Analyses of Bacterial Community Dynamics Present in Culex quinquefasciatus Collected from Tamil Nadu, India - A Metagenomic Approach

© 2018, IJPBA. All Rights Reserved 109
Available Online at www.ijpba.info
International Journal of Pharmaceutical Biological Archives 2018; 9(3):109-116
ISSN 2581 – 4303
RESEARCH ARTICLE
Analyses of Bacterial Community Dynamics Present in Culex quinquefasciatus
Collected from Tamil Nadu, India - A Metagenomic Approach
K. Suganya1
, J. Rajesh Singh2
*, P. Ganesh3
1
Department of Zoology, Annamalai University, Chidambaram, Tamil Nadu, India, 2
Department of
Biotechnology, Rajah Serfoji Government Arts College (Autonomous), Thanjavur, Tamil Nadu, India,
3
Department of Microbiology, Faculty of Science, Annamalai University, Chidambaram, Tamil Nadu, India
Received: 10 August 2018; Revised: 01 September 2018; Accepted: 20 September 2018
ABSTRACT
Culex quinquefasciatus are among the most important vectors of arboviral diseases worldwide. Recent
studiesindicatethatdiversemidgutmicrobiotaofmosquitoessignificantlyaffectsdevelopment,digestion,
metabolism, and immunity of their hosts. Here, we studied the bacterial diversity found in midgut part
of C. quinquefasciatus to understand the host and microbe interaction. The adult C. quinquefasciatus
mosquitos were collected from Loyola College Campus, Chennai, using ovitraps, and midgut part was
extracted; moreover, the DNA templates were isolated and amplified by polymerase chain reaction. The
DNA amplicons were sequenced by Illumina MiSeq gene sequencer. The total of 279,157 reads was
classified into 85, the bacterial genera of Pseudomonas, Klebsiella, Staphylococcus, and Aeromonas
predominantly found to be high when compared to the other bacterial genera. The present data strongly
encourage further investigations to verify the potential role of the detected bacteria in mosquito for the
transmission of several vectoral diseases.
Keywords: Illumina MiSeq, Klebsiella, midgut, Pseudomonas, vectoral diseases
INTRODUCTION
Mosquitoes are well known as vectors of many
human and animal pathogens worldwide. Culex
quinquefasciatus is a peridomestic mosquito
seldom found far from human residence or activity,
and readily feeds on avian, mammalian, or human
hosts. The world has seen recent outbreaks and
emergences of several tropical diseases caused
by arboviruses and transmitted by mosquitoes.
Most species are described are in the genera Culex
including several blood-feeding members able
to transmit pathogens to humans and animals,
a great concern for public health.[1]
The later
causes lymphatic filariasis (LF) in humans, and
presently, over 120 million peoples are infected
with filarial worm. LF is a major public health
problem in India and worldwide, it is estimated
that 1.3 billion people from 83 countries are living
at the risk of infections. However, in India, LF is
endemic in 17 states and six union territories, and
*Corresponding Author:
J. Rajesh Singh,
E-mail: rajgenes@gmail.com
is responsible for one-third of the global disease
burden with about 554.2 million people at risk
of infection, with 31 million parasite carriers and
23 million case of symptomatic filariasis.[2]
The
observations over 100 years have shown that the
epidemiology of dengue varies a great deal with
respect to both geography and time. This is due
to not only to modifications in human ecology
(population increase, urbanization, and more
frequent travel) but also the ecological adaptations
of certain mosquito species.[3]
Mosquitoes can acquire bacteria transtadially
(larvae to adult mosquitoes through bacteria in
water) and through sugar feeding as adults.[4]
Little is known about the midgut microflora of
Culex mosquitoes and very few studies have been
conducted to study the midgut microbiota of Culex
mosquitoes.[5,6]
Mosquitoes serve as obligate intermediate
hosts for numerous diseases that collectively
represent a major cause of human mortality
and morbidity worldwide. There have been
attempts to generate transgenic mosquitoes
refractory for the transmission of pathogens.[7]
The midgut bacterial flora of the mosquito can

Suganya, et al.: Analyses of bacterial community dynamics present in Culex quinquefasciatus collected from Tamil Nadu,
India - A metagenomic approach
IJPBA/Jul-Sep-2018(Suppl)/Vol 9/Issue 3 110
be used to introduce gene products that will
inhibit the development of pathogens inside the
mosquitoes.[8,9]
A comprehensive study has been
conducted by us on the diversity of microbiota
in the midgut lumen of C. quinquefasciatus
to ascertain their potential role in disease
transmission and for their exploitation in
vector management. Metagenomics enables us
to study microorganisms by deciphering their
genetic information from DNA that is extracted
directly from communities of environmental
microorganisms, thus bypassing the need for
culturing isolation. This discipline builds on
the successes of culture-independent surveys
of environmental samples.[10]
To understand
bacterial diversity in the midgut of mosquitoes,
several laboratory-collected mosquito studies
were conducted. Dependent and independent
culture cultivation methods are particularly useful
approaches in attempting to make a complete
assessment of the bacterial mosquito species.[11]
Bacterial communities are classically assessed
through culture-dependent methods based on
isolation on solid medium, sometimes after
enrichment by growth in liquid medium.
However, it is now obvious that the microbial
diversity is poorly represented by the cultured
fraction, and culture has been shown to
explore 1% of the whole bacterial diversity
in environmental samples.[12]
The complete
metagenomic approach will give the total gene
content of a community, thus providing data
about biodiversity function and interactions.
[13]
For the purpose of biodiversity studies,
metagenomics can focus on one common gene
shared by all members of the community. The
most commonly used culture-independent
method relies on amplification and analysis of
the 16S rRNA genes in a microbiota. Recent
metagenomic studies on mosquito midgut have
revealed the presence of a diverse microbiota,
which can significantly affect the development,
digestion, metabolism, immunity, and other
physiological functions of their hosts.
This midgut microbiota has also been suggested
to alter the competency of mosquitoes to transmit
pathogens such as arboviruses.[14-16]
In this present
study, the attempts were made to analyze the
bacterial community dynamics in midgut part
of wild-type C. quinquefasciatus by collecting
ovitraps.
MATERIALS AND METHODS
Mosquito collections
The laboratory-bred pathogen-free strains of
mosquitoes were reared in the vector control
laboratory, Department of Zoology, Annamalai
University. Mosquitoes were held at 28 ± 2°C, 70–
85% relative humidity, with a photoperiod of 12-h
light and 12-h dark. The larvae were fed on dog
biscuitsandyeastpowderinthe3:1ratio.Atthetime
of adult feeding, these mosquitoes were 3–4 days
old after emergences (maintained on raisins and
water) and were starved for 12 h before feeding.
Each time, 500 mosquitoes per cage were fed on
blood using a feeding unit filled with parafilm as
membrane for 4 h. Aedes aegypti feeding was done
from 12 noon to 4:00 pm and C. quinquefasciatus
were fed during 6:00–10:00 pm. A membrane
feeder with the bottom end fitted with parafilm was
placed with 2.0 ml of the blood sample (obtained
fromaslaughterhousebycollectinginaheparinized
vial and stored at 4°C) and kept over a netted cage
of mosquitoes. The blood was stirred continuously
using an automated stirring device, and a constant
temperature of 37°C was maintained using a water
jacket circulating system. After feeding, the fully
engorged females were separated and maintained
on raisins.[17]
Mosquitoes gut dissection
Before the dissection for midgut extraction, the
mosquitoes were surface sterilized with 70%
ethanol for 2–10 min, which effectively surface
sterilized the mosquitoes but did not affect the
midgut bacteria (unpublished data).[5]
After
surface sterilization, mosquitoes were rinsed
twice in sterile saline solution (0.85% NaCl). The
dissected midguts were placed in 200-µl aliquots
of NaCl solution prepared the day before under
sterile conditions. Eppendorf tubes were reclosed
immediately after midguts were put in the solution.
After each dissection, forceps and needles were
sterilized thoroughly in 70% ethanol to prevent
contamination.
DNA extraction from mosquito gut
Obtained midguts were stored in −80°C until
used for DNA extraction. The first is that DNA

must be extracted from the widest possible range
of microorganisms to represent the original
microbial population. The total microbial DNA
was extracted by adapting small changes in the
protocol described by Broderick et al.[18]
In brief,
the sample was suspended in 200 ml of digestion
buffer and samples were incubated with occasional
shaking in microtubes hermetically sealed for 1 h
at 37°C. The tubes were centrifuged at 13,000 rpm
for 30 min at −4°C; then, the supernatant was
transferred to sterile centrifuge tubes. The
samples were extracted with an equivalent
phenolic centrifuge:chloroform:isoamyl alcohol
(25:24:1) at 13,000 rpm for 15 min at −4°C. The
supernatant was transferred to 1.5 μl of eppondrof
tube and incubate at −80°C for 30 min. Again, it
was centrifuged at 13,000 rpm for 30 min at 4°C.
Reveal the supernatant of suspended in 20 ml of
TE buffer (ph - 8.0) store at −20°C and use more.
DNA quality and quantity
The absorption spectrum of DNA extracts
(230–280 nm and 260–230 nm) was determined
using Nanodrop(R) ND-1000 spectrophotometer
(Eurofins Genomics Bioinformatics Lab)
according to the manufacturer’s instructions.
Pure DNA is known to produce 260/280 and
260/280 nm ratios 1:80.[19]
DNA was visualized
by electrophoresis of 5-μl aliquots through 1.2%
(w/v) agarose gel containing 0.5 μg/ml ethidium
bromide, and DNAwas quantified (μg DNA0.1 g−1
fresh gut content) as previously described.
Polymerase chain reaction (PCR)
amplification
The PCR reaction of bacterial 16S rRNA
gene V3 and V4 region was performed
containing 12.5 μl of ×2 KAPA HiFi HotStart
ReadyMix, 5 μl (1 μM) of forward primer
GCCTACGGGNGGCWGCAG 3’ and reverse
primer 5’ACTACHVGGGTATCTAATCC 3’, and
2.5 μl of DNA template (5 ng/μl in 10 mM Tris
pH 8.5)toafinalvolumeof25μl.ThePCRprotocol
was performed in triplicate using the following
conditions: 5 min at 98°C for initial denaturing,
followed by 25 cycles of 98°C for 30 s, 50°C for
30 s, and 72°C for 30 s with the final extension
for 5 min at 72°C. The Illumina sequencing
adapter ligated reverse primer contained a 6-bp
barcode specific for sample identification.[20]
After amplification, PCR products were pooled
and purified using the PCR Cleanup Kit (Axygen
Biosciences, Union City, CA, USA). Bacterial
PCR products were pooled separately to sequence
in their runs, respectively.
Cluster generation and sequencing
After obtaining the peak size from Tape Station
profile, libraries were loaded onto MiSeq at
an appropriate concentration (10–20 pM) for
cluster generation and sequencing. Paired-End
sequencing allows the template fragments to
be sequenced in both the forward and reverse
direction on MiSeq. The kit reagents were used in
the binding of samples to complementary adapter
oligos on paired-end flow cell. The adapters were
designed to allow selective cleavage of the forward
strands after resynthesis of the reverse strand
during sequencing. The copied reverse strand was
then used to sequence from the opposite end of the
fragment.
Bioinformatics and statistical analysis
Bacterial sequences were analyzed using the
UPARSE pipeline.[21]
Briefly, paired-end reads
were merged into single sequences, the low-
quality merged sequences (maximum expected
error 1, 370 bp for bacterial) were removed
from downstream analysis. After removing the
chimera, sequences with ≥97% similarity were
clusteredintooperationaltaxonomicunits(OTUs).
The OTU representative sequences were assigned
using the ribosomal database project classifier to
identify bacterial taxonomies with a confidence
threshold of 0.5.[22]
The Chao1, goods coverage,
Shannon, and Simpson indexes were calculated
to estimate alpha-diversity of each sample using
MOTHUR.[23]
RESULTS
The Nanodrop readings showed that the quantity
and quality id DNA, the readings showed that the
quantity of 20.2 ng/μ1 [Table 1]. QC pass DNA
sample was processed for first amplicon generation
followed by next-generation sequencing library
preparation using Nextera XT Index Kit (illumine
Inc.). The mean of the library fragment size

distribution is 610 bp. Libraries were sequence of
MiSeq using 2×300 bp chemistry [Figure 1].
The total read counts and read bases were found to
be 139,580 and 38,889,789 in C. quinquefasciatus
gut part, after the chimera filter, it was found
to be 279,157 and 72,286,401, respectively
[Figure 2]. Metagenomic analysis of gut sample
from C. quinquefasciatus showed the presence of
different bacterial communities.
The Chao1 index was calculated to estimate the
bacterial richness in sample. The Shannon and
Simpson diversity indexes were used to evaluate
the bacterial diversities found in sample. The
Good’s coverage index represents the relative
measure of how well the sample represents the
larger environment. The results showed that the
Chao1 richness index of bacterial community was
contributed as 678.43 ± 33. Both diversity indices
showed that the least values represent that wide
range of bacterial diversities was found in midgut
part of C. quinquefasciatus [Table 2].
Bacterial community structure was examined by
relative abundance within the sample. The phylum
level distributions of bacteria are shown in
Figure 3. The phylum Proteobacteria was highly
found with the abundance of 92.95% which is
followed by Bacteroidetes (6.88%) and Firmicutes
(0.12%). Other bacterial phyla were showed very
least occurrence (0.01%) in midgut part of
C. quinquefasciatus. The results revealed that the
Proteobacteriaphylumwasmostdominantbacterial
phylum when compared with other bacterial phyla.
The class level distributions of bacteria are shown
in Figure 4. The class Gammaproteobacteria
was highly found in sample with the abundance
of 92.95% which is followed by Flavobacteriia
(6.87%). Other bacterial classes had very
C. quinquefasciatus. The results revealed that the
bacterial class
Gammaproteobacteria was most
dominant bacterial class when compared with
other bacterial classes.
The family level distributions of bacteria were
showed that the family Enterobacteriaceae was
highly found in sample with the abundance of
54.66% which is followed by Pseudomonadaceae
(22.77%), Xanthomonadaceae (10.70%),
Weeksellaceae (6.87%), and Aeromonadaceae
(4.37%). Other bacterial families showed very
C. quinquefasciatus[Figure 5].Theresultsrevealed
that the bacterial class
Enterobacteriaceae was
most dominant bacterial family when compared
with other bacterial families. Figure 6 showed that
the presence of the pathogenic species belongings
to the family Enterobacteriaceae was highly
presented in the midgut of C. quinquefasciatus. In
terms, the human pathogens were highly enriched
in the midgut of selected mosquito because its
feeding of blood from humans; moreover, it
influences the microbial communities present in
midgut.
DISCUSSION
It has been reported that the gut bacteria
of mosquitoes play a significant role in
the vector-parasite interaction.[24]
The present
Table 1: Nanodrop reading for quality checking
NanoDrop readings (ng/µ1) NanoDrop ODA260/280
NanoDrop ODA260/230
Remark
20.2 1.89 1.23 QC pass
Figure 1: Library profile of a sample of Culex quinquefasciatus on Agilent tape station using D1000 screen tape

study was undertaken to study the cultivable and
unculturable bacterial diversity found in selected
to mosquito species C. quinquefasciatus gut
sample using Illumina MiSeq studies. Similarly,
Angelakis et al., 2016, used that the Illumina
MiSeq platform for analyses the bacterial diversity
present in different mosquitos gut part. Similarly,
Satnami et al., 2017,[25]
were used Illumina MiSeq
sequencing platform for analyses the bacterial gut
diversity in heavy metal remediation earthworms.
Inthepresentstudy,wecontributedthatthepresence
of different bacterial pathogens Stenotrophomonas
geniculate, Enterobacter cloacae, Erwinia soli,
Salmonella enterica, Enterococcus asini, Bacillus
Table 2: Summary and indexing of the NGS
Sample name Goods coverage Richness estimator Diversity index
Chao1 Shannon Simpson
Culex quinquefacitatus 0.98±0.03 678.43±33 6.23±0.1 0.97±0.05
NGS: Next-generation sequencing
Figure 2: Next-generation sequencing reads counts (a) and base (b) summary
Figure 3: Relative abundance of bacterial Phylum found in midgut part of Culex quinquefasciatus
Figure 4: Relative abundance of bacterial classes found in midgut part of Culex quinquefasciatus
a b

cereus, Enterobacter turicensis, and Enterobacter
ludwigii. Similar results were also reported by
several researchers.[26-29]
Rani et al., 2009,[11]
reported that the vastness of
pathogenic bacterial population was high in the
larvae and gut part of adult Anopheles stephensi.
The results also similarly correlated with the
results obtained from the present work. The
results from the work carried out by Yadav et al.,
2016,[30]
revealed that the midgut part of different
mosquito species collected from biodiversity
hotspot, Bhalukpong, Arunachal Pradesh, India,
has harbored to several human pathogenic
bacteria. Similarly, the metagenomic results
obtained from this present study showed that
gut part of C. quinquefasciatus contains several
human pathogenic bacteria.
The prevalence of bacterial pathogen belongings
to the Enterobacteriaceae which was harbored in
gut environment of C. quinquefasciatus found to
be high and it shows that there is more prevalence
potential will be occur when C. quinquefasciatus
bites the humans. Importantly, the abundance of
Enterobacteriaceae family in the mosquito midgut
correlates significantly with the Plasmodium
infection status. This striking relationship
highlights the role of natural gut environment in
parasite transmission.[26]
The analysis of conventional cultivable bacterial
population in midgut of Aedes albopictus was
studiedbyYadavetal.,2016,reportedthat,basedon
colony morphological characteristics, we selected
113 cultivable bacterial isolates for 16S rRNA
gene sequence-based molecular identification. Of
the 113 isolates, we could identify 35 bacterial
species belonging to 18 distinct genera under four
major phyla, namely, Proteobacteria, Firmicutes,
Actinobacteria, and Bacteroidetes. Similarly,
results also obtained in this present study, which
the abundance of Proteobacteria phylum was to
be high when compared to other phyla.
CONCLUSION
The characterization of bacterial communities
present in midgut of mosquito C. quinquefasciatus
will help to overcome the health problems caused
by this mosquito to humans. Furthermore,
the understanding of mosquito and pathogen
interaction will give more sustainability to
minimize the survivability of pathogens inside
the mosquito midgut environment. Further
studies are needed to investigate by physiological
characteristics of the bacteria and their possible
interactions with mosquito by biology and vector
competence.
Figure 5: Relative abundance of bacterial Family found in midgut part of Culex quinquefasciatus
Figure 6: Krona chart explores bacterial diversity found in
midgut part of Culex quinquefasciatus

ACKNOWLEDGMENT
The authors would like to thank Dr.
A. Stalin
Antony Entomology Research Institute, Loyola
College,fortheirtimelyhelpduringthemanuscript
preparation and submission. Furthermore, we
would like to extend our thanks to Entomology
Research Institute of Loyola College, Chennai,
andYaazh Xenomics Laboratories giving excellent
technical and bioinformatics support.
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Analyses of Bacterial Community Dynamics Present in Culex quinquefasciatus Collected from Tamil Nadu, India - A Metagenomic Approach

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Analyses of Bacterial Community Dynamics Present in Culex quinquefasciatus Collected from Tamil Nadu, India - A Metagenomic Approach