Phylogenomic tree reconstruction has recently become a
routine and critical task to elucidate the evolutionary relationships
among bacterial species. The most widely used method
utilizes the concatenated core genes, universally present in a
single-copy throughout the bacterial domain. In our previous
study, a bioinformatics pipeline termed Up-to-date Bacterial
Core Genes (UBCG) was developed with a set of bacterial core
genes selected from 1,429 species covering 28 phyla. In this
study, we revised a new bacterial core gene set, named UBCG2,
that was selected from the more extensive genome sequence
set belonging to 3,508 species spanning 43 phyla. UBCG2 comprises
81 genes with nine Clusters of Orthologous Groups of
proteins (COGs) functional categories. The new gene set and
complete pipeline are available at http://leb.snu.ac.kr/ubcg2.
Citations
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The divergence of gut bacterial community on broiler chickens
has been reported as potentially possible keys to enhancing
nutrient absorption, immune systems, and increasing
poultry health and performance. Thus, we compared cecal
bacterial communities and functional predictions by sex and
body weight regarding the association between cecal microbiota
and chicken growth performance. In this study, a total
of 12 male and 12 female 1-day-old broiler chickens were
raised for 35 days in 2 separate cages. Chickens were divided
into 3 subgroups depending on body weight (low, medium,
and high) by each sex. We compared chicken cecal microbiota
compositions and its predictive functions by sex and body
weight difference. We found that bacterial 16S rRNA genes
were classified as 3 major phyla (Bacteroidetes, Firmicutes,
and Proteobacteria), accounting for > 98% of the total bacterial
community. The profiling of different bacterial taxa and
predictive metagenome functions derived from 16S rRNA
genes were performed over chicken sex and bodyweight. Male
chickens were related to the enrichment of Bacteroides while
female chickens were to the enrichment of Clostridium and
Shigella. Male chickens with high body weight were associated
with the enrichment of Faecalibacterium and Shuttleworthia.
Carbohydrate and lipid metabolisms were suggested as candidate
functions for weight gain in the males. This suggests
that the variation of cecal bacterial communities and their
functions by sex and body weight may be associated with the
differences in the growth potentials of broiler chickens.
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Highly Fermentable Fiber Alters Fecal Microbiota and Mitigates Swine Dysentery Induced by Brachyspira hyodysenteriae Emma T. Helm, Nicholas K. Gabler, Eric. R. Burrough Animals.2021; 11(2): 396. CrossRef
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Factors Influencing the Succession of the Fecal Microbiome in Broilers Dirkjan Schokker, Britt de Klerk, Randy Borg, Alex Bossers, Johanna M.J. Rebel Livestock Science.2021; 247: 104486. CrossRef
Effects of Xylanase in Corn- or Wheat-Based Diets on Cecal Microbiota of Broilers Jian Wang, Heng Cao, Chengling Bao, Yajing Liu, Bing Dong, Chunlin Wang, Zhenda Shang, Yunhe Cao, Suozhu Liu Frontiers in Microbiology.2021;[Epub] CrossRef
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A reasonable correlation between cloacal and cecal microbiomes in broiler chickens Nadia A. Andreani, Caroline J. Donaldson, Matthew Goddard Poultry Science.2020; 99(11): 6062. CrossRef
Green Tea and Pomegranate Extract Administered During Critical Moments of the Production Cycle Improves Blood Antiradical Activity and Alters Cecal Microbial Ecology of Broiler Chickens Vera Perricone, Marcello Comi, Carlotta Giromini, Raffaella Rebucci, Alessandro Agazzi, Giovanni Savoini, Valentino Bontempo Animals.2020; 10(5): 785. CrossRef
Respiratory and Gut Microbiota in Commercial Turkey Flocks with Disparate Weight Gain Trajectories Display Differential Compositional Dynamics Kara J. M. Taylor, John M. Ngunjiri, Michael C. Abundo, Hyesun Jang, Mohamed Elaish, Amir Ghorbani, Mahesh KC, Bonnie P. Weber, Timothy J. Johnson, Chang-Won Lee, Edward G. Dudley Applied and Environmental Microbiology.2020;[Epub] CrossRef
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Effects of Rearing Conditions and Sex on Cecal Microbiota in Ducks Chunhong Zhu, Wenjuan Xu, Zhiyun Tao, Weitao Song, Hongxiang Liu, Shuangjie Zhang, Huifang Li Frontiers in Microbiology.2020;[Epub] CrossRef
Effects of Eimeria maxima and Clostridium perfringens infections on cecal microbial composition and the possible correlation with body weight gain in broiler chickens Mingmin Lu, Robert W. Li, Hongyan Zhao, Xianghe Yan, Hyun S. Lillehoj, Zhifeng Sun, SungTak Oh, Yueying Wang, Charles Li Research in Veterinary Science.2020; 132: 142. CrossRef
Family matters: skin microbiome reflects the social group and spatial proximity in wild zebra finches Kathrin Engel, Helga Pankoke, Sebastian Jünemann, Hanja B. Brandl, Jan Sauer, Simon C. Griffith, Jörn Kalinowski, Barbara A. Caspers BMC Ecology.2020;[Epub] CrossRef
Dissection of the cecal microbial community in chickens after Eimeria tenella infection Hong-Liang Chen, Xin-Yu Zhao, Guang-Xun Zhao, Hai-Bin Huang, Hao-Rui Li, Chun-Wei Shi, Wen-Tao Yang, Yan-Long Jiang, Jian-Zhong Wang, Li-Ping Ye, Quan Zhao, Chun-Feng Wang, Gui-Lian Yang Parasites & Vectors.2020;[Epub] CrossRef
Dietary supplementation with fermented defatted “alperujo” induces modifications of the intestinal mucosa and cecal microbiota of broiler chickens Agustín Rebollada-Merino, María Ugarte-Ruiz, Marta Hernández, Pedro Miguela-Villoldo, David Abad, Pedro Cuesta-Álvaro, David Rodríguez-Lázaro, Lucía de Juan, Lucas Domínguez, Antonio Rodríguez-Bertos Poultry Science.2020; 99(11): 5308. CrossRef
Changes in the gut microbiota mediate the differential regulatory effects of two glucose oxidases produced by Aspergillus niger and Penicillium amagasakiense on the meat quality and growth performance of broilers Shengru Wu, Xiaodong Chen, Taohuan Li, Hao Ren, Lixin Zheng, Xiaojun Yang Journal of Animal Science and Biotechnology.2020;[Epub] CrossRef
Sanguinarine modulate gut microbiome and intestinal morphology to enhance growth performance in broilers Zhu-Ying Liu, Xiao-Long Wang, Shu-Qi Ou, De-Xing Hou, Jian-Hua He, Michael H. Kogut PLOS ONE.2020; 15(6): e0234920. CrossRef
Characterization of heat stress affecting the growth performance, blood biochemical profile, and redox status in male and female broilers at market age Shaojun He, Qirun Yin, Yongjie Xiong, Jing Li, Deyi Liu Tropical Animal Health and Production.2020; 52(6): 3833. CrossRef
Influential factors on the composition of the conventionally raised broiler gastrointestinal microbiomes K.M. Feye, M.F.A. Baxter, G. Tellez-Isaias, M.H. Kogut, S.C. Ricke Poultry Science.2020; 99(2): 653. CrossRef
Genome reconstruction of a novel carbohydrate digesting bacterium from the chicken caecal microflora Ankit T. Hinsu, Ramesh J. Pandit, Shriram H. Patel, Androniki Psifidi, Fiona M. Tomley, Subrata K. Das, Damer P. Blake, Chaitanya G. Joshi Meta Gene.2019; 20: 100543. CrossRef
Functioning of the Intestinal Ecosystem: From New Technologies in Microbial Research to Practical Poultry Feeding – A Review Zenon Zduńczyk Annals of Animal Science.2019; 19(2): 239. CrossRef
Faecalibacterium diversity in dairy cow milk Keith W. Savin, Jody Zawadzki, Martin J. Auldist, Jianghui Wang, Doris Ram, Simone Rochfort, Benjamin G. Cocks, Christopher Staley PLOS ONE.2019; 14(8): e0221055. CrossRef
Olfactory Communication via Microbiota: What Is Known in Birds? Öncü Maraci, Kathrin Engel, Barbara A. Caspers Genes.2018; 9(8): 387. CrossRef