High-throughput sequencing of microbial diversity in implant-associated infection

The diversity of hydrogen-producing bacteria and methanogens within an in situ coal seam

BACKGROUND

Biogenic and biogenic-thermogenic coalbed methane (CBM) are important energy reserves for unconventional natural gas. Thus, to investigate biogenic gas formation mechanisms, a series of fresh coal samples from several representative areas of China were analyzed to detect hydrogen-producing bacteria and methanogens in an in situ coal seam. Complete microbial DNA sequences were extracted from enrichment cultures grown on coal using the Miseq high-throughput sequencing technique to study the diversity of microbial communities. The species present and differences between the dominant hydrogen-producing bacteria and methanogens in the coal seam are then considered based on environmental factors.

RESULTS

Sequences in the Archaea domain were classified into four phyla and included members from Euryarchaeota, Thaumarchaeota, Woesearchaeota, and Pacearchaeota. The Bacteria domain included members of the phyla: Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, Acidobacteria, Verrucomicrobia, Planctomycetes, Chloroflexi, and Nitrospirae. The hydrogen-producing bacteria was dominated by the genera: Clostridium, Enterobacter, Klebsiella, Citrobacter, and Bacillus; the methanogens included the genera: Methanorix, Methanosarcina, Methanoculleus, Methanobrevibacter, Methanobacterium, Methanofollis, and Methanomassiliicoccus.

CONCLUSION

Traces of hydrogen-producing bacteria and methanogens were detected in both biogenic and non-biogenic CBM areas. The diversity and abundance of bacteria in the biogenic CBM areas are relatively higher than in the areas without biogenic CBM. The community structure and distribution characteristics depend on coal rank, trace metal elements, temperature, depth and groundwater dynamic conditions. Biogenic gas was mainly composed of hydrogen and methane, the difference and diversity were caused by microbe-specific fermentation of substrates; as well as by the environmental conditions. This discovery is a significant contribution to extreme microbiology, and thus lays the foundation for research on biogenic CBM.

Evaluation of the accuracy and sensitivity of high‑throughput sequencing technology using known microbiota

Next generation sequencing provides an excellent platform to explore microbiota in any given environment, and little work is required to evaluate the accuracy and sensitivity of high‑throughput sequencing technology. In the present study, a known microbiota containing Escherichia coli, Lactobacillus plantarum, Streptococcus thermophilus, Bifidobacterium bifidum, Bacillus subtilis, Enterococcus faecalis and Salmonella typhimurium was used to evaluate the high‑throughput sequencing technology. The results suggested that there were 122.7 operational taxonomic units (OTUs) in all groups, which is 17.5‑fold (the whole OTU number/the actual bacterial number) greater compared with the actual microbial number in each group, and the Venn method indicated that only 46.38% (64/138), 58.70% (81/138), 86.13% (118/137), 83.57% (117/140) and 89.29% (125/140) of the common OTUs were identified in groups A, B, C, D and E, of which the majority of OTUs did not belong to known bacteria. In addition, the DNA extraction and amplification efficiency failed to identify bacteria at the phylum, class, order, family, genus and species levels, which may further increase false information of microbial analysis. In conclusion, the present study provided basic datato investigate the potential drawbacks of high‑throughput sequencing technology, which will help researchers to avoid exaggerating the bacterial number when this technology is applied to study microbiota in particular environments.