Nitrification of a tropical peat soil cultivated with oil palm (Elaeis guineensis Jacq.) by Ariffin, Mohd Rizal

“…Planctomycetaceae order from the phylum Planctomycetes (anammox bacteria) were also abundant in number suggesting anaerobic ammonium oxidation is possible in tropical peat soil cultivated with oil palm. …”
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Bacterial and methanogenic archaeal community changes during treatment of palm oil mill effluent and biological indicators for final discharge by Mohd Nor, Diana

“…However, the bacterial community compositions in the different final discharges exhibited almost similar patterns in that the phylum Proteobacteria was dominant in all the samples. …”
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Inhaled Corticosteroids Selectively Alter the Microbiome and Host Transcriptome in the Small Airways of Patients with Chronic Obstructive Pulmonary Disease by William Yip, Xuan Li, Graeme J. Koelwyn, Stephen Milne, Fernando Sergio Leitao Filho, Chen Xi Yang, Ana I. Hernández Cordero, Julia Yang, Cheng Wei Tony Yang, Tawimas Shaipanich, Stephan F. van Eeden, Janice M. Leung, Stephen Lam, Kelly M. McNagny, Don D. Sin

“…Longitudinal changes in the microbiome at a community, phylum and genus level were correlated with changes in host gene expression using a Spearman’s rank correlation test. …”
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Multi-Omics Analysis of the Microbiome and Metabolome Reveals the Relationship Between the Gut Microbiota and Wooden Breast Myopathy in Broilers by Kelang Kang, Kelang Kang, Nanxuan Zhou, Nanxuan Zhou, Weishi Peng, Weishi Peng, Fang Peng, Fang Peng, Mengmeng Ma, Mengmeng Ma, Liwei Li, Liwei Li, Fuyi Fu, Fuyi Fu, Shuhan Xiang, Shuhan Xiang, Haihan Zhang, Haihan Zhang, Haihan Zhang, Xi He, Xi He, Xi He, Xi He, Zehe Song, Zehe Song, Zehe Song, Zehe Song

“…The diversity of the intestinal microflora was decreased in birds with severe WB, with decreases in Chao 1, and observed species indices. At the phylum level, birds with severe WB had a lower Firmicutes/Bacteroidetes ratio (P = 0.098) and a decreased abundance of Verrucomicrobia (P < 0.05). …”
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Effects of fermented soybean meal substitution for fish meal on intestinal flora and intestinal health in pearl gentian grouper by Aobo Pang, Aobo Pang, Aobo Pang, Cong Peng, Cong Peng, Cong Peng, Ruitao Xie, Zhuoduo Wang, Beiping Tan, Beiping Tan, Beiping Tan, Tingting Wang, Tingting Wang, Tingting Wang, Wei Zhang, Wei Zhang, Wei Zhang

“…Photobacterium was the dominant phylum in all experimental groups, and the proportion of these bacteria gradually decreased with increasing FSBM substitution. …”
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Effects of Heated Drinking Water during the Cold Season on Serum Biochemistry, Ruminal Fermentation, Bacterial Community, and Metabolome of Beef Cattle by Tengfei He, Guang Yi, Xilin Wang, Yan Sun, Jiangong Li, Zhenlong Wu, Yao Guo, Fang Sun, Zhaohui Chen

“…Compared to RTW, the HW mainly had a higher relative abundance of <i>Firmicutes</i> (<i>p</i> = 0.07) at the phylum level and had a lower abundance of <i>Prevotella</i> (<i>p</i> < 0.01), <i>norank_f_p-215-o5</i> (<i>p</i> = 0.03), and a higher abundance of <i>NK4A214_group</i> (<i>p</i> = 0.01) and <i>Lachnospiraceae_NK3A20_group</i> (<i>p</i> = 0.05) at the genus level. …”
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Comparative Analysis of the Endophytic Bacterial Diversity of Populus euphratica Oliv. in Environments of Different Salinity Intensities by Haitao Yue, Luyu Zhao, Duo Yang, Minwei Zhang, Jieyi Wu, Zhongkai Zhao, Xiangxiang Xing, Liwen Zhang, Yanan Qin, Fei Guo, Jie Yang, Tuerxunnayi Aili

“…Notably, Firmicutes (relative abundance >5%) was a different dominant phylum in the samples from the high-saline environment compared with the relatively low-saline-environment group. …”
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Fecal bacterial microbiome diversity in chronic HIV-infected patients in China by Yang Sun, Yingfei Ma, Ping Lin, Yi-Wei Tang, Liying Yang, Yinzhong Shen, Renfan Zhang, Li Liu, Jun Cheng, Jiashen Shao, Tangkai Qi, Yan Tang, Rentian Cai, Liqian Guan, Bin Luo, Meiyan Sun, Ben Li, Zhiheng Pei, Hongzhou Lu

“…Relative abundance at the phylum and genus levels were calculated. Alpha diversity was determined by Chao 1 and observed-species indices, and beta diversity was determined by double principal component analysis using the estimated phylogeny-based unweighted Unifrac distance matrices. …”
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Effects of High Dietary Carbohydrate Levels on Growth Performance, Enzyme Activities, Expression of Genes Related to Liver Glucose Metabolism, and the Intestinal Microbiota of <i>L... by Luzhe Zheng, Zhanzhan Wang, Bo Zhang, Lulu Yan, Pengfei Wang, Chao Zhao, Heizhao Lin, Lihua Qiu, Chuanpeng Zhou

“…High-throughput 16S rRNA gene sequencing showed that high dietary carbohydrate intake changed the composition and structure of the intestinal microbiota. At the phylum level of the intestinal microbiota, high dietary carbohydrates decreased the relative abundance of Firmicutes and increased the relative abundance of Proteobacteria and Bacteroidetes. …”
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Effects of Dietary Indole-3-carboxaldehyde Supplementation on Growth Performance, Intestinal Epithelial Function, and Intestinal Microbial Composition in Weaned Piglets by Ruofan Zhang, Ruofan Zhang, Guowen Huang, Guowen Huang, Yuting Ren, Yuting Ren, Haifeng Wang, Yanxin Ye, Yanxin Ye, Jiaqing Guo, Jiaqing Guo, Mengting Wang, Mengting Wang, Weiyun Zhu, Weiyun Zhu, Kaifan Yu, Kaifan Yu

“…In addition, dietary ICA supplementation modulated the intestinal flora, increasing the richness estimators and diversity index, decreasing the abundances of phylum Fibrobacterota and genera Alloprevotella, Prevotella, and Parabacteroides, and enriching the abundance of genera Butyrivibrio. …”
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Children with idiopathic short stature have significantly different gut microbiota than their normal height siblings: a case-control study by Liora Lazar, Liora Lazar, Adi Eshel, Lelyan Moadi, Michal Yackobovitch-Gavan, Michal Yackobovitch-Gavan, Michal Yackobovitch-Gavan, Meytal Bar-Maisels, Meytal Bar-Maisels, Biana Shtaif, Biana Shtaif, Michal Nevo, Moshe Phillip, Moshe Phillip, Moshe Phillip, Sondra Turjeman, Omry Koren, Galia Gat-Yablonski, Galia Gat-Yablonski, Galia Gat-Yablonski

“…Outcome measures from fecal analysis of both siblings included GM composition analyzed by 16S rRNA sequencing, fecal metabolomics, and monitoring the growth of germ-free (GF) mice after fecal transplantation.ResultsFecal analysis of ISS children identified higher predicted levels of genes encoding enzymes for pyrimidine, purine, flavin, coenzyme B, and thiamine biosynthesis, lower levels of several amino acids, and a significantly higher prevalence of the phylum Euryarchaeota compared to their normal-height siblings (p&lt;0.001). …”
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Long-Term Cultivation and Meta-Omics Reveal Methylotrophic Methanogenesis in Hydrocarbon-Impacted Habitats by Yi-Fan Liu, Jing Chen, Zhong-Lin Liu, Zhao-Wei Hou, Bo Liang, Li-Ying Wang, Lei Zhou, Li-Bin Shou, Dan-Dan Lin, Shi-Zhong Yang, Jin-Feng Liu, Xiao-Lin Wu, Ji-Dong Gu, Bo-Zhong Mu

“…However, according to the metatranscriptomic analyses, methane was predicted to be produced mainly via H2-dependent methylotrophic methanogenesis, primarily from necromass-derived trimethylamine mediated by Methanomethyliaceae within the candidate phylum Verstraetearchaeota. These findings reveal that H2-dependent methylotrophic methanogens, as well as methylotrophic methanogens, may play important ecological roles in the carbon cycle of hydrocarbon enriched subsurface ecosystems.…”
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Evidence for a Causal Role for Escherichia coli Strains Identified as Adherent-Invasive (AIEC) in Intestinal Inflammation by Hatem Kittana, João C. Gomes-Neto, Kari Heck, Anthony F. Juritsch, Jason Sughroue, Yibo Xian, Sara Mantz, Rafael R. Segura Muñoz, Liz A. Cody, Robert J. Schmaltz, Christopher L. Anderson, Rodney A. Moxley, Jesse M. Hostetter, Samodha C. Fernando, Jennifer Clarke, Stephen D. Kachman, Clayton E. Cressler, Andrew K. Benson, Jens Walter, Amanda E. Ramer-Tait

“…Many species in this phylum are thought to contribute to disease under certain conditions, including adherent-invasive Escherichia coli (AIEC) strains, which are enriched in some patients. …”
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Analysis of fecal microbiota and related clinical indicators in ICU patients with sepsis by Huaying Chen, Huiheng Liu, Yujing Sun, Meiqin Su, Jinzhou Lin, Junsheng Wang, Jueying Lin, Xiaoyan Zhao

“…There were significant differences in APACHE II score, length of ICU stay, lactate level, and oxygenation index of patients between the Death or DAMA group and Clinical Improvement group (all P < 0.05). For phylum level, the abundance of Firmicutes, Actinobacteria, and Bacteroidetes decreased in the ND group compared with the ND_HC group, while the abundance of Proteobacteria increased (P < 0.05). …”
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The Threat of Potentially Pathogenic Bacteria in the Feces of Bats by Yuyuan Huang, Yamin Sun, Qianni Huang, Xianglian Lv, Ji Pu, Wentao Zhu, Shan Lu, Dong Jin, Liyun Liu, Zhengli Shi, Jing Yang, Jianguo Xu

“…The results revealed that the bat microbiome was most commonly dominated by Proteobacteria, while the strictly anaerobic phylum Bacteroidetes occupied 35.3% of the relative abundance in Rousettus spp. and 36.3% in Hipposideros spp., but less than 2.7% in the other three bat species (Taphozous spp., Rhinolophus spp., and Myotis spp.). …”
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Mineral waters of Serbia and development of phototrophic microbial communities near points of emergence and on wellheads by Vladimir Šaraba, Slađana Popović, Olivera Krunić, Gordana Subakov Simić, Željko Kljajić, Milojko Lazić

“…Although many representative taxa are found on only one of the studied localities, such as Synechococcus bigranulatus and Pseudanabaena thermalis, those of the genera Leptolyngbya, Phormidium and Cosmarium laeve, as well as genera of the phylum Bacillariophyta, occur at several sampling sites. …”
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Full-length transcriptome analysis provides insights into larval shell formation in Mulinia lateralis by Xiaolin Guo, Xixi Li, Feng Zhao, Danwen Liu, Zujing Yang, Moli Li, Yajuan Li, Huilan Wei, Hao Wang, Zhenkui Qin, Zhifeng Zhang, Zhifeng Zhang, Zhenmin Bao, Zhenmin Bao

“…Mollusca is the second largest animal phylum and represents one of the most evolutionarily successful animal groups. …”
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Expression Analysis and the Roles of the <i>Sec1</i> Gene in Regulating the Composition of Mouse Gut Microbiota by Zhanshi Ren, Hairui Fan, Shanshen Gu, Haoyu Liu, Zhengchang Wu, Haifei Wang, Wenbin Bao, Shenglong Wu

“…Analysis of gut microbial composition in <i>Sec1</i> knockout mice revealed that at the phylum level, <i>Bacteroidetes</i> accounted for 68.8%and 68.3% of gut microbial composition in the <i>Sec1⁻</i>^/− and <i>Sec1⁺</i>^/+ groups, respectively, and <i>Firmicutes</i> accounted for 27.1% and 19.7%, respectively; while <i>Firmicutes</i>/<i>Bacteroidetes</i> were significantly higher in <i>Sec1⁻</i>^/− mice than in <i>Sec1⁺</i>^/+ mice (39.4% vs. 28.8%). …”
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Evolution of the Gut Microbiome in HIV-Exposed Uninfected and Unexposed Infants during the First Year of Life by Conner L. Jackson, Daniel N. Frank, Charles E. Robertson, Diana Ir, Jennifer M. Kofonow, Mahlodi P. Montlha, Eleonora A. M. L. Mutsaerts, Marta C. Nunes, Shabir A. Madhi, Debashis Ghosh, Adriana Weinberg

“…Microbial composition significantly differed, including 12 genera, 5 families and 1 phylum at 6 weeks; 12 genera and 2 families at 28 weeks; and 2 genera and 2 families at 62 weeks of life. …”
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Succession of the Intestinal Microflora Structure of Haliotis discus hannai During the Weaning Period by Li NIAN, Zhipeng WANG, Haitao ZHANG, Xuguang HOU, Zhansheng GUO

“…In terms of the composition and structure at the phylum level, the dominant bacterial groups in diatom-fed abalone and weaning abalone were relatively consistent, including Proteobacteria, Bacteroidetes, and Firmicutes. …”
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