Article
Biotechnology & Applied Microbiology
Balazs Kakuk, Roland Wirth, Gergely Maroti, Mark Szuhaj, Gabor Rakhely, Krisztian Laczi, Kornel L. Kovacs, Zoltan Bagi
Summary: The early response of the mixed mesophilic microbial community to H-2 gas injection was investigated to uncover the first responses of the microbial community. The study found that certain Archaea increased hydrogenotrophic methanogenesis activity in response to H-2 exposure, while the pathway in Methanosarcina was downregulated. Additionally, H-2 injection altered the metabolism of certain Bacteria, impacting the syntrophic community interactions between Archaea and Bacteria.
MICROBIAL CELL FACTORIES
(2021)
Article
Microbiology
Jing Yang, Qiang Zhang, Jun Zhang, Yan Ouyang, Zepeng Sun, Xinlong Liu, Feng Qaio, Li-Qun Xu, Yunfei Niu, Jian Li
Summary: Chronic obstructive pulmonary disease (COPD) is a respiratory disease caused by the interaction between genes and environmental conditions. The composition of airway bacteria changes significantly during acute exacerbations in COPD patients, accompanied by alterations in host inflammatory responses.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Microbiology
Lu Qian, Xiaoli Yu, Hang Gu, Fei Liu, Yijun Fan, Cheng Wang, Qiang He, Yun Tian, Yisheng Peng, Longfei Shu, Shanquan Wang, Zhijian Huang, Qingyun Yan, Jianguo He, Guangli Liu, Qichao Tu, Zhili He
Summary: This study investigates the diversity, function, and coupling mechanism of microbially driven biogeochemical cycling along the sediment depth of mangrove wetlands. The results show that the metabolic pathways involved in methane, nitrogen, and sulfur cycling are influenced by pH and acid volatile sulfide. S-driven denitrifiers play an important role in N2O emissions and there are potential coupling mechanisms between ANMEs and SRB in the mangrove sediment.
Article
Engineering, Environmental
Chen-Wei Zheng, Yi-Hao Luo, Yen-Jung Sean Lai, Zehra Esra Ilhan, Aura Ontiveros-Valencia, Rosa Krajmalnik-Brown, Yan Jin, Haiwei Gu, Xiangxing Long, Dandan Zhou, Bruce E. Rittmann
Summary: Traditional research methods for the biodegradation of emerging organic pollutants are slow and labor-intensive, but new metagenome, metatranscriptome, and metabolome technologies offer a faster and more efficient approach. By integrating these three "omics" approaches, it is possible to link gene abundance and expression with the biotransformation of the pollutants and the formation of metabolites. In this study, the tri-omics approach was used to study the biotransformation pathways of cetyltrimethylammonium bromide (CTAB) under aerobic conditions. The analysis revealed three parallel first-step oxygenation pathways and identified key intermediates and enzymes involved in the biotransformation of CTAB. This study highlights the potential of the tri-omics approach for future research on complex organic biodegradation by microbial communities.
Article
Microbiology
Joshua C. Gil, Sarah M. Hird
Summary: This study investigated the accuracy of simulated metagenomes in a nonmodel system, the Canada goose, and revealed some unique functional characteristics of the microbiome in this nonmodel organism. It also highlighted the limitations of simulated metagenomes in specific gene prediction.
MICROBIOLOGY SPECTRUM
(2022)
Review
Oncology
Paul Vinu Salachan, Karina Dalsgaard Sorensen
Summary: The role of microbiota in human health and disease, including cancer types, is established, but its specific role in prostate cancer development, progression, and treatment response is less understood. The lack of better risk stratification tools may be due to gaps in knowledge regarding bacterial infections and inflammation signatures as risk factors. Further research is needed to find the biological link between microbiome and prostate carcinogenesis.
JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH
(2022)
Article
Ecology
Juan Pablo Isaza, Vanessa Sandoval-Figueredo, Maria Camila Rodelo, Andrea Munoz-Garcia, Ingrid Figueroa-Galvis, Javier Vanegas
Summary: This study characterized the metatranscriptome of bacteria associated with nutrient cycling and xenobiotic degradation in a mangrove contaminated by wastewater in the Colombian Caribbean. Firmicutes and Proteobacteria were found to be the predominant phyla, with gene expression mainly related to carbohydrate metabolism and genetic information processing. Functional annotation revealed high transcriptional activity in metabolic pathways and biogeochemical cycles, indicating a dominance of anaerobic processes and decomposition of organic matter. The degradation of benzoate was identified as the pathway with the highest transcriptional activity in xenobiotic degradation. The dominance of few taxonomic groups may suggest selection by wastewater and potential future loss of ecosystem resilience.
REGIONAL STUDIES IN MARINE SCIENCE
(2021)
Article
Engineering, Environmental
Vicente Gomez-Alvarez, Sallamaari Siponen, Ari Kauppinen, Anna-Maria Hokajarvi, Ananda Tiwari, Anniina Sarekoski, Ilkka T. Miettinen, Eila Torvinen, Tarja Pitkanen
Summary: The study used next-generation sequencing technologies to analyze the water microbiome in five waterworks in Finland. The presence and type of disinfectant residual exert selective pressure on the microbial community. The microbial community in non-disinfected drinking water systems is important and maintaining disinfectant residual is crucial for reducing microbial numbers and diversity.
Article
Chemistry, Multidisciplinary
Na Zhao, Jiabao Cao, Jiayue Xu, Beibei Liu, Bin Liu, Dingqiang Chen, Binbin Xia, Liang Chen, Wenhui Zhang, Yuqing Zhang, Xuan Zhang, Zhimei Duan, Kaifei Wang, Fei Xie, Kun Xiao, Wei Yan, Lixin Xie, Hongwei Zhou, Jun Wang
Summary: Utilizing RNA sequencing and third-generation sequencing technology for pathogen identification can improve the ratio of microbial reads and accelerate clinical diagnosis, showing significant potential.
Article
Biology
Mingwei Cai, Changhai Duan, Xinxu Zhang, Jie Pan, Yang Liu, Cuijing Zhang, Meng Li
Summary: Theionarchaea, a recently described archaeal class within the Euryarchaeota, was found in sediment ecosystems with potential metabolic capabilities including detoxifying proteins and amino acids. Through metagenomics and metatranscriptomics, Theionarchaea's role in marine ecosystems and its syntrophic relationship with fermenters and methanogens were revealed.
SCIENCE CHINA-LIFE SCIENCES
(2022)
Article
Microbiology
Shiyu Tao, Huicong Zou, Jingjing Li, Hong Wei
Summary: This study provides a comprehensive understanding of the intestinal virome in early-weaned piglets, revealing the differences in virome profiles between healthy piglets and piglets with diarrhea. Potential biomarkers for diarrhea in early-weaned piglets were identified, laying the foundation for the development of strategies to prevent and treat early-weaning-induced piglet diarrhea.
MICROBIOLOGY SPECTRUM
(2022)
Article
Microbiology
Pradeep K. Malik, Shraddha Trivedi, Atul P. Kolte, Archit Mohapatra, Siddharth Biswas, Ashwin V. K. Bhattar, Raghavendra Bhatta, Habibar Rahman
Summary: A study compared the rumen microbial community and functional differences in adult male cattle and buffaloes fed on the same diet. The results showed no difference in microbiota composition and methane yield between the two host species, but some differences were observed in functional abundance. However, feeding cattle and buffaloes on the same diet resulted in similar microbiota composition, metabolic functionality, and methane yield.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Microbiology
Mika Uehara, Takashi Inoue, Minori Kominato, Sumitaka Hase, Erika Sasaki, Atsushi Toyoda, Yasubumi Sakakibara
Summary: We developed an analysis method that integrates metagenomes and metatranscriptomes from multiple intestinal sites to elucidate how microbial function varies along the intestinal tract. This method enables spatial covariation analysis of the functional activity of microbiomes and accurate identification of gene expression changes among intestinal sites, including changes in the expression of unknown bacterial genes. Moreover, we applied this method to the investigation of the common marmoset intestine, which is anatomically and pharmacologically similar to that of humans. Our findings indicate the expression pattern of the microbiome varies in response to changes in the internal environment along the intestinal tract, and this microbial change may affect the intestinal environment.
Article
Nutrition & Dietetics
Song-Song Xu, Xiu-Ling Zhang, Sha-Sha Liu, Shu-Tang Feng, Guang-Ming Xiang, Chang-Jiang Xu, Zi-Yao Fan, Kui Xu, Nan Wang, Yue Wang, Jing-Jing Che, Zhi-Guo Liu, Yu-Lian Mu, Kui Li
Summary: This study established an animal model of metabolic syndrome similar to humans and analyzed metabolic parameters, atherosclerotic lesions, gut microbiome, and host transcriptome. The results showed that diet-induced gut microbiota dysbiosis activated host chronic inflammatory responses and upregulated the expression of genes related to arachidonic acid-dependent signaling pathways, revealing an intimate linkage between arachidonic acid metabolism and atherothrombosis.
FRONTIERS IN NUTRITION
(2022)
Article
Veterinary Sciences
Yunjuan Peng, Ting Xie, Zhuosui Wu, Wenxiao Zheng, Tao Zhang, Samantha Howe, Jianmin Chai, Feilong Deng, Ying Li, Jiangchao Zhao
Summary: This study reanalyzed the composition and expression activity of gut archaea in ruminants and monogastric animals using metagenomic and metatranscriptomic data. The results showed significant differences in the alpha and beta diversity of each host species, suggesting that metatranscriptomic data better represent the functional status of archaea.
FRONTIERS IN VETERINARY SCIENCE
(2022)
Article
Biology
Mingwei Cai, Changhai Duan, Xinxu Zhang, Jie Pan, Yang Liu, Cuijing Zhang, Meng Li
Summary: Theionarchaea, a recently described archaeal class within the Euryarchaeota, was found in sediment ecosystems with potential metabolic capabilities including detoxifying proteins and amino acids. Through metagenomics and metatranscriptomics, Theionarchaea's role in marine ecosystems and its syntrophic relationship with fermenters and methanogens were revealed.
SCIENCE CHINA-LIFE SCIENCES
(2022)
Article
Environmental Sciences
Mingwei Cai, Xiuran Yin, Xiaoyu Tang, Cuijing Zhang, Qingfei Zheng, Meng Li
Summary: The study investigated methanogens in vegetated coastal ecosystems and found that mangroves have more diverse methane-producing archaea compared to saltmarshes and seagrasses, where methylotrophic methanogenesis is predominant. The research identified 13 groups of methanogenic archaea being transcribed in VCEs, with Methanosarcinales being the most predominant. This suggests potential distinct methane production contributions in different VCEs to global warming.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Microbiology
Zhichao Zhou, Patricia Q. Tran, Adam M. Breister, Yang Liu, Kristopher Kieft, Elise S. Cowley, Ulas Karaoz, Karthik Anantharaman
Summary: Advances in microbiome science have been driven by the ability to study and infer microbial ecology from genomes. METABOLIC is a scalable software that allows for the study of microbial ecology and biogeochemistry using genomes at the resolution of individual organisms and/or microbial communities. It provides annotation of microbial genomes, metabolic pathway analyses, and determination of microbial contributions to biogeochemical transformations and cycles. METABOLIC is a versatile tool that can be used with various metagenomic datasets, from diverse environments such as marine subsurface, terrestrial subsurface, and human gut.
Article
Ecology
Xiuran Yin, Guowei Zhou, Mingwei Cai, Qing-Zeng Zhu, Tim Richter-Heitmann, David A. Aromokeye, Yang Liu, Rolf Nimzyk, Qingfei Zheng, Xiaoyu Tang, Marcus Elvert, Meng Li, Michael W. Friedrich
Summary: The study found that multiple low-abundance archaeal groups are actually catabolic protein degraders, while the functional role of widespread extracellular peptidases is not an optimal tool to identify protein catabolism. In addition, the catabolic degradation of sedimentary protein is not a common feature of the abundant archaeal community in temperate and permanently cold marine sediments.
Article
Biochemistry & Molecular Biology
Xinxu Zhang, Yuhan Huang, Yang Liu, Wei Xu, Jie Pan, Xiaowei Zheng, Huan Du, Cuijing Zhang, Zhongyi Lu, Dayu Zou, Zongbao Liu, Mingwei Cai, Jinbo Xiong, Yaxin Zhu, Zhiyang Dong, Hongchen Jiang, Hailiang Dong, Juquan Jiang, Zhuhua Luo, Li Huang, Meng Li
Summary: This study analyzed 146 Thermoprofundales genomes and revealed five subgroups with distinct habitat preferences. Most of the microorganisms from Subgroups B and D are thermophiles inhabiting hydrothermal vents and hot spring sediments, while those from Subgroup E are adapted to surface environments with sunlight. The study also discovered that Thermoprofundales may have the ability to produce H2 gas, and the peripheral arm structure of Subgroup E plays an important role in evolution.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Ecology
Cui-Jing Zhang, Yu-Rong Liu, Guihong Cha, Yang Liu, Xin-Quan Zhou, Zhongyi Lu, Jie Pan, Mingwei Cai, Meng Li
Summary: Methylmercury (MeHg) is a potent neurotoxin that bioaccumulates along food chains. The diversity and distribution of putative microbial Hg-methylators in mangrove ecosystems were investigated using metagenomic and metatranscriptomic analyses. Asgard archaea, including Lokiarchaeota, were identified as potential novel Hg-methylating microorganisms. These findings suggest the important role of Asgard archaea in hgcA evolution and MeHg production.
Article
Microbiology
Huan Du, Jie Pan, Dayu Zou, Yuhan Huang, Yang Liu, Meng Li
Summary: This study identified a substantial number of potential microbial metabolic interactions in mangrove sediments using metabolic modeling-based approach. The concept of microbial active functional module (mAFM) was proposed to describe a group of microbes with high metabolic interactions, contributing to element transformations in the sediments. The results greatly expanded the understanding of microbial interactions and their roles in biogeochemical cycling in mangrove sediments.
Article
Environmental Sciences
Zongbao Liu, Xiulin Wan, Cuijing Zhang, Mingwei Cai, Yueping Pan, Meng Li
Summary: This study investigated the occurrence, host range, and potential mobility of antibiotic resistance genes (ARGs) in six mangrove ecosystems in southeastern China. The research identified a total of 348 ARG subtypes, with some being associated with clinically relevant antibiotics. The results also revealed more than 42 bacterial phyla as potential hosts of ARGs.
JOURNAL OF ENVIRONMENTAL MANAGEMENT
(2023)
Article
Microbiology
Yang Tong, Xinying Wu, Yang Liu, Huiyu Chen, Yan Zhou, Li Jiang, Meng Li, Suwen Zhao, Yan Zhang
Summary: Many bacteriophages evade bacterial immune recognition by substituting adenine with 2,6-diaminopurine (Z) in their genomes. A naturally existing PurZ variant, PurZ0, which uses guanosine triphosphate as the phosphate donor, has been identified and characterized. The structure of PurZ0 is highly analogous to that of archaeal PurA, suggesting it is an intermediate in the evolution from archaeal PurA to phage PurZ.
NATURE MICROBIOLOGY
(2023)
Editorial Material
Multidisciplinary Sciences
Meng Li, Changhai Duan
CHINESE SCIENCE BULLETIN-CHINESE
(2023)
Article
Microbiology
Huan Du, Jie Pan, Cuijing Zhang, Xilan Yang, Cheng Wang, Xiaolan Lin, Jinhui Li, Wan Liu, Haokui Zhou, Xiaoli Yu, Shuming Mo, Guoqing Zhang, Guoping Zhao, Wu Qu, Chengjian Jiang, Yun Tian, Zhili He, Yang Liu, Meng Li
Summary: The study compares the microbial features of mangrove ecosystems in China and South America, finding analogous assembly patterns and key functional guilds. The entire communities exhibit significant distance-decay patterns and are strongly influenced by stochastic processes, while the assembly of specialists may be related to the behaviors of organisms in the mangrove ecosystems. Sulfate-reducing prokaryotes dominate the mangrove microbiomes and play important roles in maintaining community structure and functions.
MICROBIOLOGY SPECTRUM
(2023)
