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Mehwish Durrani
Rubina Nazli
Nabila Sher
Muhammad Abubakr
Johar Ali


OBJECTIVE: To find out the self-motivated cadence of intestinal microbiota by zinc obtainability with help of next generation sequencing.

METHODS: This cross-sectional study was conducted on infants aging 1-4 months from Peshawar, Pakistan. Out of 50 infants enrolled in study, data of 46 healthy infants [23 breast-fed (BF) and 23 formula-fed (FF)] were available for final analysis. Their blood and stool samples were collected and analyzed for zinc and fecal DNA extraction, for metagenomic shot gun sequencing using next generation.

RESULTS:  Mean age of infants was 78.40±35.88 days. Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria are the four dominating major phyla found in the gut microbiota of the sample population. In breast-fed infants, mean plasma zinc was 0.138 ± 0.118 mg/L whereas, in formula-fed infants it was 0.120±0. 026 mg/L. Correlation of zinc levels with gut microbes revealed that Phylum Bacteroidetes was very low in breast-fed while in formula-fed infants it was negligible to an extent that cannot be correlated with zinc. It was also observed that there is abundance of Proteobacteria (BF: r=-0.276, p=0.264) and (FF: r= -0.043, p= 0.873) in both the zinc deficient groups whereas, Firmicutes content was (BF: r= 0.392, p=0.207) and (FF: r= -0.030, p= 0.905).

CONCLUSION: Both breast-fed and formula-fed infants had low gut microbial diversity due to low zinc levels emphasizing the need to address and rectify this problem. The improved zinc status of the infants will enable the researchers to establish and ascertain the association of zinc status with the diversity of microbiome.

Article Details

How to Cite
Durrani, M., R. Nazli, N. Sher, M. Abubakr, and J. Ali. “GUT MICROBIOME PROFILE IN ZINC DEFICIENT INFANTS USING NEXT GENERATION SEQUENCING”. KHYBER MEDICAL UNIVERSITY JOURNAL, Vol. 13, no. 1, Mar. 2021, pp. 4-9, doi:10.35845/kmuj.2021.20739.
Original Articles


1. Timmerman HM, Rutten NB, Boekhorst J, Saulnier DM, Kortman GA, Contractor N, et al. Intestinal colonisation patterns in breast-fed and formula-fed infants during the first 12 weeks of life reveal sequential microbiota signatures. Sci Rep 2017 Aug 21;7(1):8327. DOI: 10.1038/s41598-017-08268-4.
2. Ho NT, Li F, Lee-Sarwar KA, Tun HM, Brown BP, Pannaraj PS, et al. Meta-analysis of effects of exclusive breastfeeding on infant gut microbiota across populations. Nat Commun 2018 Oct 9;9(1):4169. DOI: 10.1038/s41467-018-06473-x.
3. Pannaraj PS, Li F, Cerini C, Bender JM, Yang S, Rollie A, et al. Association between breast milk bacterial communities and establishment and development of the infant gut microbiome. JAMA Pediatrics 2017;171(7):647-54. DOI: 10.1001/jamapediatrics.2017.0378.
4. Jiménez E, Delgado S, Maldonado A, Arroyo R, Albújar M, García N, et al. Staphylococcus epidermidis: a differential trait of the fecal microbiota of breast-fed infants. BMC Microbiol 2008;8(1):143. DOI: 10.1186/1471-2180-8-143.
5. Azad MB, Konya T, Persaud RR, Guttman DS, Chari RS, Field CJ, et al. Impact of maternal intrapartum antibiotics, method of birth and breastfeeding on gut microbiota during the first year of life: a prospective cohort study. Br J Obs Gynaecol (BJOG) 2016;123(6):983-93. DOI: 10.1111/1471-0528.13601.
6. Turnbaugh PJ, Ley RE, Hamady M, Fraser-Liggett CM, Knight R, Gordon JI. The human microbiome project. Nature 2007;449(7164):804. DOI: 10.1038/nature06244.
7. Civardi E, Garofoli F, Mazzucchelli I, Angelini M, Manzoni P, Stronati M. Enteral nutrition and infections: the role of human milk. Early Hum Dev 2014 Mar;90 Suppl 1:S57-9. DOI: 10.1016/S0378-3782(14)70019-2.
8. Mueller E, Blaser M. Breast milk, formula, the microbiome and overweight. Nature Rev Endocrinol 2018;14(9):510-1. DOI: 10.1038/s41574-018-0066-5.
9. Palmer C, Bik EM, DiGiulio DB, Relman DA, Brown PO. Development of the human infant intestinal microbiota. PLoS Biol 2007;5(7):e177. DOI: 10.1371/journal.pbio.0050177.
10. Gale C, Logan KM, Santhakumaran S, Parkinson JR, Hyde MJ, Modi N. Effect of breastfeeding compared with formula feeding on infant body composition: a systematic review and meta-analysis. Am J Clin Nutr 2012;95(3):656-69. DOI: 10.3945/ajcn.111.027284.
11. Khodayar-Pardo P, Mira-Pascual L, Collado MC, Martinez-Costa C. Impact of lactation stage, gestational age and mode of delivery on breast milk microbiota. J Perinatol 2014;34(8):599-605. DOI: 10.1038/jp.2014.47.
12. Hunt KM, Foster JA, Forney LJ, Schutte UM, Beck DL, Abdo Z, et al. Characterization of the diversity and temporal stability of bacterial communities in human milk. PLoS One 2011;6(6):e21313. DOI: 10.1371/journal.pone.0021313.
13. Sudo N, Sawamura S, Tanaka K, Aiba Y, Kubo C, Koga Y. The requirement of intestinal bacterial flora for the development of an IgE production system fully susceptible to oral tolerance induction. J Immunol 1997;159(4):1739-45.
14. Bezirtzoglou E, Tsiotsias A, Welling GW. Microbiota profile in feces of breast- and formula-fed newborns by using fluorescence in situ hybridization (FISH). Anaerobe 2011;17(6):478-82. DOI: 10.1016/j.anaerobe.2011.03.009.
15. Watson L, Cartwright D, Jardine LA, Pincus D, Koorts P, Kury S, et al. Transient neonatal zinc deficiency in exclusively breastfed preterm infants. J Paediatr Child Health 2018;54(3):319-22. DOI: 10.1111/jpc.13780.
16. Aumeistere L, Ciprovica I, Zavadska D, Bavrins K, Borisova A. Zinc Content in Breast Milk and Its Association with Maternal Diet. Nutrients 2018;10(10). DOI: 10.3390/nu10101438.
17. Arıca S, Arıca V, Dag H, Kaya A, Hatipoglu S, Fenercioglu A, et al. Serum zinc levels in children of 0-24 months diagnosed with pneumonia admitted to our clinic. Int J Clin Exp Med 2011;4(3):227-33.
18. Ackland ML, Michalczyk AA. Zinc and infant nutrition. Arch Biochem Biophys 2016;611:51-7. DOI: 10.1016/
19. Solomons NW, Vossenaar M. Nutrient density in complementary feeding of infants and toddlers. E J Clin Nutr 2013;67(5):501-6. DOI: 10.1038/ejcn.2013.46.
20. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 2014;30(15):2114-20.
21. Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods 2012;9(4):357-9. DOI: 10.1038/nmeth.1923.
22. Truong DT, Franzosa EA, Tickle TL, Scholz M, Weingart G, Pasolli E, et al. MetaPhlAn2 for enhanced metagenomic taxonomic profiling. Nat Methods 2015;12(10):902-3. DOI: 10.1038/nmeth.3589.
23. Reed S, Knez M, Uzan A, Stangoulis JCR, Glahn RP, Koren O, et al. Alterations in the Gut (Gallus gallus) Microbiota Following the Consumption of Zinc Biofortified Wheat (Triticum aestivum)-Based Diet. J Agric Food Chem 2018;66(25):6291-9. DOI: 10.1021/acs.jafc.8b01481.
24. Del Chierico F, Vernocchi P, Petrucca A, Paci P, Fuentes S, Praticò G, et al. Phylogenetic and metabolic tracking of gut microbiota during perinatal development. PLoS One 2015;10(9):e0137347. DOI: 10.1371/journal.pone.0137347.
25. Reed S, Neuman H, Moscovich S, Glahn RP, Koren O, Tako E. Chronic Zinc Deficiency Alters Chick Gut Microbiota Composition and Function. Nutrients 2015;7(12):9768-84. DOI: 10.3390/nu7125497.