SQMtools: automated processing and visual analysis of ’omics data with R and anvi’o

Puente-Sánchez, Fernando; García-García, Natalia; Tamames, Javier

doi:10.1101/2020.04.23.057133

Cited by 14 publications

(18 citation statements)

References 23 publications

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“…Functional annotation was performed using DIAMOND (Buchfink et al ., 2015) against the KEGG database (Kanehisa et al ., 2016). Read mapping against contigs was then performed using Bowtie2 (Langmead and Salzberg, 2012) in order to quantify the abundance of genes among the different samples, and transformed to transcripts per million (TPM) values (Puente-Sánchez et al ., 2020). To identify genes involved in 3-CA degradation, the analysis focused on the following KEGG metabolic pathways from the xenobiotics biodegradation and metabolism category: chlorocyclohexane and chlorobenzene degradation (KO: 00361), benzoate degradation (KO: 00362), polycyclic aromatic hydrocarbon degradation (KO: 00624), and aminobenzoate degradation (KO: 00627).…”

Section: Methodsmentioning

confidence: 99%

Metagenomics and Metatranscriptomics Suggest Pathways of 3-Chloroaniline Degradation in Wastewater Reactors

Seshan

Santillan

Constancias

et al. 2021

Preprint

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Biological wastewater treatment systems are often affected by major shifts in influent quality, including the input of various toxic chemicals. Yet the mechanisms underlying adaptation of activated sludge process performance when challenged with a sustained toxin input have not been studied in a controlled and replicated experiment. Three replicate bench-scale bioreactors were subjected to a chemical disturbance in the form of 3-chloroaniline (3-CA) input over 132 days, following an acclimation period of 58 days, while three control reactors received no 3-CA input. The nitrification process was initially affected by 3-CA input; yet all three treatment reactors evolved to biologically degrade 3-CA within three weeks of the experiment, resulting in partial nitrification recovery. 16S rRNA amplicon sequencing revealed that ammonia oxidizers were initially impacted by 3-CA, and a new ammonia oxidizing community emerged with the onset of 3-CA degradation. Combining process and microbial community data from amplicon sequencing with potential functions gleaned from assembled metagenomics and metatranscriptomics data, 3-CA degradation was shown to likely occur via a phenol monooxygenase followed by ortho-cleavage of the aromatic ring. The relative abundance of genera Gemmatimonas, Saprospiraceae OLB8 and Taibaiella correlated significantly with 3-CA degradation. This study demonstrated the impact of a sustained stress on the activated sludge community and wastewater treatment process and its subsequent recovery. Using a combination of techniques in a controlled and replicated experiment, we showed that microbial communities can evolve degradative capacity following a sustained xenobiotic input, specific functions like nitrification can fully or partially recover and targeted culture-independent approaches can be used to elucidate the mechanisms of adaptation.

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Section: Methodsmentioning

confidence: 99%

Metagenomics and Metatranscriptomics Suggest Pathways of 3-Chloroaniline Degradation in Wastewater Reactors

Seshan

Santillan

Constancias

et al. 2021

Preprint

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“…Functional annotation was performed using DIAMOND 76 against the KEGG database 81 . Read mapping against contigs was then performed using Bowtie2 82 in order to quantify the abundance of genes among the different samples, and transformed in transcripts per million (tpm) values to be consistent with prior works 83 . Nitrification genes were then quantified as follows: amo as the tpm sum from entries K10944 ( pmoA-amoA ), K10945 ( pmoB-amoB ) and K10946 ( pmoC-amoC ); hao as the tpm from entry K10535; and nxr / nar as tpm sum from entries K00370 ( narG, narZ, nxrA ) and K00371 ( narH, narY, nxrB ).…”

Section: Methodsmentioning

confidence: 99%

Sustained organic loading disturbance favors nitrite accumulation in bioreactors with variable resistance, recovery and resilience of nitrification and nitrifiers

Santillan

Phua

Constancias

et al. 2020

Sci Rep

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Sustained disturbances are relevant for environmental biotechnology as they can lead to alternative stable states in a system that may not be reversible. Here, we tested the effect of a sustained organic loading alteration (food-to-biomass ratio, F:M, and carbon-to-nitrogen ratio, C:N) on activated sludge bioreactors, focusing on the stability of nitrification and nitrifiers. Two sets of replicate 5-L sequencing batch reactors were operated at different, low and high, F:M (0.19–0.36 mg COD/mg TSS/d) and C:N (3.5–6.3 mg COD/mg TKN) conditions for a period of 74 days, following 53 days of sludge acclimation. Recovery and resilience were tested during the last 14 days by operating all reactors at low F:M and C:N (henceforth termed F:M–C:N). Stable nitrite accumulation (77%) was achieved through high F:M–C:N loading with a concurrent reduction in the abundance of Nitrospira. Subsequently, only two of the three reactors experiencing a switch back from high to low F:M–C:N recovered the nitrite oxidation function, with an increase in Nitrobacter as the predominant NOB, without a recovery of Nitrospira. The AOB community was more diverse, resistant and resilient than the NOB community. We showed that functional recovery and resilience can vary across replicate reactors, and that nitrification recovery need not coincide with a return to the initial nitrifying community structure.

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“…The pipelines used the co-assembly mode option where reads from all samples were pooled before the assembly using the Megahit [ 16 ] step was performed. The SQMtools package on R version 4.0.3 [ 17 ] was used to analyze both taxonomic and functional profiling data generated from SqueezeMeta pipelines [ 18 ].…”

Section: Main Textmentioning

confidence: 99%

Shotgun metagenomic analysis reveals new insights into bacterial community profiles in tempeh

et al. 2020

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Objective Amplicon sequencing targeting 16S ribosomal RNA (rRNA) has been widely used to profile the microbial community from fermented food samples. However, polymerase chain reaction (PCR) steps on amplicon sequencing analysis and intragenomic heterogeneity within 16S rRNA are believed to contribute to bias in estimating microbial community composition. As potential paraprobiotics sources, a comprehensive profiling study of tempeh microbial ecology could contribute to tempeh product development. This study employed a shotgun metagenomic approach, where metagenome fragments from tempeh samples were sequenced directly for taxonomic and functional profiling analysis. Results Taxonomic profiling showed that Proteobacteria, Firmicutes, and Bacteroidetes were the dominant phyla from the shotgun metagenomic analysis in all tempeh samples. In terms of composition, this shotgun metagenomic study revealed that Proteobacteria was the most abundant phylum. Functional profiling showed that iron complex outer-membrane recepter protein (KEGG ID: K02014) was the most transcribed gene based on this metagenomic analysis. The metagenome-assembled genomes (MAGs) results from the binning pipeline could reveal almost complete whole genome sequence of Lactobacillus fermentum, Enterococcus cecorum, Escherichia coli, Klebsiella pneumoniae, and Acinetobacter baumannii.

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SQMtools: automated processing and visual analysis of ’omics data with R and anvi’o

Cited by 14 publications

References 23 publications

Metagenomics and Metatranscriptomics Suggest Pathways of 3-Chloroaniline Degradation in Wastewater Reactors

Metagenomics and Metatranscriptomics Suggest Pathways of 3-Chloroaniline Degradation in Wastewater Reactors

Sustained organic loading disturbance favors nitrite accumulation in bioreactors with variable resistance, recovery and resilience of nitrification and nitrifiers

Shotgun metagenomic analysis reveals new insights into bacterial community profiles in tempeh

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