**Author details**

Madangchanok Imchen and Ranjith Kumavath\*

\*Address all correspondence to: rnkumavath@gmail.com; rnkumavath@cukerala.ac.in

Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, India

## **References**


[4] Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, Mende DR. A human gut microbial gene catalog established by metagenomic sequencing. Nature. 2010;**464**(7285):59

[18] Williams BL, Hornig M, Parekh T, Lipkin WI. Application of novel PCR-based methods for detection, quantitation, and phylogenetic characterization of Sutterella species in intestinal biopsy samples from children with autism and gastrointestinal disturbances.

Metagenomics of Antimicrobial Resistance in Gut Microbiome

http://dx.doi.org/10.5772/intechopen.76214

11

[19] Smith SE, Li J, Garbett K, Mirnics K, Patterson PH. Maternal immune activation alters fetal brain development through interleukin-6. Journal of Neuroscience. 2007;**27**(40):

[20] Hu Y, Gao GF, Zhu B. The antibiotic resistome: Gene flow in environments, animals and

[21] Bennett PM. Plasmid encoded antibiotic resistance: Acquisition and transfer of antibiotic resistance genes in bacteria. British Journal of Pharmacology. 2008;**153**(S1):S347-S357

[22] Dobrindt U, Hochhut B, Hentschel U, Hacker J. Genomic islands in pathogenic and envi-

[23] Hu Y, Zhu Y, Ma Y, Liu F, Lu N, Yang X, Luan C, Yi Y, Zhu B. Genomic insights into intrinsic and acquired drug resistance mechanisms in Achromobacter xylosoxidans.

[24] Rice LB. Tn916 family conjugative transposons and dissemination of antimicrobial resistance determinants. Antimicrobial Agents and Chemotherapy. 1998;**42**(8):1871-1877 [25] Rowe-Magnus DA, Mazel D. The role of integrons in antibiotic resistance gene capture.

[26] Fournier PE, Vallenet D, Barbe V, Audic S, Ogata H, Poirel L, Richet H, Robert C, Mangenot S, Abergel C, Nordmann P. Comparative genomics of multidrug resistance in Acine-

[27] Nordgård L, Brusetti L, Raddadi N, Traavik T, Averhoff B, Nielsen KM. An investigation of horizontal transfer of feed introduced DNA to the aerobic microbiota of the gastroin-

[28] Van Schaik W. The human gut resistome. Philosophical Transactions of Royal Society B.

[29] Hu Y, Yang X, Li J, Lv N, Liu F, Wu J, Lin IY, Wu N, Weimer BC, Gao GF, Liu Y. The bacterial mobile resistome transfer network connecting the animal and human microbi-

[30] Stecher B, Denzler R, Maier L, Bernet F, Sanders MJ, Pickard DJ, Barthel M, Westendorf AM, Krogfelt KA, Walker AW, Ackermann M. Gut inflammation can boost horizontal gene transfer between pathogenic and commensal Enterobacteriaceae. Proceedings of

[31] Machado AMD, Sommer MO. Human intestinal cells modulate conjugational transfer of multidrug resistance plasmids between clinical Escherichia coli isolates. PLoS One.

omes. Applied and Environmental Microbiology. 2016;**82**(22):6672-6681

ronmental microorganisms. Nature Reviews. Microbiology. 2004;**2**(5):414

Antimicrobial Agents and Chemotherapy. 2015;**59**(2):1152-1161

*International Journal of Medical Microbiology*. 2002;**292**(2):115-125

tobacter baumannii. PLoS Genetics. 2006;**2**(1):e7

2015;**370**(1670):20140087

2014;**9**(6):e100739

testinal tract of rats. BMC Research Notes. 2012;**5**(1):170

the National Academy of Sciences. 2012;**109**(4):1269-1274

MBio. 2012;**3**(1):e00261-11

human beings. Frontiers of Medicine. 2017:1-8

10695-10702


[18] Williams BL, Hornig M, Parekh T, Lipkin WI. Application of novel PCR-based methods for detection, quantitation, and phylogenetic characterization of Sutterella species in intestinal biopsy samples from children with autism and gastrointestinal disturbances. MBio. 2012;**3**(1):e00261-11

[4] Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, Mende DR. A human gut microbial gene catalog established by

[5] Roeselers G, Bouwman J, Levin E. The human gut microbiome, diet, and health:"post hoc non ergo propter hoc". Trends in Food Science & Technology. 2016;**57**:302-305 [6] Hooper LV, Midtvedt T, Gordon JI. How host-microbial interactions shape the nutrient environment of the mammalian intestine. Annual Review of Nutrition. 2002;*22*(1):283-307

[7] Savage DC. Gastrointestinal microflora in mammalian nutrition. Annual Review of

[8] Bäckhed F, Ley RE, Sonnenburg JL, Peterson DA, Gordon JI. Host-bacterial mutualism

[9] Hsiao EY, McBride SW, Hsien S, Sharon G, Hyde ER, McCue T, Codelli JA, Chow J, Reisman SE, Petrosino JF, Patterson PH. Microbiota modulate behavioral and physiological abnormalities associated with neurodevelopmental disorders. Cell. 2013;

[10] Wostmann BS, Larkin C, Moriarty A, Bruckner-Kardoss E. Dietary intake, energy metabolism, and excretory losses of adult male germfree Wistar rats. Laboratory Animal

[11] Caporaso JG, Lauber CL, Costello EK, Berg-Lyons D, Gonzalez A, Stombaugh J, Knights D, Gajer P, Ravel J, Fierer N, Gordon JI. Moving pictures of the human microbiome.

[12] Franzosa EA, Huang K, Meadow JF, Gevers D, Lemon KP, Bohannan BJ, Huttenhower C. Identifying personal microbiomes using metagenomic codes. Proceedings of the

[13] Clemente JC, Ursell LK, Parfrey LW, Knight R. The impact of the gut microbiota on

[14] Schloissnig S, Arumugam M, Sunagawa S, Mitreva M, Tap J, Zhu A, Waller A, Mende DR, Kultima JR, Martin J, Kota K. Genomic variation landscape of the human gut micro-

[15] Boukthir S, Matoussi N, Belhadj A, Mammou S, Dlala SB, Helayem M, Rocchiccioli F, Bouzaidi S, Abdennebi M. Abnormal intestinal permeability in children with autism. La

[16] Malkova NV, Collin ZY, Hsiao EY, Moore MJ, Patterson PH. Maternal immune activation yields offspring displaying mouse versions of the three core symptoms of autism.

[17] Shi L, Smith SE, Malkova N, Tse D, Su Y, Patterson PH. Activation of the maternal immune system alters cerebellar development in the offspring. Brain, Behavior, and

metagenomic sequencing. Nature. 2010;**464**(7285):59

in the human intestine. Science. 2005;**307**(5717):1915-1920

National Academy of Sciences. 2015;**112**(22):E2930-E2938

human health: An integrative view. Cell. 2012;**148**(6):1258-1270

Nutrition. 1986;**6**(1):155-178

**155**(7):1451-1463

10 Metagenomics for Gut Microbes

Science. 1983;**33**(1):46-50

Genome Biology. 2011;**12**(5):R50

biome. Nature. 2013;**493**(7430):45

Tunisie medicale. 2010;**88**(9):685-686

Immunity. 2009;**23**(1):116-123

Brain, Behavior, and Immunity. 2012;**26**(4):607-616


[32] Mills S, Shanahan F, Stanton C, Hill C, Coffey A, Ross RP. Movers and shakers: Influence of bacteriophages in shaping the mammalian gut microbiota. Gut Microbes. 2013;**4**(1):4-16

[46] Buelow E,Gonzalez TB, Versluis D, Oostdijk EA, Ogilvie LA, van Mourik MS, Oosterink E, van Passel MW, Smidt H, D'andrea MM, de Been M. Effects of selective digestive decontamination (SDD) on the gut resistome. Journal of Antimicrobial Chemotherapy.

Metagenomics of Antimicrobial Resistance in Gut Microbiome

http://dx.doi.org/10.5772/intechopen.76214

13

[47] Pérez-Cobas AE, Artacho A, Knecht H, Ferrús ML, Friedrichs A, Ott SJ, Moya A, Latorre A, Gosalbes MJ. Differential effects of antibiotic therapy on the structure and function of

[48] Forslund K, Sunagawa S, Coelho LP, Bork P. Metagenomic insights into the human gut

[49] Raymond F, Ouameur AA, Déraspe M, Iqbal N, Gingras H, Dridi B, Leprohon P, Plante PL, Giroux R, Bérubé È, Frenette J. The initial state of the human gut microbiome deter-

[50] Jakobsson HE, Jernberg C, Andersson AF, Sjölund-Karlsson M, Jansson JK, Engstrand L. Short-term antibiotic treatment has differing long-term impacts on the human throat

[51] Imchen M, Kumavath R. Vaccination to Combat as an Approach to Reduce the Antibacterial Resistance..! International Journal of Vaccines and Vaccination. 2017;**4**(1):

[52] Kale-Pradhan PB, Jassaly HK, Wilhelm SM. Role of lactobacillus in the prevention of antibiotic-associated diarrhea: A meta-analysis. Pharmacotherapy: The Journal of

[53] Khoruts A, Dicksved J, Jansson JK, Sadowsky MJ. Changes in the composition of the human fecal microbiome after bacteriotherapy for recurrent Clostridium difficile-associ-

[54] Lee CR, Cho IH, Jeong BC, Lee SH. Strategies to minimize antibiotic resistance. International Journal of Environmental Research and Public Health. 2013;**10**(9):4274-4305

[55] Deehan EC, Walter J. The fiber gap and the disappearing gut microbiome: Implications for human nutrition. Trends in Endocrinology & Metabolism. 2016;**27**(5):239-242

[56] Logan AC, Jacka FN, Prescott SL. Immune-microbiota interactions: Dysbiosis as a global

[57] Salyers AA, Gupta A, Wang Y. Human intestinal bacteria as reservoirs for antibiotic

[58] Gibson MK, Crofts TS, Dantas G. Antibiotics and the developing infant gut microbiota

[59] Cox LM, Yamanishi S, Sohn J, Alekseyenko AV, Leung JM, Cho I, Kim SG, Li H, Gao Z, Mahana D, Rodriguez JGZ. Altering the intestinal microbiota during a critical develop-

mental window has lasting metabolic consequences. Cell. 2014;**158**(4):705-721

resistome and the forces that shape it. BioEssays. 2014;**36**(3):316-329

mines its reshaping by antibiotics. The ISME Journal. 2016;**10**(3):707

Human Pharmacology and Drug Therapy. 2010;**30**(2):119-126

ated diarrhea. Journal of Clinical Gastroenterology. 2010;**44**(5):354-360

health issue. Current Allergy and Asthma Reports. 2016;**16**(2):13

resistance genes. Trends in Microbiology. 2004;**12**(9):412-416

and resistome. Current Opinion in Microbiology. 2015;**27**:51-56

human gut microbiota. PLoS One. 2013;**8**(11):e80201

and gut microbiome. PLoS One. 2010;**5**(3):e9836

00074. DOI: 10.15406/ijvv.2017.04.00074

2014;**69**(8):2215-2223


[46] Buelow E,Gonzalez TB, Versluis D, Oostdijk EA, Ogilvie LA, van Mourik MS, Oosterink E, van Passel MW, Smidt H, D'andrea MM, de Been M. Effects of selective digestive decontamination (SDD) on the gut resistome. Journal of Antimicrobial Chemotherapy. 2014;**69**(8):2215-2223

[32] Mills S, Shanahan F, Stanton C, Hill C, Coffey A, Ross RP. Movers and shakers: Influence of bacteriophages in shaping the mammalian gut microbiota. Gut Microbes.

[33] Kim MS, Park EJ, Roh SW, Bae JW. Diversity and abundance of single-stranded DNA viruses in human feces. Applied and Environmental Microbiology. 2011;**77**(22):8062-8070

[34] Reyes A, Semenkovich NP, Whiteson K, Rohwer F, Gordon JI. Going viral: Next generation sequencing applied to human gut phage populations. Nature Reviews. Micro-

[35] Goren MG, Carmeli Y, Schwaber MJ, Chmelnitsky I, Schechner V, Navon-Venezia S. Transfer of carbapenem-resistant plasmid from Klebsiella pneumoniae ST258 to

[37] Cheng W, Chen H, Su C, Yan S. Abundance and persistence of antibiotic resistance genes in livestock farms: A comprehensive investigation in eastern China. Environment

[38] Zhu YG, Johnson TA, Su JQ, Qiao M, Guo GX, Stedtfeld RD, Hashsham SA, Tiedje JM. Diverse and abundant antibiotic resistance genes in Chinese swine farms. Proceedings

[39] Kazimierczak KA, Scott KP, Kelly D, Aminov RI. Tetracycline resistome of the organic

[40] Hu Y, Yang X, Lu N, Zhu B. The abundance of antibiotic resistance genes in human guts has correlation to the consumption of antibiotics in animal. Gut Microbes. 2014;

[41] Hu Y, Yang X, Qin J, Lu N, Cheng G, Wu N, Pan Y, Li J, Zhu L, Wang X, Meng Z. Metagenome-wide analysis of antibiotic resistance genes in a large cohort of human gut

[42] Forslund K, Sunagawa S, Kultima JR, Mende DR, Arumugam M, Typas A, Bork P. Country-specific antibiotic use practices impact the human gut resistome. Genome

[43] Ghosh TS, Gupta SS, Nair GB, Mande SS. In silico analysis of antibiotic resistance genes in the gut microflora of individuals from diverse geographies and age-groups. PLoS

[44] Bengtsson-Palme J, Angelin M, Huss M, Kjellqvist S, Kristiansson E, Palmgren H, Larsson DJ, Johansson A. The human gut microbiome as a transporter of antibiotic resistance genes between continents. Antimicrobial Agents and Chemotherapy. 2015;

[45] Arnold KE, Williams NJ, Bennett M. Disperse abroad in the land': The role of wildlife in the dissemination of antimicrobial resistance. Biology Letters. 2016;**12**(8):20160137

pig gut. Applied and Environmental Microbiology. 2009;*75*(6):1717-1722

Escherichia coli in patient. Emerging Infectious Diseases. 2010;**16**(6):1014

[36] Yap MNF. The double life of antibiotics. Missouri Medicine. 2013;110(4):320

of the National Academy of Sciences. 2013;**110**(9):3435-3440

microbiota. Nature Communications. 2013;**4**:2151

Research. 2013;**23**(7):1163-1169

One. 2013;**8**(12):e83823

**59**(10):6551-6560

2013;**4**(1):4-16

12 Metagenomics for Gut Microbes

biology. 2012;**10**(9):607

International. 2013;**61**:1-7

**5**(2):245-249


[60] Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, Contreras M, Magris M, Hidalgo G, Baldassano RN, Anokhin AP, Heath AC. Human gut microbiome viewed across age and geography. Nature. 2012;**486**(7402):222

[72] Bäckhed F, Roswall J, Peng Y, Feng Q, Jia H, Kovatcheva-Datchary P, Li Y, Xia Y, Xie H, Zhong H, Khan MT. Dynamics and stabilization of the human gut microbiome during

Metagenomics of Antimicrobial Resistance in Gut Microbiome

http://dx.doi.org/10.5772/intechopen.76214

15

[73] Dominguez-Bello MG, Costello EK, Contreras M, Magris M, Hidalgo G, Fierer N, Knight R. Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proceedings of the National Academy of Sciences.

[74] Moore AM, Ahmadi S, Patel S, Gibson MK, Wang B, Ndao IM, Deych E, Shannon W, Tarr PI, Warner BB, Dantas G. Gut resistome development in healthy twin pairs in the first

[75] Lozoff B, Brittenham GM, Wolf AW, McClish DK, Kuhnert PM, Jimenez E, Jimenez R, Mora LA, Gomez I, Krauskoph D. Iron deficiency anemia and iron therapy effects on

[76] Wang WL, Xu SY, Ren ZG, Tao L, Jiang JW, Zheng SS. Application of metagenomics in the human gut microbiome. World journal of gastroenterology: WJG. 2015;**21**(3):803 [77] Sommer MO, Dantas G, Church GM. Functional characterization of the antibiotic resis-

infant developmental test performance. Pediatrics. 1987;**79**(6):981-995

tance reservoir in the human microflora. Science. 2009;**325**(5944):1128-1131

the first year of life. Cell Host & Microbe. 2015;**17**(5):690-703

2010;**107**(26):11971-11975

year of life. Microbiome. 2015;**3**(1):27


[72] Bäckhed F, Roswall J, Peng Y, Feng Q, Jia H, Kovatcheva-Datchary P, Li Y, Xia Y, Xie H, Zhong H, Khan MT. Dynamics and stabilization of the human gut microbiome during the first year of life. Cell Host & Microbe. 2015;**17**(5):690-703

[60] Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, Contreras M, Magris M, Hidalgo G, Baldassano RN, Anokhin AP, Heath AC. Human gut microbiome viewed

[61] La Rosa PS, Warner BB, Zhou Y, Weinstock GM, Sodergren E, Hall-Moore CM, Stevens HJ, Bennett WE, Shaikh N, Linneman LA, Hoffmann JA. Patterned progression of bacterial populations in the premature infant gut. Proceedings of the National Academy of

[62] Palmer C, Bik EM, DiGiulio DB, Relman DA, Brown PO. Development of the human

[63] Alicea-Serrano AM, Contreras M, Magris M, Hidalgo G, Dominguez-Bello MG. Tetracycline resistance genes acquired at birth. Archives of Microbiology. 2013;**195**(6):447-451

[64] Moore AM, Patel S, Forsberg KJ, Wang B, Bentley G, Razia Y, Qin X, Tarr PI, Dantas G. Pediatric fecal microbiota harbor diverse and novel antibiotic resistance genes. PLoS

[65] Arboleya S, Sánchez B, Milani C, Duranti S, Solís G, Fernández N, Clara G, Ventura M, Margolles A, Gueimonde M. Intestinal microbiota development in preterm neonates

[66] Bennet R, Eriksson M, Nord CE, ZetterstrÖm R. Fecal bacterial microflora of newborn infants during intensive care management and treatment with five antibiotic regimens.

[67] Tanaka S, Kobayashi T, Songjinda P, Tateyama A, Tsubouchi M, Kiyohara C, Shirakawa T, Sonomoto K, Nakayama J. Influence of antibiotic exposure in the early postnatal period on the development of intestinal microbiota. FEMS Immunology & Medical

[68] Makino H, Kushiro A, Ishikawa E, Kubota H, Gawad A, Sakai T, Oishi K, Martin R, Ben-Amor K, Knol J, Tanaka R. Mother-to-infant transmission of intestinal bifidobacterial strains has an impact on the early development of vaginally delivered infant's micro-

[69] Abrahamsson TR, Rautava S, Moore AM, Neu J, Sherman PM. The time for a confirmative necrotizing enterocolitis probiotics prevention trial in the extremely low birth weight infant in North America is now! The Journal of Pediatrics. 2014;**165**(2):389-394

[70] Härtel C, Pagel J, Rupp J, Bendiks M, Guthmann F, Rieger-Fackeldey E, Heckmann M, Franz A, Schiffmann JH, Zimmermann B, Hepping N. Prophylactic use of lactobacillus acidophilus/Bifidobacterium infantis probiotics and outcome in very low birth weight

[71] Jones RM, Luo L, Ardita CS, Richardson AN, Kwon YM, Mercante JW, Alam A, Gates CL, Wu H, Swanson PA, Lambeth JD. Symbiotic lactobacilli stimulate gut epithelial proliferation via Nox-mediated generation of reactive oxygen species. The EMBO

and effect of perinatal antibiotics. The Journal of Pediatrics. 2015;**166**(3):538-544

across age and geography. Nature. 2012;**486**(7402):222

infant intestinal microbiota. PLoS Biology. 2007;**5**(7):e177

The Pediatric Infectious Disease Journal. 1986;**5**(5):533-539

infants. The Journal of Pediatrics. 2014;**165**(2):285-289

Sciences. 2014;**111**(34):12522-12527

One. 2013;**8**(11):e78822

14 Metagenomics for Gut Microbes

Microbiology. 2009;**56**(1):80-87

biota. PLoS One. 2013;**8**(11):e78331

Journal. 2013;**32**(23):3017-3028


**Section 2**

**Metagenomic Applications**
