Profiling temporal dynamics of acetogenic communities in anaerobic digesters using next-generation sequencing and T-RFLP

AbstractAcetogens play a key role in anaerobic degradation of organic material and in maintaining biogas process efficiency. Profiling this community and its temporal changes can help evaluate process stability and function, especially under disturbance/stress conditions, and avoid complete process failure. The formyltetrahydrofolate synthetase (FTHFS) gene can be used as a marker for acetogenic community profiling in diverse environments. In this study, we developed a new high-throughput FTHFS gene sequencing method for acetogenic community profiling and compared it with conventional terminal restriction fragment length polymorphism of the FTHFS gene, 16S rRNA gene-based profiling of the whole bacterial community, and indirect analysis via 16S rRNA profiling of the FTHFS gene-harbouring community. Analyses and method comparisons were made using samples from two laboratory-scale biogas processes, one operated under stable control and one exposed to controlled overloading disturbance. Comparative analysis revealed satisfactory detection of the bacterial community and its changes for all methods, but with some differences in resolution and taxonomic identification. FTHFS gene sequencing was found to be the most suitable and reliable method to study acetogenic communities. These results pave the way for community profiling in various biogas processes and in other environments where the dynamics of acetogenic bacteria have not been well studied.

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Profiling acetogenic community dynamics in anaerobic digesters - comparative analyses using next-generation sequencing and T-RFLP

10.1101/2021.01.26.427894 ◽

2021 ◽

Author(s):

Abhijeet Singh ◽

Bettina Müller ◽

Anna Schnürer

Keyword(s):

Bacterial Community ◽

16S Rrna ◽

High Throughput ◽

Community Dynamics ◽

Temporal Dynamics ◽

Gene Sequencing ◽

Process Efficiency ◽

Rrna Gene ◽

Anaerobic Digesters ◽

Community Profiling

ABSTRACTAcetogens play a key role in anaerobic degradation of organic material and in maintaining biogas process efficiency. Profiling this community and its temporal changes can help evaluate process stability and function, especially under disturbance/stress conditions, and avoid complete process failure. The formyltetrahydrofolate synthetase (FTHFS) gene can be used as a marker for acetogenic community profiling in diverse environments. In this study, we developed a new high-throughput FTHFS gene sequencing method for acetogenic community profiling and compared it with conventional T-RFLP of the FTHFS gene, 16S rRNA gene-based profiling of the whole bacterial community, and indirect analysis via 16S rRNA profiling of the FTHFS gene-harbouring community. Analyses and method comparisons were made using samples from two laboratory-scale biogas processes, one operated under stable control and one exposed to controlled overloading disturbance. Comparative analysis revealed satisfactory detection of the bacterial community and its changes for all methods, but with some differences in resolution and taxonomic identification. FTHFS gene sequencing was found to be the most suitable and reliable method to study acetogenic communities. These results pave the way for community profiling in various biogas processes and in other environments where the dynamics of acetogenic bacteria have not been well studied.GRAPHICAL ABSTRACTONE SENTENCE SUMMARYOur high-throughput FTHFS gene AmpSeq method for barcoded samples and unsupervised analysis with AcetoScan accurately reveals temporal dynamics of acetogenic community structure in anaerobic digesters.

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Detection of Viable and Total Bacterial Community in the Pit Mud of Chinese Strong-Flavor Liquor Using Propidium Monoazide Combined With Quantitative PCR and 16S rRNA Gene Sequencing

Frontiers in Microbiology ◽

10.3389/fmicb.2020.00896 ◽

2020 ◽

Vol 11 ◽

Author(s):

Guangxun Tan ◽

Rui Zhou ◽

Wenqian Zhang ◽

Yuanliang Hu ◽

Zhiyong Ruan ◽

...

Keyword(s):

Bacterial Community ◽

16S Rrna ◽

16S Rrna Gene ◽

Gene Sequencing ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Propidium Monoazide ◽

Pit Mud ◽

Total Bacterial Community ◽

Rrna Gene Sequencing

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Prokaryotic community profiling of local algae wastewaters using advanced 16S rRNA gene sequencing

Environmental Science and Pollution Research ◽

10.1007/s11356-017-0078-z ◽

2017 ◽

Vol 25 (1) ◽

pp. 704-711 ◽

Cited By ~ 5

Author(s):

Alya Limayem ◽

Andrew Micciche ◽

Bina Nayak ◽

Shyam Mohapatra

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Gene Sequencing ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Prokaryotic Community ◽

Community Profiling ◽

Rrna Gene Sequencing

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Multicenter assessment of microbial community profiling using 16S rRNA gene sequencing and shotgun metagenomic sequencing

Journal of Advanced Research ◽

10.1016/j.jare.2020.07.010 ◽

2020 ◽

Vol 26 ◽

pp. 111-121 ◽

Cited By ~ 1

Author(s):

Dongsheng Han ◽

Peng Gao ◽

Rui Li ◽

Ping Tan ◽

Jiehong Xie ◽

...

Keyword(s):

Microbial Community ◽

16S Rrna ◽

16S Rrna Gene ◽

Gene Sequencing ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Metagenomic Sequencing ◽

Community Profiling ◽

Shotgun Metagenomic Sequencing ◽

Rrna Gene Sequencing

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Correction: Temporal dynamics of in-situ fiber-adherent bacterial community under ruminal acidotic conditions determined by 16S rRNA gene profiling

PLoS ONE ◽

10.1371/journal.pone.0204600 ◽

2018 ◽

Vol 13 (9) ◽

pp. e0204600

Author(s):

Renee M. Petri ◽

Poulad Pourazad ◽

Ratchaneewan Khiaosa-ard ◽

Fenja Klevenhusen ◽

Barbara U. Metzler-Zebeli ◽

...

Keyword(s):

Bacterial Community ◽

16S Rrna ◽

16S Rrna Gene ◽

Temporal Dynamics ◽

Gene Profiling ◽

Rrna Gene

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Performance Comparison of Illumina and Ion Torrent Next-Generation Sequencing Platforms for 16S rRNA-Based Bacterial Community Profiling

Applied and Environmental Microbiology ◽

10.1128/aem.02206-14 ◽

2014 ◽

Vol 80 (24) ◽

pp. 7583-7591 ◽

Cited By ~ 175

Author(s):

Stephen J. Salipante ◽

Toana Kawashima ◽

Christopher Rosenthal ◽

Daniel R. Hoogestraat ◽

Lisa A. Cummings ◽

...

Keyword(s):

Bacterial Community ◽

16S Rrna ◽

Amplicon Sequencing ◽

Error Rates ◽

Personal Genome ◽

Rrna Gene ◽

Ion Torrent ◽

Community Profiling ◽

Sequencing Platforms ◽

Ion Torrent Platform

ABSTRACTHigh-throughput sequencing of the taxonomically informative 16S rRNA gene provides a powerful approach for exploring microbial diversity. Here we compare the performances of two common “benchtop” sequencing platforms, Illumina MiSeq and Ion Torrent Personal Genome Machine (PGM), for bacterial community profiling by 16S rRNA (V1-V2) amplicon sequencing. We benchmarked performance by using a 20-organism mock bacterial community and a collection of primary human specimens. We observed comparatively higher error rates with the Ion Torrent platform and report a pattern of premature sequence truncation specific to semiconductor sequencing. Read truncation was dependent on both the directionality of sequencing and the target species, resulting in organism-specific biases in community profiles. We found that these sequencing artifacts could be minimized by using bidirectional amplicon sequencing and an optimized flow order on the Ion Torrent platform. Results of bacterial community profiling performed on the mock community and a collection of 18 human-derived microbiological specimens were generally in good agreement for both platforms; however, in some cases, results differed significantly. Disparities could be attributed to the failure to generate full-length reads for particular organisms on the Ion Torrent platform, organism-dependent differences in sequence error rates affecting classification of certain species, or some combination of these factors. This study demonstrates the potential for differential bias in bacterial community profiles resulting from the choice of sequencing platform alone.

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