“…Similarly, in our previous study, we also noted an increase in antibiotic resistance in bacteria isolated across the MBE and described a novel cefotaxime-resistant strain of Corynebacterium godavarianum from the Godavari River, India [ 66 , 67 ]. The recent study by Yadav et al [ 68 ] involving shotgun metagenomic analysis based on the MinION sequencing supports the observed elevated levels of antibiotic resistance genes during mass bathing. Fig.…”
The unprecedented COVID-19 pandemic has had major impact on human health worldwide. Whilst national and international COVID-19 lockdown and travel restriction measures have had widespread negative impact on economies and mental health, they may have beneficial effect on the environment, reducing air and water pollution. Mass bathing events (MBE) also known as Kumbh Mela are known to cause perturbations of the ecosystem affecting resilient bacterial populations within water of rivers in India. Lockdowns and travel restrictions provide a unique opportunity to evaluate the impact of minimum anthropogenic activity on the river water ecosystem and changes in bacterial populations including antibiotic-resistant strains. We performed a spatiotemporal meta-analysis of bacterial communities of the Godavari River, India. Targeted metagenomics revealed a 0.87-fold increase in the bacterial diversity during the restricted activity of lockdown. A significant increase in the resilient phyla, viz.
Proteobacteria
(70.6%),
Bacteroidetes
(22.5%),
Verrucomicrobia
(1.8%),
Actinobacteria
(1.2%) and
Cyanobacteria
(1.1%), was observed. There was minimal incorporation of allochthonous bacterial communities of human origin. Functional profiling using imputed metagenomics showed reduction in infection and drug resistance genes by − 0.71-fold and − 0.64-fold, respectively. These observations may collectively indicate the positive implications of COVID-19 lockdown measures which restrict MBE, allowing restoration of the river ecosystem and minimise the associated public health risk.
Supplementary Information
The online version contains supplementary material available at 10.1007/s00248-021-01781-0.
“…Similarly, in our previous study, we also noted an increase in antibiotic resistance in bacteria isolated across the MBE and described a novel cefotaxime-resistant strain of Corynebacterium godavarianum from the Godavari River, India [ 66 , 67 ]. The recent study by Yadav et al [ 68 ] involving shotgun metagenomic analysis based on the MinION sequencing supports the observed elevated levels of antibiotic resistance genes during mass bathing. Fig.…”
The unprecedented COVID-19 pandemic has had major impact on human health worldwide. Whilst national and international COVID-19 lockdown and travel restriction measures have had widespread negative impact on economies and mental health, they may have beneficial effect on the environment, reducing air and water pollution. Mass bathing events (MBE) also known as Kumbh Mela are known to cause perturbations of the ecosystem affecting resilient bacterial populations within water of rivers in India. Lockdowns and travel restrictions provide a unique opportunity to evaluate the impact of minimum anthropogenic activity on the river water ecosystem and changes in bacterial populations including antibiotic-resistant strains. We performed a spatiotemporal meta-analysis of bacterial communities of the Godavari River, India. Targeted metagenomics revealed a 0.87-fold increase in the bacterial diversity during the restricted activity of lockdown. A significant increase in the resilient phyla, viz.
Proteobacteria
(70.6%),
Bacteroidetes
(22.5%),
Verrucomicrobia
(1.8%),
Actinobacteria
(1.2%) and
Cyanobacteria
(1.1%), was observed. There was minimal incorporation of allochthonous bacterial communities of human origin. Functional profiling using imputed metagenomics showed reduction in infection and drug resistance genes by − 0.71-fold and − 0.64-fold, respectively. These observations may collectively indicate the positive implications of COVID-19 lockdown measures which restrict MBE, allowing restoration of the river ecosystem and minimise the associated public health risk.
Supplementary Information
The online version contains supplementary material available at 10.1007/s00248-021-01781-0.
“…Most studies targeting bacteria and archaea filtered between 0.1 and 4 L of water through membranes with 0.22 µm pore size to capture the biomass [27,37,47,50,54,59,63,66,[68][69][70][71]73]. Filtration can take hours to complete [27], and sometimes water prefiltration through membranes with a pore size between 0.4 and 11 µm was used to remove suspended solids [37,76]. However, prefiltration will exclude biomass attached to suspended solids or otherwise entrapped, unless all the filter membranes are extracted for the analysis.…”
Section: Biomass Collection and Concentrationmentioning
confidence: 99%
“…As a minimum, the purified genetic material needs repair and preparation of the fragmented DNA/RNA strand ends followed by ligation (i.e., attachment) of the sequencing adaptors which interact with the flow cell nanopores. This can be done with ligation sequencing kits that were popular choices to sequence DNA [43,45,46,49,52,53,55,60,61,67,70,72,76] and derived amplicons [31,32,34,35,44,58,59,73,74], or amplicons of complementary DNA (cDNA, see below) [28]. Semmouri et al [33] evaluated the MinION potential for direct RNA nanopore sequencing using the corresponding kit.…”
Section: End Repair and Ligation Of Sequencing Adaptorsmentioning
confidence: 99%
“…Guppy includes such post-processing features, i.e., barcoding/demultiplexing, adapter trimming, and alignment. Other popular application choices in the reviewed studies include qcat [83] for demultiplexing (i.e., to assign reads to their barcodes when several barcoded samples are run on a single flow cell) [44,45,[59][60][61]67,76] and Porechop [84] for adaptor trimming [45,46,48,52,55,58,[60][61][62]64,67,69,72,74,76]. However, qcat and Porechop are no longer supported, and the use of Guppy is recommended.…”
Section: Demultiplexing and Adaptor Trimmingmentioning
confidence: 99%
“…Reddington et al [37] compared MG-RAST, Kraken2 [94] and One Codex [95] and found that One Codex was unsuitable for their purpose, as it resulted in a high proportion of unclassified reads when analyzing river metagenomes. Kaiju [96] is another classification tool used in several shotgun sequencing studies [45,61,76]. The ARTIC bioinformatics pipeline [97] was used in wastewater epidemiology studies [41,42] for SARS-CoV-2 variant calling from nanopore sequencing data.…”
In 2014, Oxford Nanopore Technologies (ONT) introduced an affordable and portable sequencer called MinION. We reviewed emerging applications in water research and assessed progress made with this platform towards ubiquitous genetics. With >99% savings in upfront costs as compared to conventional platforms, the MinION put sequencing capacity into the hands of many researchers and enabled novel applications with diverse remits, including in countries without universal access to safe water and sanitation. However, to realize the MinION’s fabled portability, all the auxiliary equipment items for biomass concentration, genetic material extraction, cleanup, quantification, and sequencing library preparation also need to be lightweight and affordable. Only a few studies demonstrated fully portable workflows by using the MinION onboard a diving vessel, an oceanographic research ship, and at sewage treatment works. Lower nanopore sequencing read accuracy as compared to alternative platforms currently hinders MinION applications beyond research, and inclusion of positive and negative controls should become standard practice. ONT’s EPI2ME platform is a major step towards user-friendly bioinformatics. However, no consensus has yet emerged regarding the most appropriate bioinformatic pipeline, which hinders intercomparison of study results. Processing, storing, and interpreting large data sets remains a major challenge for ubiquitous genetics and democratizing sequencing applications.
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