, Erik L. H. Cammeraat, Albert Sole-Benet, Roberto Lazaro, Lourdes Luna, Joseph Nesme, Soren J. Sorensen, Karsten Kalbitz, Kornelia Smalla, Cordula Vogel
Summary: In this study, the effects of different plant species on microbes, EPS production, and soil aggregation were investigated in two sites in southern Spain. It was found that plant species and site influenced the microbial communities in the rhizoplane, with site being the most important factor. Higher carbonate content in soil reduced the plant-specific effects on microbial communities and subsequent soil aggregation. This study highlights the importance of plant-microbe interactions in soil ecosystem dynamics and the role of soil properties in moderating these interactions.
SOIL BIOLOGY & BIOCHEMISTRY
(2021)
Article
Immunology
Hongzhang Shen, Juanjuan Zhu, Fuqiang Ye, Dongchao Xu, Liangliang Fang, Jianfeng Yang, Huijie Lv, Qifeng Lou, Hangbin Jin, Ming Ni, Xiaofeng Zhang
Summary: The study revealed that a history of invasive endoscopic sphincterotomy (EST) significantly influences the biliary microbiota, leading to a marked shift in the composition of biliary bacteria. The bacterial genus Pyramidobacter was specifically associated with a history of EST.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Andres Felipe Vasquez, Alejandro Reyes Munoz, Jorge Duitama, Andres Gonzalez Barrios
Summary: The research successfully identified potential anticancer drug candidates using a computational strategy that involved deconstruction of natural product libraries and development of pharmacophore models. This approach resulted in a set of 20 diverse, developable, synthesizable, and potent hit compounds.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2021)
Article
Multidisciplinary Sciences
Luis Alberto Chica Cardenas, Viviana Clavijo, Martha Vives, Alejandro Reyes
Summary: This study aimed to analyze the diversity and variability of bacterial communities in the ceca of chickens, identifying common bacteria with important metabolic functions. Despite variations in parameters, commonalities in the microbial community were found across different studies.
Article
Virology
Gamaliel Lopez-Leal, Alejandro Reyes-Munoz, Rosa Isela Santamaria, Miguel A. Cevallos, Carlos Perez-Monter, Santiago Castillo-Ramirez
Summary: This study characterized a bacteriophage Ab11510-phi isolated from a multidrug-resistant Acinetobacter baumannii strain, revealing its narrow host range and classification within the Vieuvirus genus. Furthermore, the study highlighted the high level of mosaicism in Ab11510-phi and emphasized the importance of comparative genomics and phylogenetic analysis for proper characterization of phage diversity.
ARCHIVES OF VIROLOGY
(2021)
Article
Multidisciplinary Sciences
Camilo Quiroga-Gonzalez, Luis Alberto Chica Cardenas, Monica Ramirez, Alejandro Reyes, Camila Gonzalez, Pablo R. Stevenson
Summary: The study revealed an increase in gut microbial diversity in reintroduced woolly monkeys after release, associated with changes in diet. There was a clear separation in microbial composition before and after release, with the timing of liberation being the major factor of variation.
SCIENTIFIC REPORTS
(2021)
Article
Microbiology
Leda Restrepo, Cristobal Dominguez-Borbor, Leandro Bajana, Irma Betancourt, Jenny Rodriguez, Bonny Bayot, Alejandro Reyes
Summary: The study demonstrates the potential of probiotics in controlling pathogenic bacterial populations in shrimp's gastrointestinal tract, particularly against AHPND-causing Vibrio pathogens. However, the risk of probiotic strain becoming pathogenic when working with AHPND-causing Vibrio pathogens needs to be carefully evaluated.
Article
Food Science & Technology
Madhushri S. Varunjikar, Carlos Moreno-Ibarguen, Juan S. Andrade-Martinez, Hui-Shan Tung, Ikram Belghit, Magnus Palmblad, Pal A. Olsvik, Alejandro Reyes, Josef D. Rasinger, Kai K. Lie
Summary: The study shows that both DNA and protein-based approaches can efficiently tackle current challenges in feed and food authentication analyses.
Review
Microbiology
Juan Sebastian Andrade-Martinez, Laura Carolina Camelo Valera, Luis Alberto Chica Cardenas, Laura Forero-Junco, Gamaliel Lopez-Leal, J. Leonardo Moreno-Gallego, Guillermo Rangel-Pineros, Alejandro Reyes
Summary: Over a century of bacteriophage research has uncovered fundamental aspects of their biology, ecology, and evolution. The introduction of community-level studies through metagenomics has revealed unprecedented insights on the impact that phages have on ecological and physiological processes. The availability of computational tools has greatly contributed to our knowledge of phage diversity and ecology, but the ongoing surge in software programs makes it challenging to keep up with them.
MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS
(2022)
Article
Multidisciplinary Sciences
Gloria Ines Lafaurie, Yineth Neuta, Rafael Rios, Mauricio Pacheco-Montealegre, Roquelina Pianeta, Diana Marcela Castillo, David Herrera, Jinnethe Reyes, Lorena Diaz, Yormaris Castillo, Mariano Sanz, Margarita Iniesta
Summary: Microbiological criteria for differentiating between stages and grades of periodontal diseases are currently lacking. This study found associations between specific microbial species and periodontitis, but these associations varied between the two countries studied. Further research using advanced sequencing techniques could provide more insight into the differences between stages of periodontitis.
Article
Virology
Liliane S. S. Oliveira, Alejandro Reyes, Bas E. E. Dutilh, Arthur Gruber
Summary: The study developed protocols for the rational design of profile HMMs, which can automatically identify informative sequence motifs and construct profile HMMs. These methods were applied to detect and classify different viral groups and related transposable elements.
Article
Microbiology
Alejandro Castellanos, Leda Restrepo, Leandro Bajana, Irma Betancourt, Bonny Bayot, Alejandro Reyes
Summary: AHPND is a disease causing significant losses in the shrimp farming industry, with global losses exceeding $2.6 billion. The most common etiological agent is V. parahaemolyticus strains carrying the PirAB(vp) toxin. By analyzing South American AHPND-causing V. parahaemolyticus isolates at the genomic level, it was found that they have high similarity but do not cluster with other Mexican strains, suggesting different genetic backgrounds and possible acquisition of the pVA1-type plasmid through horizontal gene transfer at different times.
MICROBIOLOGY SPECTRUM
(2023)
Letter
Biotechnology & Applied Microbiology
Evelien M. M. Adriaenssens, Simon Roux, J. Rodney Brister, Ilene Karsch-Mizrachi, Jens H. H. Kuhn, Arvind Varsani, Tong Yigang, Alejandro Reyes, Cedric Lood, Elliot J. J. Lefkowitz, Matthew B. B. Sullivan, Robert A. A. Edwards, Peter Simmonds, Luisa Rubino, Sead Sabanadzovic, Mart Krupovic, Bas E. E. Dutilh
NATURE BIOTECHNOLOGY
(2023)
Correction
Biotechnology & Applied Microbiology
Evelien M. M. Adriaenssens, Simon Roux, J. Rodney Brister, Ilene Karsch-Mizrachi, Jens H. Kuhn, Arvind Varsani, Tong Yigang, Alejandro Reyes, Cedric Lood, Elliot J. Lefkowitz, Matthew B. B. Sullivan, Robert A. A. Edwards, Peter Simmonds, Luisa Rubino, Sead Sabanadzovic, Mart Krupovic, Bas E. E. Dutilh
NATURE BIOTECHNOLOGY
(2023)
Article
Environmental Sciences
Daniel Bautista, Diana Garcia, Lorena Davila, Alejandro Caro-Quintero, Alba Marina Cotes, Adriana Gonzalez, A. Paola Zuluaga
Summary: Cape gooseberry (Physalis peruviana) is Colombia's second most exported fruit, with a market worth 37.8 million USD in 2021. Fusarium oxysporum f sp. physalis (Foph) is a devastating pathogen causing significant losses. This study found that soil microbiomes can have a suppressive effect against Foph, with a decrease in disease incidence and severity observed in seedlings grown in propagated soils.
ENVIRONMENTAL MICROBIOLOGY REPORTS
(2023)
Article
Biochemical Research Methods
Guillermo Rangel-Pineros, Alexandre Almeida, Martin Beracochea, Ekaterina Sakharova, Manja Marz, Alejandro Reyes Munoz, Martin Hoelzer, Robert D. Finn
Summary: VIRify is a computational pipeline that accurately characterizes the functional and taxonomic aspects of viral communities based on sequencing data. It utilizes viral profile hidden Markov models to identify and classify viral contigs, providing taxonomic classifications at different ranks.
PLOS COMPUTATIONAL BIOLOGY
(2023)