Article
Ecology
Rhianna R. Hohbein, Nathan P. Nibbelink
Summary: This study aimed to approximate country-wide connectivity for Andean bears in Colombia using a novel approach that validates the model with publicly available web and social media records. The model was found to be most sensitive to changes in resistance values of agricultural landcover and mid-elevational zones, but still provided valuable insights for conservation practitioners in Colombia. Further research on Andean bear movements through agricultural landscapes is needed to improve understanding of connectivity for this species in Colombia.
Article
Microbiology
Zhen Li, Ran Cui, Yu-Bei Wang, Ya-Biao Luo, Peng-Xiang Xue, Qi-Guo Tang, Mei-Ying Fang
Summary: This study investigated the composition and function of the gastrointestinal microbiota in Tan sheep and Dorper sheep, and its relationship with meat quality traits, specifically the fatty acid content. It identified specific bacterial species in different gastrointestinal segments and their association with glucose, lipid, and amino acid metabolism. Additionally, it found that 16 microbial species were essential for the fatty acid content in the muscle, especially C12:0.
Article
Multidisciplinary Sciences
Yu Dong, Rui Xu, Xiaowei Chen, Chuanli Yang, Fei Jiang, Yan Shen, Qiong Li, Fujin Fang, Yongjun Li, Xiaobing Shen
Summary: This study aims to investigate the gut microbiota profile of adults with coronary atherosclerosis and provides insights for future research. High-throughput sequencing of fecal samples from 35 patients with coronary atherosclerosis and 32 healthy adults in Nanjing, China, revealed differences in gut microbiota composition and diversity between the two groups. Megamonas, Streptococcus, Veillonella, Ruminococcus_torques_group, Prevotella_2, and Tyzzerella_4 were identified as potential biomarkers for coronary atherosclerosis.
Article
Microbiology
Alberto Jacome-Hernandez, Araceli Lamelas, Damaris Desgarennes, Carmen Huerta, Magdalena Cruz-Rosales, Mario E. Favila
Summary: The taxonomic composition of gut bacterial communities in Scarabaeinae beetles is influenced by factors such as beetle tribe and habitat. Forest-dwelling beetles exhibit higher bacterial diversity compared to grassland beetles, suggesting a correlation between bacterial diversity and food resource availability in complex habitats.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Immunology
Gang Du, Wei Dong, Qing Yang, Xueying Yu, Jinghong Ma, Weihong Gu, Yue Huang
Summary: This study investigated alterations in fecal microbiota and inflammatory cytokine responses in Huntington's disease (HD) patients. The results showed that HD patients had changes in microbiota diversity and structure, with some microbial components correlated with clinical characteristics and cytokine levels. The findings provide insight into the pathogenesis of HD and the potential role of gut dysbiosis in the disease.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Microbiology
Aoyun Li, Bingxian Liu, Feiran Li, Yuanyuan He, Lei Wang, Muhammad Fakhar-e-Alam Kulyar, Huade Li, Yuhang Fu, Huaisen Zhu, Yaping Wang, Xiong Jiang
Summary: This study found that the gut bacterial community remains relatively stable in diarrheic giraffes, but the gut fungal community shows significant changes between healthy and diarrheic states. Diarrhea causes significant alterations in gut microbial composition, with more pronounced changes observed in the gut bacterial community.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Immunology
Xiaochen Qiao, Kun Zhang, Xiaoyan Li, Zhi Lv, Wenhao Wei, Ruhao Zhou, Lei Yan, Yongchun Pan, Sen Yang, Xiaojuan Sun, Pengcui Li, Chaojian Xu, Yi Feng, Zhi Tian
Summary: This study assessed the correlation between gut microbiota (GM) and bone loss in disuse-induced osteoporosis (DIO). The results showed that changes in GM abundance and fecal metabolites were associated with DIO-induced bone loss, providing new insights into the pathogenesis of DIO. Further research is needed to explore the detailed regulatory role of GM and metabolites in DIO-induced bone loss.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Medicine, Research & Experimental
Bolin Li, Pengli Du, Yao Du, Danyang Zhao, Yanru Cai, Qian Yang, Zijing Guo
Summary: The study showed that luteolin significantly reduced colonic damage and inflammation in UC rats, and altered the diversity and composition of gut microbiota. The findings suggest that gut microbiota could serve as promising biomarkers for understanding how luteolin improves UC.
Article
Evolutionary Biology
Nedda F. Saremi, Jonas Oppenheimer, Christopher Vollmers, Brendan O'Connell, Shard A. Milne, Ashley Byrne, Li Yu, Oliver A. Ryder, Richard E. Green, Beth Shapiro
Summary: This study presents an annotated de novo assembly of the nuclear genome of a captive-born female Andean bear, which will serve as a valuable resource for exploring the phylogenetic history of extinct and extant bear species, as well as future population genetics studies of Andean bears.
JOURNAL OF HEREDITY
(2021)
Article
Nutrition & Dietetics
Huibin Pan, Lixia Huo, Weiyun Shen, Zhuquan Dai, Ying Bao, Chaohui Ji, Jie Zhang
Summary: This study demonstrated the ameliorative effects of BBR on pathological injury, inflammation, intestinal barrier function, gut microbiota, and metabolites in CLP rats. It also revealed that BBR may improve sepsis by regulating immune cell levels and gut microbiota composition.
FRONTIERS IN NUTRITION
(2022)
Article
Microbiology
Yao Ling, Wen-Jing Li, Fei-Fei Li, Xiao-Bao Xue, Yuan-Yi Gao, Li Wang, Ke Liang, Xin-Jiang Li
Summary: This study describes the gut microbiota diversity of four species of grasshoppers and finds that the gut microbiota is correlated with the cellulose and hemicellulose digestibility of grasshoppers. This is important for developing grasshopper digestive tracts as bioreactors for cellulose decomposition, improving the utilization of agricultural straw, and producing clean biomass energy.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Gastroenterology & Hepatology
Zhaowei Yang, Zhong Chen, Xinliu Lin, Siyang Yao, Mo Xian, Xiaoping Ning, Wanyi Fu, Mei Jiang, Naijian Li, Xiaojun Xiao, Mulin Feng, Zexuan Lian, Wenqing Yang, Xia Ren, Zhenyu Zheng, Jiefeng Zhao, Nili Wei, Wenju Lu, Marjut Roponen, Bianca Schaub, Gary W. K. Wong, Zhong Su, Charles Wang, Jing Li
Summary: Rural environments and microbiota are linked to a reduction in the prevalence of allergies. This study found that rural children have fewer allergies and a unique gut microbiota with fewer Bacteroides and more Prevotella. Indoor dusts in rural environments have higher endotoxin levels and a greater diversity of bacteria and fungi compared to indoor urban dusts.
Article
Pharmacology & Pharmacy
Xinyuan Liu, Mengqian Dun, Tongtong Jian, Yuqing Sun, Mingyu Wang, Guoying Zhang, Jianya Ling
Summary: In this study, the effects of Cordyceps militaris extracts (CE) and cordycepin (CCS) on T2DM mice were analyzed using gut microbiome and metabolomics methods. The results showed that the CCS and CE groups had decreased glucose and lipid metabolism parameters, oxidative stress biomarkers, and inflammation cytokines. Comparative analysis of fecal samples indicated a higher abundance of Firmicutes/Bacteroidetes in the experimental groups. These findings suggest that C. militaris could be used as a food supplement to alleviate T2DM.
FRONTIERS IN PHARMACOLOGY
(2023)
Article
Immunology
Li Xi, Yumin Song, Jincheng Han, Xinxi Qin
Summary: This study using 16S rDNA amplicon sequencing revealed distinct differences in gut microbial composition and diversity between diarrheic and healthy Baer's Pochard. The gut bacterial community of diarrheic Baer's Pochard showed a decrease in alpha diversity with evident changes in taxonomic compositions compared to healthy individuals. This is the first report to investigate the alterations in gut microbiota of Baer's Pochard under different health states, providing valuable insight into gut microbial composition and diversity in this species.
MICROBIAL PATHOGENESIS
(2021)
Article
Immunology
Rui-kun Zhang, Kun Yan, Hai-feng Chen, Yang Zhang, Gui-jin Li, Xiao-gang Chen, Lin-pu Ge, Feng Cheng, Zhi-neng Chen, Xin-miao Yao
Summary: This study investigated the effect of traditional Chinese medicine (TCM) intervention on the structure and function of the gut microbiota (GM) in patients with osteoporosis (OP). After three months of treatment, patients in the TCM group showed improved bone mineral density (BMD) compared to the control group. The GM composition and metabolites also underwent significant changes. This suggests that TCM may promote the rehabilitation of OP patients through modulation of the GM.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2023)
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
Biotechnology & Applied Microbiology
David A. Ayala-Usma, Martha Cardenas, Romain Guyot, Maryam Chaib De Mares, Adriana Bernal, Alejandro Reyes Munoz, Silvia Restrepo
Summary: This study presents the first genome-wide analysis of Phytophthora betacei and expands the genomic resources for Phytophthora infestans. It highlights the differences in genome size, transposable element activity, and phylogenetic relationships between the two species. Additionally, it provides insights into the genome biology and evolutionary history of Phytophthora species in subclade 1c.
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.
Article
Biotechnology & Applied Microbiology
Jaime E. Gutierrez, Nohora Gutierrez-Hoyos, Juan Sebastian Gutierrez, Martha J. Vives, V. Sivasubramanian
Summary: Bioaugmentation using a microbial consortium with predominance of microalgae showed significant reduction in pollutants in the Mallorquin tropical swamp, without disrupting the original phytoplankton community. This study confirmed the effectiveness of phycoremediation for on-site bioremediation of natural water bodies, marking the first successful intervention at this scale in a natural swamp in Colombia.
INDIAN JOURNAL OF MICROBIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Jaime E. Gutierrez, Nohora Gutierrez-Hoyos, Juan S. Gutierrez Benedetti, Martha J. Vives, V Sivasubramanian
Summary: This study characterized a cyanobacterial bloom in a reservoir in the tropical zone of northern Colombia. It identified Microcystis sp. as the dominant microorganism and detected the presence of microcystin in the water. A bioaugmentation process using a microbial consortium with a predominance of microalgae (MCPM) successfully broke the dominance of cyanobacteria and restored the richness and density of phytoplankton. The density of cyanobacteria decreased significantly after 15 days of MCPM bioaugmentation. A remarkable removal of Microcystis sp. (34% to 53%) was observed between the first and sixteenth day, and from the sixteenth to fifty-eighth day, the removal reached 92% to 100%. The bioaugmentation process lasted for a total of 58 days.
JOURNAL OF CHEMICAL TECHNOLOGY AND BIOTECHNOLOGY
(2022)
Article
Multidisciplinary Sciences
Viviana Clavijo, Tatiana Morales, Martha Josefina Vives-Flores, Alejandro Reyes Munoz
Summary: The microbiota in broiler chicken intestines has a significant impact on the animals' health and productivity. Phages, as a potential alternative to antibiotics, selectively target pathogens without disrupting the microbiota. This study characterizes the commensal microbial community in broiler chickens treated with a Salmonella phage treatment. The results show that the phage treatment does not disrupt the normal development of the microbiota's structure but leads to a reduction in Campylobacter and an increase in Butyricimonas, Helicobacter, and Rikenellaceae.
SCIENTIFIC REPORTS
(2022)
Article
Virology
Bas E. Dutilh, Arvind Varsani, Yigang Tong, Peter Simmonds, Sead Sabanadzovic, Luisa Rubino, Simon Roux, Alejandro Reyes Munoz, Cedric Lood, Elliot J. Lefkowitz, Jens H. Kuhn, Mart Krupovic, Robert A. Edwards, J. Rodney Brister, Evelien M. Adriaenssens, Matthew B. Sullivan
Summary: The development of virus taxonomy relies on advances in metagenomic analysis and other technologies, which have brought a wealth of previously unknown virus sequence data and provided unprecedented insights into the vastness of the virosphere. Properly classifying viruses is crucial to understanding the diversity of viruses, and the inclusion of uncultivated viruses has already improved this process.
CURRENT OPINION IN VIROLOGY
(2021)
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
Humanities, Multidisciplinary
Patricia Zalamea, Martha Vives, Ferney Rodriguez
Summary: Understanding the visual representation of the COVID-19 pandemic, both in scientific diagrams and non-scientific expressions, provides insights into how it has been perceived and socially adapted by online audiences. A multidisciplinary perspective combining art history, microbiology, and physics offers a fresh outlook on representation as a way for humans to engage with and comprehend a critical historical event triggered by an invisible virus. Historical understanding of past pandemics helps in understanding the unique iconography of the current one. The comparison between global and local forms of representation highlights the political connotations of imagery and its power to inform or misinform depending on its context and usage.
COGENT ARTS & HUMANITIES
(2022)
Article
Immunology
Sara J. Clasen, Michael E. W. Bell, Andrea Borbon, Du-Hwa Lee, Zachariah M. Henseler, Jacobo de la Cuesta-zuluaga, Katarzyna Parys, Jun Zou, Yanling Wang, Veronika Altmannova, Nicholas D. Youngblut, John R. Weir, Andrew T. Gewirtz, Youssef Belkhadir, Ruth E. Ley
Summary: Flagellin, the protein subunit of bacterial flagellum, can either stimulate or evade the innate immune receptor Toll-like receptor 5 (TLR5) through pattern recognition. Weak agonism of flagellins from commensal bacteria brings up the question of how TLR5 response is tuned. This study discovered a class of flagellin-TLR5 interaction called silent recognition, which enables flagellin binding to preformed TLR5 dimers and significantly increases TLR5 signaling.
SCIENCE IMMUNOLOGY
(2023)
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
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)