Peer-reviewed journal publications
*Corresponding author, †Co-first authors.
- Y. Hirakata, R. Mei, K. Morinaga, T. Katayama, H. Tamaki, X. Meng, T. Watari, T. Yamaguchi, M. Hatamoto, and M.K. Nobu*, 2023. Discovery of anaerobic bacterial scavengers of dead cells. The ISME Journal. 10.1038/s41396-023-01538-2.
Cultivation and characterization of syntrophic Bacteroidota species that scavenge dead cells using distinct strategies and contribute to the cycle of life and death in oxygen-depleted environments.
- R. Mei, M. Kaneko, H. Imachi, and M.K. Nobu*, 2023. The origin and evolution of methanogenesis and Archaea are intertwined. PNAS Nexus. 10.1093/pnasnexus/pgad023.
New evidence for the antiquity of methanogenesis and its influence on the transition from ancestral archaea to the diversity prominent today.
- R. Mei and W-T. Liu*, 2022. Meta-omics supervised characterization of respiration activities associated with microbial immigrants in anaerobic sludge digesters. Environmental Science & Technology. 10.1021/acs.est.2c01029.
Meta-omics-supervised characterization of microbial immigrants in anaerobic sludge digesters and revealed their activities of anaerobic respiration.
- J. Kim†, R. Mei†, F.P. Wilson, H. Yuan, B.T.W. Bocher, and W-T. Liu*, 2020. Ecogenomics-based mass balance model reveals the effects of fermentation conditions on microbial activity. Frontiers in Microbiology. 10.3389/fmicb.2020.595036.
Identification of optimal fermentation conditions and active microbial populations by applying an ecogenomics-based mass balance approach to organic waste fermentation cultures.
- M.K. Nobu†, T. Narihiro†, R. Mei, Y. Kamagata, P-H. Lee, P.K. Lee, M.J., McInerney, and W-T. Liu*, 2020. Catabolism and interactions of uncultured organisms shaped by eco-thermodynamics in methanogenic bioprocesses. Microbiome. 10.1186/s40168-020-00885-y.
Discovery of diverse uncultured populations driving H2-sensitive metabolisms that are critical for microorganisms overcome a critical obstacle in methanogenic carbon cycles.
- L. Ye*, R. Mei, W-T. Liu, H. Ren, and X. Zhang*, 2020. Machine learning-aided analyses of thousands of draft genomes reveal specific features of activated sludge processes. Microbiome. 10.1186/s40168-020-0794-3.
Recovery of 2,000+ archaeal and bacterial genomes from full-scale activated sludge processes. Identification of functional features vital for microbes to thrive in activated sludge using a machine learning approach.
- R. Mei, M.K. Nobu, T. Narihiro, and W-T. Liu*, 2020. Metagenomic and
metatranscriptomic analyses revealed uncultured Bacteroidales populations as
the dominant proteolytic amino acid degraders in anaerobic digesters. Frontiers
in Microbiology. 10.3389/fmicb.2020.593006.
Meta-omics characterization of a proteolytic amino acids degrading Bacteroidetes bacterium that is abundant and prevalent in anaerobic wastewater treatment processes.
- T.Y.C. Lam†, R. Mei†, Z. Wu, P.K. Lee, W-T. Liu*, and P-H. Lee*, 2020. Superior resolution characterization of microbial diversity in anaerobic digesters using full-length 16S rRNA gene amplicon sequencing. Water Research, 10.1016/j.watres.2020.115815.
Full-length 16S rRNA gene amplicon sequencing using PacBio Sequel for an accurate phylogenetic investigation of microbiomes in full-scale anaerobic digesters.
- R. Mei, M.K. Nobu, and W-T. Liu*, 2020. Identifying anaerobic amino acids degraders through the comparison of short-term and long-term enrichments. Environmental Microbiology Reports. 10.1111/1758-2229.12821.
Continuous enrichment targeting amino acids-degrading populations in methanogenic environments. A clear community shift was observed and described using a culturability index.
- H. Sun, R. Mei, X. Zhang, H. Ren, W-T. Liu, and L. Ye*, 2020. Bacterial enrichment in highly-selective acetate-fed bioreactors and its application in rapid biofilm formation. Water Research. 10.1016/j.watres.2019.115359.
Identification of novel Acinetobacter species that contribute to sludge granulation and biofilm formation process in highly-selective bioreactors.
- R. Mei and W-T. Liu*, 2019. Quantifying the contribution of microbial immigration in engineered water systems. Microbiome. 10.1186/s40168-019-0760-0.
A perspective on why evaluating the impact of microbial immigration on diversity and function within ecosystems is challenging. An ecogenomics-based mass balance approach may offer a solution.
- R. Mei, J. Kim, F.P. Wilson, B.T.W. Bocher, and W-T. Liu*, 2019. Coupling growth kinetics model and machine learning quantifies microbial immigration impacts and identifies key environmental parameters in a biological wastewater treatment process. Microbiome. 10.1186/s40168-019-0682-x.
Quantifying microbial immigration may improve the accuracy of a supervised learning regressor in predicting system performance based on community composition.
- H. Yuan, R. Mei, J. Liao, and W-T. Liu*, 2019. Nexus of stochastic and
deterministic processes on microbial community assembly in biological systems. Frontiers in Microbiology. 10.3389/fmicb.2019.01536.
Study the core microbial populations and the shift in community composition in lab-scale activated sludge reactors.
- A.M. Zealand, R. Mei, P. Papachristodoulou, A. P. Roskilly, W-T. Liu, and D.W. Graham*, 2019. Molecular microbial ecology of stable versus failing rice
straw anaerobic digesters. Microbial Biotechnology. 10.1111/1751-7915.13438.
Assessment of how feeding frequency and organic loading rate impacts microbial communities and biogas production in the treatment of waste rice straw.
- R. Mei, M.K. Nobu, T. Narihiro, J. Yu, A. Sathyagal, E. Willman, and W-T. Liu*, 2018. Novel Geobacter species and diverse methanogens contribute to enhanced methane production in media-added methanogenic reactors. Water Research. 10.1016/j.watres.2018.10.026.
Identification of a phylogenetically novel Geobacter species that could lead to enhanced methane production in softdrink wastewater treatment.
- T. Narihiro†, M.K. Nobu†, B.T.W. Bocher, R. Mei, and W-T. Liu*, 2018. Co‐occurrence network analysis reveals thermodynamics‐driven microbial
interactions in methanogenic bioreactors. Environmental Microbiology
Reports. 10.1111/1758-2229.12689.
Characterization of the interaction of microbial populations in petrochemical wastewater treatment bioreactors, focusing on organisms from multiple niches orchestrating in metabolic networks.
- A.M. Zealand, R. Mei, P. Papachristodoulou, A. P. Roskilly, W-T. Liu, and D.W. Graham*, 2018. Microbial community composition and diversity in rice
straw digestion bioreactors with and without dairy manure. Applied
Microbiology and Biotechnology. 10.1007/s00253-018-9243-7.
Assessment of how adding dairy manure impacts microbial communities and biogas production in the treatment of waste rice straw.
- M.K. Nobu†, T. Narihiro†, M. Liu, K. Kuroda, R. Mei, and W-T. Liu*, 2017. Thermodynamically diverse syntrophic aromatic compound catabolism. Environmental Microbiology. 10.1111/1462-2920.13922.
Investigation of the catabolic diversity and flexibility of bacteria that circumvent thermodynamic restrictions to metabolize biochemically recalcitrant and environmentally relavent aromatic compounds.
- R. Mei, M.K. Nobu, T. Narihiro, K. Kuroda, J. Sierra, Z. Wu, L, Ye, P.K. Lee, P-H. Lee, J.B. van Lier, M.J., McInerney, Y. Kamagata, and W-T. Liu*, 2017. Operation-driven heterogeneity and overlooked feed-associated populations in anaerobic digester microbiome. Water Research. 10.1016/j.watres.2017.07.050.
Analysis of global anaerobic digester microbiome, uncovering vast heterogeneity and inferring the cause.
- K. Kuroda†, M.K. Nobu†, R. Mei, T. Narihiro, B.T.W. Bocher, T. Yamaguchi, and W-T. Liu*, 2016. A single-granule-level approach reveals ecological heterogeneity in
an upflow anaerobic sludge blanket reactor. PLOS ONE. 10.1371/journal.pone.0167788.
Investigation of the heterogeneity of individual granular micro-ecosystems in lab- and full-scale petrochemical wastewater treatment bioreactors.
- R. Mei, T. Narihiro, M.K. Nobu, and W-T. Liu*, 2016. Effects of heat shocks on microbial community structure and microbial activity of a methanogenic enrichment degrading benzoate. Letters in Applied Microbiology. 10.1111/lam.12629.
Demonstration of how a microbial consortium resists and recovers from heat shock with varying intensity.
- M.K. Nobu, T. Narihiro, K. Kuroda, R. Mei, and W-T. Liu*, 2016. Chasing the
elusive Euryarchaeota class WSA2: genomes reveal a uniquely fastidious
methyl-reducing methanogen. The ISME Journal. 10.1038/ismej.2016.33.
The first detailed metagenomic characterization of a methanogen class that is prevalent in anoxic ecosystems.
- R. Mei, T. Narihiro, M.K. Nobu, K. Kuroda, and W-T. Liu*, 2016. Evaluating digestion efficiency in full-scale anaerobic digesters by identifying active microbial populations through the lens of microbial activity. Scientific Reports. 10.1038/srep34090.
High-throughput, quantitative determination of how microbial species behave after migrating from one ecosystem to another, which is associated with the performance of wastewater treatment.
- T. Narihiro, N. Kim, R. Mei, M.K. Nobu, and W-T. Liu*, 2015. Microbial
community analysis of anaerobic reactors treating soft drink wastewater. PLOS ONE. 10.1371/journal.pone.0119131.
Description of the microbial community in an efficient system treating softdrink wastewater.
- X. Pan, S. Geng, X. Lv, R. Mei, J. Jiangyang, Y. Wang, L. Xu, X. Liu, Y. Tang, G. Wang, and X. Wu*, 2015. Defluviimonas alba sp. nov., isolated from an oilfield. International Journal of Systematic and Evolutionary Microbiology. 10.1099/ijs.0.000181.
Description of a novel bacterial species isolated from oilfield.
- S. Geng, X. Pan, R. Mei, Y. Wang, X. Liu, X. Wang, Y. Tang, and X. Wu*, 2015. Glycocaulis alkaliphilus sp. nov., a dimorphic prosthecate bacterium
isolated from crude oil. International Journal of Systematic and Evolutionary Microbiology. 10.1099/ijs.0.000023.
Description of a novel bacterial species isolated from crude oil.
- S. Geng, X. Pan, R. Mei, Y. Wang, J. Sun, X. Liu, Y. Tang, and X. Wu*, 2015. Paradevosia shaoguanensis gen. nov., sp. nov., isolated from a coking wastewater. Current Microbiology. 10.1007/s00284-014-0689-2.
Description of a novel bacterial species isolated from coking wastewater.
- X. Pan, S. Geng, R. Mei, Y. Wang, H. Cai, X. Liu, Y. Tang, Y. Nie, S. Ye, and X. Wu*, 2014. Nitratireductor shengliensis sp. nov., isolated from
an oil-polluted saline soil. Current Microbiology. 10.1007/s00284-014-0624-6.
Description of a novel bacterial species isolated from oil-polluted saline soil.
- S. Geng, X. Pan, R. Mei, Y. Wang, J. Sun, X. Liu, Y. Tang, and X. Wu*, 2014. Ottowia shaoguanensis sp. nov., isolated from coking wastewater. Current Microbiology. 10.1007/s00284-013-0481-8.
Description of a novel bacterial species isolated from coking wastewater.
Book chapter
- T. Narihiro, M.K. Nobu, R. Mei, and W-T. Liu*, 2015. Microbial community involved in anaerobic purified terephthalic acid treatment process. Anaerobic
Biotechnology: Environmental Protection and Resource Recovery, Imperial
College Press, London. 10.1142/9781783267910_0003.
Summary of the microbial ecology involved in the treatment of an important aromatic compound in the petrochemical industry.