Metagenomic data of free cyanide and thiocyanate degrading bacterial communities

Comparison of targeted metagenomics and IS-Pro methods for analysing the lung microbiome

Background

Targeted metagenomics and IS-Pro method are two of the many methods that have been used to study the microbiome. The two methods target different regions of the 16 S rRNA gene. The aim of this study was to compare targeted metagenomics and IS-Pro methods for the ability to discern the microbial composition of the lung microbiome of COPD patients.

Methods

Spontaneously expectorated sputum specimens were collected from COPD patients. Bacterial DNA was extracted and used for targeted metagenomics and IS-Pro method. The analysis was performed using QIIME2 (targeted metagenomics) and IS-Pro software (IS-Pro method). Additionally, a laboratory cost per isolate and time analysis was performed for each method.

Results

Statistically significant differences were observed in alpha diversity when targeted metagenomics and IS-Pro methods’ data were compared using the Shannon diversity measure (p-value = 0.0006) but not with the Simpson diversity measure (p-value = 0.84). Distinct clusters with no overlap between the two technologies were observed for beta diversity. Targeted metagenomics had a lower relative abundance of phyla, such as the Proteobacteria, and higher relative abundance of phyla, such as Firmicutes when compared to the IS-Pro method. Haemophilus, Prevotella and Streptococcus were most prevalent genera across both methods. Targeted metagenomics classified 23 % (144/631) of OTUs to a species level, whereas IS-Pro method classified 86 % (55/64) of OTUs to a species level. However, unclassified OTUs accounted for a higher relative abundance when using the IS-Pro method (35 %) compared to targeted metagenomics (5 %). The two methods performed comparably in terms of cost and time; however, the IS-Pro method was more user-friendly.

Conclusions

It is essential to understand the value of different methods for characterisation of the microbiome. Targeted metagenomics and IS-Pro methods showed differences in ability in identifying and characterising OTUs, diversity and microbial composition of the lung microbiome. The IS-Pro method might miss relevant species and could inflate the abundance of Proteobacteria. However, the IS-Pro kit identified most of the important lung pathogens, such as Burkholderia and Pseudomonas and may work in a more diagnostics-orientated setting. Both methods were comparable in terms of cost and time; however, the IS-Pro method was easier to use.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-021-02288-x.

Functional Analysis of a Polluted River Microbiome Reveals a Metabolic Potential for Bioremediation

The objective of this study is to understand the functional and metabolic potential of the microbial communities along the Apatlaco River and highlight activities related to bioremediation and its relationship with the Apatlaco’s pollutants, to enhance future design of more accurate bioremediation processes. Water samples were collected at four sampling sites along the Apatlaco River (S1–S4) and a whole metagenome shotgun sequencing was performed to survey and understand the microbial metabolic functions with potential for bioremediation. A HMMER search was used to detect sequence homologs related to polyethylene terephthalate (PET) and polystyrene biodegradation, along with bacterial metal tolerance in Apatlaco River metagenomes. Our results suggest that pollution is a selective pressure which enriches microorganisms at polluted sites, displaying metabolic capacities to tolerate and transform the contamination. According to KEGG annotation, all sites along the river have bacteria with genes related to xenobiotic biodegradation. In particular, functions such as environmental processing, xenobiotic biodegradation and glycan biosynthesis are over-represented in polluted samples, in comparison to those in the clean water site. This suggests a functional specialization in the communities that inhabit each perturbated point. Our results can contribute to the determination of the partition in a metabolic niche among different Apatlaco River prokaryotic communities, that help to contend with and understand the effect of anthropogenic contamination.

Process performance determination data in thiocyanate biodegradation systems: Use of sulphate production

This data article presents the utilization of sulphates as an indirect technique for the assessment of microbial growth, activity and SCN^- biodegradation efficiency since the TDO were observed to be unable to utilise the produced sulphates as a source of sulphur (Mekuto e al., 2017) [1] The TDO demonstrated complete SCN^- biodegradation while also utilizing the produced ammonium. The production of SO₄^2- from SCN^- biodegradation had a good correlation in comparison to the traditional methods of assessing microbial growth and activity i.e. direct cell counts (DCC), heterotrophic counts (CFU) and fluorescein production from fluorescein diacetate (FDA). The concentration of the produced SO₄^2- demonstrated a similar logarithmic trend with the FDA, DCC and CFU techniques, thus confirming that the production of SO₄^2- from SCN^- biodegradation systems can be utilised as an indirect technique for the assessment of microbial growth, activity and SCN^- biodegradation performance.

Microbial communities associated with the co-metabolism of free cyanide and thiocyanate under alkaline conditions

This study focused on the identification of free cyanide (CDO) and thiocyanate (TDO) degrading microbial communities using a culture-dependent and independent approach. Culturable microbial species were isolated from the CDOs (n = 13) and TDOs (n = 18). The CDOs were largely dominated by Bacillus sp. while the TDOs were dominated by Bacillus sp., Klebsiella oxytoca, Providencia sp. and Pseudomonas sp. However, 16S rRNA amplicon gene-sequencing revealed the complexity and diversity of the microbial communities in contrast to the organisms that were detected using culture-dependent technique. Overall, the organisms were mainly dominated by Myroides odoratimimus and Proteus sp. at 37.82 and 30.5% for CDOs, and 35.26 and 17.58% for TDOs, respectively. The co-culturing of the CDOs and TDOs resulted in biochemical changes of key metabolic enzymes, and this resulted in the complete degradation of CN- and SCN- simultaneously; a phenomenon which has not been witnessed, especially under alkaline conditions. Current ongoing studies are focused on the application of these organisms for the biodegradation of CN- and SCN- in a continuous system, under changing operational parameters, to assess their effectiveness in the biodegradation of CN- and SCN-.