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Journal Article 8

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2024 1

2023 2

2022 1

2020 1

2019 2

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Metagenomics 7

-caproate 1

n-caproate 1

Ammonia inhibition 1

Antibiotic resistance 1

Antibiotic resistance genes 1

Bacterial community 1

Bathyarchaeota 1

Chain elongation 1

Comparative genomics 1

Culturomics 1

Decentralized sewage treatment facilities 1

Enzyme 1

Fatty acid biosynthesis 1

Hyperthermophilic adaptation 1

Landfill leachate 1

Medium chain fatty acids 1

Metabolomics 1

Network analysis 1

Partial nitrification-denitrification 1

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Culturomics and metagenomics: In understanding of environmental resistome

Monika Nowrotek, Łukasz Jałowiecki, Monika Harnisz, Grażyna Anna Płaza

Frontiers of Environmental Science & Engineering 2019, Volume 13, Issue 3, doi: 10.1007/s11783-019-1121-8

Abstract:

State of the art of culturomics and metagenomics to study resistome

The combination of culturomics and metagenomics

Keywords： Culturomics     Metagenomics     Antibiotic resistance     Resistome    

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METAGENOMICS COMBINED WITH HIGH-THROUGHPUT SEQUENCING REVEALS THE METHANOGENIC POTENTIAL OF FRESH CORN

Frontiers of Agricultural Science and Engineering 2023, Volume 10, Issue 3,   Pages 403-423 doi: 10.15302/J-FASE-2022471

Abstract:

● Methane production from fresh straw was 7.50% higher than dry straw.

Keywords： fresh corn straw     high solid anaerobic digestion     metagenomics     microbial communities     thermophilic    

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Distribution of antibiotic resistance genes and their association with bacteria and viruses in decentralized sewage treatment facilities

Frontiers of Environmental Science & Engineering 2022, Volume 16, Issue 3, doi: 10.1007/s11783-021-1469-4

Abstract:

• Distribution of ARGs in decentralized sewage facilities were investigated.

Keywords： Decentralized sewage treatment facilities     Antibiotic resistance genes     Virus     Metagenomics     Network    

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Core Metabolic Features and Hot Origin of Bathyarchaeota Article

Xiaoyuan Feng, Yinzhao Wang, Rahul Zubin, Fengping Wang

Engineering 2019, Volume 5, Issue 3,   Pages 498-504 doi: 10.1016/j.eng.2019.01.011

Abstract:

The archaeal phylum Bathyarchaeota comprises highly diversified subgroups and is considered to be one of the most abundant microorganisms on earth. The metabolic features and evolution of this phylum still remain largely unknown. In this article, a comparative metabolic analysis of 15 newly reconstructed and 36 published metagenomic assembled genomes (MAGs) spanning 10 subgroups was performed, revealing the core metabolic features of Bathyarchaeota—namely, protein, lipid, and benzoate degradation; glycolysis; and the Wood–Ljungdahl (WL) pathway, indicating an acetyl-CoA-centralized metabolism within this phylum. Furthermore, a partial tricarboxylic acid (TCA) cycle, acetogenesis, and sulfur-related metabolic pathways were found in specific subgroups, suggesting versatile metabolic capabilities and ecological functions of different subgroups. Intriguingly, most of the MAGs from the Bathy-21 and -22 subgroups, which are placed at the phylogenetic root of all bathyarchaeotal lineages and likely represent the ancient Bathyarchaeota types, were found in hydrothermal environments and encoded reverse gyrase, suggesting a hyperthermophilic feature. This work reveals the core metabolic features of Bathyarchaeota, and indicates a hot origin of this archaeal phylum.

Keywords： Bathyarchaeota     Metagenomics     Comparative genomics     Hyperthermophilic adaptation    

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Taxonomic and functional variations in the microbial community during the upgrade process of a full-scale landfill leachate treatment plant – from conventional to partial nitrification-denitrification

Binbin Sheng, Depeng Wang, Xianrong Liu, Guangxing Yang, Wu Zeng, Yiqing Yang, Fangang Meng

Frontiers of Environmental Science & Engineering 2020, Volume 14, Issue 6, doi: 10.1007/s11783-020-1272-7

Abstract: Abstract • Upgrade process was investigated in a full-scale landfill leachate treatment plant. • The optimization of DO can technically achieve the shift from CND to PND process. • Nitrosomonas was mainly responsible for ammonium oxidation in PND system. • An obviously enrichment of Thauera was found in the PND process. • Enhanced metabolic potentials on organics was found during the process update. Because of the low access to biodegradable organic substances used for denitrification, the partial nitrification-denitrification process has been considered as a low-cost, sustainable alternative for landfill leachate treatment. In this study, the process upgrade from conventional to partial nitrification-denitrification was comprehensively investigated in a full-scale landfill leachate treatment plant (LLTP). The partial nitrification-denitrification system was successfully achieved through the optimizing dissolved oxygen and the external carbon source, with effluent nitrogen concentrations lower than 150 mg/L. Moreover, the upgrading process facilitated the enrichment of Nitrosomonas (abundance increased from 0.4% to 3.3%), which was also evidenced by increased abundance of amoA/B/C genes carried by Nitrosomonas. Although Nitrospira (accounting for 0.1%–0.6%) was found to stably exist in the reactor tank, considerable nitrite accumulation occurred in the reactor (reaching 98.8 mg/L), indicating high-efficiency of the partial nitrification process. Moreover, the abundance of Thauera, the dominant denitrifying bacteria responsible for nitrite reduction, gradually increased from 0.60% to 5.52% during the upgrade process. This process caused great changes in the microbial community, inducing continuous succession of heterotrophic bacteria accompanied by enhanced metabolic potentials toward organic substances. The results obtained in this study advanced our understanding of the operation of a partial nitrification-denitrification system and provided a technical case for the upgrade of currently existing full-scale LLTPs.

Keywords： Landfill leachate     Process upgrade     Partial nitrification-denitrification     Bacterial community     Metagenomics    

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Alterations in the Gut Microbiome in Liver Recipients with Post-transplant Diabetes Mellitus Article

Qi Ling, Yuqiu Han, Yue Ma, Xiaosen Wang, Zheng Zhu, Jingyu Wang, Jiaying Cao, Lin Xiaohan, Jun Wang, Baohong Wang

Engineering 2023, Volume 31, Issue 12,   Pages 98-111 doi: 10.1016/j.eng.2023.09.006

Abstract: Here, by combining high-throughput shotgun metagenomics sequencing and metabolomics profiling, we characterized

Keywords： Post-transplant diabetes mellitus     Tacrolimus     Metagenomics     Metabolomics    

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Chain Elongation Using Native Soil Inocula: Exceptional n-Caproate Biosynthesis Performance and Microbial Mechanisms

Lin Deng,Yang Lv,Tian Lan,Qing-Lian Wu,Wei-Tong Ren,Hua-Zhe Wang,Bing-Jie Ni,Wan-Qian Guo,

Engineering doi: 10.1016/j.eng.2023.10.017

Abstract: Moreover, metagenomics analysis revealed a higher abundance of functional genes in key microbial species

Keywords： Soil     Chain elongation     n     -caproate     Reverse beta-oxidation     Fatty acid biosynthesis     Metagenomics    

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Unveiling the Mechanism Underlying the Effects of Ammonia on n-Caproate Production: Influenced Pathways, Key Enzymes, and Microbiota Functions Article

Qing-Lian Wu, Ke-Xin Yuan, Wei-Tong Ren, Lin Deng, Hua-Zhe Wang, Xiao-Chi Feng, He-Shan Zheng, Nan-Qi Ren, Wan-Qian Guo

Engineering 2024, Volume 35, Issue 4,   Pages 180-190 doi: 10.1016/j.eng.2023.08.018

Abstract:

n-caproate, which is produced via chain elongation (CE) using waste biomass, can supply various fossil-derived products, thus advancing the realization of carbon neutrality. Ammonia released from the degradation of nitrogen-rich waste biomass can act as a nutrient or an inhibitor in anaerobic bioprocesses, including CE, with the distinction being primarily dependent on its concentration. Currently, the optimal concentration of ammonia and the threshold of toxicity for open-culture n-caproate production using ethanol as an electron donor, along with the underlying mechanisms, remain unclear. This study revealed that the optimal concentration of ammonia for n-caproate production was 2 g∙L−1, whereas concentrations exceeding this threshold markedly suppressed the CE performance. Exploration of the mechanism revealed the involvement of two forms of ammonia (i.e., ammonium ions and free ammonia) in this inhibitory behavior. High ammonia levels (5 g∙L−1) induced excessive ethanol oxidation and suppressed the reverse β-oxidation (RBO) process, directly leading to the enhanced activities of enzymes (phosphotransacetylase and acetate kinase) responsible for acetate formation and diminished activities of butyryl-coenzyme A (CoA): acetyl-CoA transferase, caproyl-CoA: butyryl-CoA transferase, and caproyl-CoA: acetyl-CoA transferase that are involved in the syntheses of n-butyrate and n-caproate. Furthermore, the composition of the microbial community shifted from Paraclostridium dominance (at 0.1 g∙L−1 ammonia) to a co-dominance of Fermentimonas, Clostridium sensu stricto 12, and Clostridium sensu stricto 15 at 2 g∙L−1 ammonia. However, these CE-functional bacteria were mostly absent in the presence of excessive ammonia (5 g∙L−1 ammonia). Metagenomic analysis revealed the upregulation of functions such as RBO, fatty acid synthesis, K+ efflux, adenosine triphosphatase (ATPase) metabolism, and metal cation export in the presence of 2 g∙L−1 ammonia, collectively contributing to enhanced n-caproate production. Conversely, the aforementioned functions (excluding metal cation export) and K+ influx were suppressed by excessive ammonia, undermining both ammonia detoxification and n-caproate biosynthesis. The comprehensive elucidation of ammonia-driven mechanisms influencing n-caproate production, as provided in this study, is expected to inspire researchers to devise effective strategies to alleviate ammonia-induced inhibition.

Keywords： Ammonia inhibition     Medium chain fatty acids     n-caproate     Enzyme     Metagenomics    

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Title Author Date Type Operation

Culturomics and metagenomics: In understanding of environmental resistome

Monika Nowrotek, Łukasz Jałowiecki, Monika Harnisz, Grażyna Anna Płaza

Journal Article

METAGENOMICS COMBINED WITH HIGH-THROUGHPUT SEQUENCING REVEALS THE METHANOGENIC POTENTIAL OF FRESH CORN

Journal Article

Distribution of antibiotic resistance genes and their association with bacteria and viruses in decentralized sewage treatment facilities

Journal Article

Core Metabolic Features and Hot Origin of Bathyarchaeota

Xiaoyuan Feng, Yinzhao Wang, Rahul Zubin, Fengping Wang

Journal Article

Taxonomic and functional variations in the microbial community during the upgrade process of a full-scale landfill leachate treatment plant – from conventional to partial nitrification-denitrification

Binbin Sheng, Depeng Wang, Xianrong Liu, Guangxing Yang, Wu Zeng, Yiqing Yang, Fangang Meng

Journal Article

Alterations in the Gut Microbiome in Liver Recipients with Post-transplant Diabetes Mellitus

Qi Ling, Yuqiu Han, Yue Ma, Xiaosen Wang, Zheng Zhu, Jingyu Wang, Jiaying Cao, Lin Xiaohan, Jun Wang, Baohong Wang

Journal Article

Chain Elongation Using Native Soil Inocula: Exceptional n-Caproate Biosynthesis Performance and Microbial Mechanisms

Lin Deng,Yang Lv,Tian Lan,Qing-Lian Wu,Wei-Tong Ren,Hua-Zhe Wang,Bing-Jie Ni,Wan-Qian Guo,

Journal Article

Unveiling the Mechanism Underlying the Effects of Ammonia on n-Caproate Production: Influenced Pathways, Key Enzymes, and Microbiota Functions

Qing-Lian Wu, Ke-Xin Yuan, Wei-Tong Ren, Lin Deng, Hua-Zhe Wang, Xiao-Chi Feng, He-Shan Zheng, Nan-Qi Ren, Wan-Qian Guo

Journal Article