The Gut-microbiome : a potential ally under siege from AMR

The world of gut microbiota

Our intestine is packed with millions of microorganisms that have co-evolved with us to form a complex ecosystem that is known as the intestinal or gut microbiota. The gut microbiota community is densely populated by diverse bacteria, archaea, viruses, fungi and protozoa from several hundred different species, with bacterial microbiota from primarily four phyla being the dominant class: Bacteroidetes, Firmicutes, Actinobacteria, and Proteobacteria (1). This microbial community performs essential functions for the host physiology in metabolism, nutrient absorption, immunity, and neuronal development among others, whereas aberrations in the microbial makeup can lead to a variety of diseases(2). Thus, it is also known as the “invisible organ”. Diet, geographical location, and ethnicity are all important determinants of gut microbiota diversity and overall composition(3,4).

The effect of antibiotics on gut microbiota

This naturally co-evolving, symbiotic process has been severely impacted in recent decades by administration of antibiotics. Although antibiotics are a major tool in fighting diseases, they are also known to negatively impact gut health. Multiple studies have shown that antibiotics cause microbial dysbiosis — an imbalance in the gut microflora population leading to numerous diseases like diabetes, obesity, inflammatory bowel diseases among others(5). Due to the broad-spectrum activities of certain antibiotics, subsets of commensal microbes are also killed or inhibited leading to changes in the microbiome. The antibiotic vancomycin is known to decrease faecal microbial diversity and absolute number of Gram-positive bacteria(6). Antibiotics also disrupt and alter the gut metabolome (small molecules like arabinitol and sugars like sucrose)(7). Apart from directly affecting gut microbiota, antibiotics can also have indirect effects on the microflora and their host. By altering the bacterial metabolites and thus the signals transmitted from gut microbiota to the host, antibiotics can also impact host immunity. Not only gut immunity, antibiotics also bring about impairment of systemic immunity including that of pulmonary defence against pathogens(8).

The transmission, and development of AMR in gut microbiota

Antibiotic resistance has been declared as one of the top 10 global public health crisis by WHO. Between 2000 & 2015, global antibiotic usage increased by 65%(9). It is predicted that approximately 10 million people will die from AMR annually by 2050(10). One direct adverse effect of the antibiotic administration is the selection and spread of AMR genes in gut microbiota. Any habitat that provides a niche for bacterial flora to thrive also holds the potential for giving rise to antimicrobial resistance (AMR) genes. The human intestine with its suitable conditions like nutrient richness, appropriate temperature, high bacterial density, and abundant bacterial interactions provides such environment. Gut microbiota can acquire AMR in primarily two ways: (1) “starting from scratch”- caused by spontaneous mutation or external environmental factors, (2) “less to more”- spread of AMR genes through horizontal gene transfer (HGT)(11). Among the external factors, the inappropriate, over-the-counter use and broad, non-targeted, prophylactic antibiotic treatment prescribed by medical practitioners along with cross-contamination in hospitals through inefficient disinfection of wards and equipment are some of the prime methods of AMR transmission(12). Use of antibiotics during pregnancy affect the foetus in the uterus too and subsequently facilitating AMR development in infants’ intestinal microbiota(13). Furthermore, the pervasive use of antibiotics to enhance growth rate and the prophylactic treatment of industrially housed food-producing animals, aquaculture, and planting industry provide more avenues for AMR strains to proliferate(14). Multiple studies have shown that farm workers’ intestines contain a large amount of antibiotic resistance genes due to exchange with the surrounding environment as compared to their family members(15–17). Raw fruits and vegetables are another source through which AMR genes reach the intestines of the consumers(18).

The transfer of resistance genes is mainly mediated by HGT in intestines that can take place through one of four ways: (a) Transformation — the process by which a bacterium absorbs environmental DNA (eDNA) and integrates it into its own genome. One of the culprits of food poisoning in humans, Campylobacter jejuni gain resistance to antibiotics like kanamycin and chloramphenicol through this method (19). (b) Transduction — By using phage as a medium, a donor bacteria may transfer part of its DNA to a recipient bacteria to cause gene recombination. (c ) Conjugation- genetic transfer and recombination through cell-cell contact between bacteria. The high density of intestinal bacteria greatly aid in this process and indeed conjugation of bacterial genes through plasmids is the main reason for widespread occurrence of AMR genes in the gut microbiota. For example, the multi-drug resistant E.coli develops resistance to colistin through conjugation with Enterobacteriaceae (20). (d) Membrane vesicle fusion- Bacteria secrete outer membrane vesicles (OMV) to escape the effects of various antibiotics. These OMVs might carry antibiotic degrading enzymes or resistance genes which can be picked up by surrounding bacteria to become resistant themselves(21).

Current data shows that the transfer of resistance genes is enhanced in environments subject to anthropogenic antibiotic exposure(22,23). Thus, we need to adopt a One Health strategy that strictly controls and monitors the multiple links of humans, animals, and environment to prevent spread of AMR and parallelly adopt methods that encourage the diversification and growth of the host’s own microbiota profile.

The road ahead- Microbiome therapeutics

Despite AMR bacteria causing problems in the human intestine, the solution may also lie within it. With the bidirectional interaction between host and gut microbiota and their important role in maintaining human health and immunity, these native microbiota hold immense potential to be used as therapeutics for disease management. Strategies such as fecal microbiota transplantation (FMT) or probiotics that rely on the administration of exogenous microbes to replace disease-causing microbes with beneficial ones could be used to manage dysbiosis-related disorders(24). Bacteriocins, produced by commensal microbiota is another therapeutic method under active research that can be used to reduce deleterious pathogens from the microbiome instead of antibiotics(25). The microbiome therapeutic industry is estimated to reach $838.2 million by 2026 and several companies are at the forefront of this research. Ferring and Rebiotix’s live biotherapeutic (bacterial suspension of live spores) RBX2660 has shown 70.4% efficiency in treating recurrent CDI over placebo(26). Another such innovation funded by CARB-X is the USA-based Vedanta’s VE707 microbiome programme, an oral preventative agent consisting of a consortium of commensal bacteria designed to decolonize gut-dwelling multi-drug resistant organisms in patients at high risk for infection such as those undergoing solid organ or bone marrow transplants. If successful, it can save $2 billion in healthcare associated costs(27).

Indian Scenario

Research into human microbiome though lagging compared to the rest of the world, is fast catching up in India. Currently pro-biotics form the majority of products in this sector. As of 2021 the Indian human microbiome market was valued at USD 139 million with projected growth to USD 282 million by 2031, with a growth rate of 6.9% (28).

One of India’s first start-ups working on human microbiome-based prognostic, diagnostic and therapeutic tools is Xome Life Sciences. Xome uses a combination of computational analyses, laboratory experiments and sensitivity studies to design their products. The company is currently focusing on developing such solutions for screening and quantitative monitoring of celiac disease and for screening and monitoring dental caries and oral health. (29)

The field of microbiome is greatly aided by developments in genomics and metabolomics. C-CAMP has been playing a supporting role in enhancing the research base when it comes to microbiome. For example, the Discovery to Innovation Accelerator (DIA) team of C-CAMP was part of a study highlighting the link of Nrf2 pathway to gut barrier integrity. (28) While the next generation genomics facility was instrumental in revealing unique features of Indian distal gut microbiota through metagenomics analysis.(30)

For Indian innovations in the microbiome area to achieve the projected growth a combination of support infrastructure in the form of omics facilities, reference libraries for microbes along with dedicated programs for innovators is required. Research in this area can have implication in nutrition, human health through the AMR link, as well as discovery of novel therapeutic molecules.

Disclaimer: The blog is a compilation of information on a given topic that is drawn from credible sources; however, this does not claim to be an exhaustive document on the subject. It is not intended to be prescriptive, nor does it represent the opinion of C-CAMP or its partners. The blog is intended to encourage discussion on an important topic that may be of interest to the larger community and stakeholders in associated domains.

References

1. Ducarmon QR, Zwittink RD, Hornung BVH, Schaik W Van. Gut Microbiota and Colonization Resistance against Bacterial Enteric Infection. Antimicrob Agents Chemother. 2019;

2. Cho I, Blaser MJ. The human microbiome: At the interface of health and disease. Nat Rev Genet. 2012;13(4):260–70.

3. Zmora N, Suez J, Elinav E. You are what you eat: diet, health and the gut microbiota. Nat Rev Gastroenterol Hepatol [Internet]. 2019;16(1):35–56. A

4. Prideaux L, Kang S, Wagner J, Buckley M, Mahar JE, De Cruz P, et al. Impact of ethnicity, geography, and disease on the microbiota in health and inflammatory bowel disease. Inflamm Bowel Dis. 2013;19(13):2906–18.

5. Zhang S, Chen DC, Chen LM. Facing a new challenge: The adverse effects of antibiotics on gut microbiota and host immunity. Chin Med J (Engl). 2019;132(10):1135–8.

6. Willing BP, Russell SL, Finlay BB. Shifting the balance: Antibiotic effects on host-microbiota mutualism. Nat Rev Microbiol. 2011;9(4):233–43.

7. Choo JM, Kanno T, Zain NMM, Leong LEX, Abell GCJ, Keeble JE, et al. Divergent Relationships between Fecal Microbiota and Metabolome following Distinct Antibiotic-Induced Disruptions. mSphere. 2017;2(1).

8. Bergonzelli GE, Granato D, Pridmore RD, Marvin-Guy LF, Donnicola D, Corthésy-Theulaz IE. GroEL of Lactobacillus johnsonii La1 (NCC 533) is cell surface associated: Potential role in interactions with the host and the gastric pathogen Helicobacter pylori. Infect Immun. 2006;74(1):425–34.

9. Klein EY, Van Boeckel TP, Martinez EM, Pant S, Gandra S, Levin SA, et al. Global increase and geographic convergence in antibiotic consumption between 2000 and 2015. Proc Natl Acad Sci U S A. 2018;115(15):E3463–70.

10. Neill JO’. Antimicrobial Resistance: Tackling a crisis for the health and wealth of nations. The Review on Antimicrobial Resistance. 2014.

11. Zhang Y, Xu S, Yang Y, Chou SH, He J. A ‘time bomb’ in the human intestine — the multiple emergence and spread of antibiotic-resistant bacteria. Environ Microbiol. 2022;24(3):1231–46.

12. Desta K, Woldeamanuel Y, Azazh A, Mohammod H, Desalegn D, Shimelis D, et al. High gastrointestinal colonization rate with extended-spectrum β-lactamase-producing Enterobacteriaceae in hospitalized patients: Emergence of carbapenemase-producing K. Pneumoniae in Ethiopia. PLoS One. 2016;11(8):1–14.

13. Nogacka AM, Salazar N, Arboleya S, Suárez M, Fernández N, Solís G, et al. Early microbiota, antibiotics and health. Cell Mol Life Sci. 2018;75(1):83–91.

14. Wegener HC. Antibiotics in animal feed and their role in resistance development. Curr Opin Microbiol. 2003;6(5):439–45.

15. Sun J, Liao XP, D’Souza AW, Boolchandani M, Li SH, Cheng K, et al. Environmental remodeling of human gut microbiota and antibiotic resistome in livestock farms. Nat Commun [Internet]. 2020;11(1):1–11.

16. Luiken REC, Van Gompel L, Bossers A, Munk P, Joosten P, Hansen RB, et al. Farm dust resistomes and bacterial microbiomes in European poultry and pig farms. Environ Int [Internet]. 2020;143(May):105971.

17. Van Gompel L, Luiken REC, Hansen RB, Munk P, Bouwknegt M, Heres L, et al. Description and determinants of the faecal resistome and microbiome of farmers and slaughterhouse workers: A metagenome-wide cross-sectional study. Environ Int [Internet]. 2020;143(June):105939.

18. Strategy H, Human F, Lopes R, Fuentes-castillo D, Fontana H, Rodrigues L, et al. Endophytic Lifestyle of Global Clones of Extended-Spectrum b -Lactamase-Producing Priority Pathogens in Fresh Vegetables : mSystems. 2021;

19. Bae J, Oh E, Jeon B. Enhanced Transmission of Antibiotic Resistance in Campylobacter jejuni Biofilms by Natural Transformation. Antimicrob Agents Chemother. 2014;

20. Zhu W, Lawsin A, Lindsey RL, Batra D, Knipe K, Yoo BB, et al. Conjugal Transfer, Whole-Genome Sequencing, and Plasmid Analysis of Four mcr-1-Bearing Isolates from U.S. Patients. Antimicrob Agents Chemother. 2019;(11):1–5.

21. Kim SW, Park S Bin, Im SP, Lee JS, Jung JW, Won T, et al. Outer membrane vesicles from β -lactam-resistant Escherichia coli enable the survival of β -lactam- susceptible E . coli in the presence of β -lactam antibiotics. Sci Rep [Internet]. 2018;(March):1–13.

22. Kristiansson E, Fick J, Janzon A, Grabic R, Rutgersson C, Weijdegård B, et al. Pyrosequencing of antibiotic-contaminated river sediments reveals high levels of resistance and gene transfer elements. PLoS One. 2011;6(2).

23. Knapp CW, Dolfing J, Ehlert PAI, Graham DW. Evidence of increasing antibiotic resistance gene abundances in archived soils since 1940. Environ Sci Technol. 2010;44(2):580–7.

24. Gagliardi A, Totino V, Cacciotti F, Iebba V, Neroni B, Bonfiglio G, et al. Rebuilding the Gut Microbiota Ecosystem. Int J Environ Res Public Health. 2018;

25. Yadav M, Chauhan NS. Microbiome therapeutics : exploring the present scenario and challenges. Gastroenterol Rep. 2021;(July):1–19.

26. Rebiotix a Ferring Company. Ferring and Rebiotix Present Landmark Phase 3 Data Demonstrating Superior Efficacy of Investigational RBX2660 Versus Placebo to Reduce Recurrence of C . difficile Infection [Internet]. 2021.

27. CARB-X. CARB-X funds Vedanta Biosciences to accelerate the development of a new category of oral therapeutics to help a patient’s microbiota fight drug-resistant bacteria [Internet]. 2019.

28.https://www.transparencymarketresearch.com/india-human-microbiome-market.html

29. https://www.wipo.int/wipo_magazine/en/ip-at-work/2022/indian-microbiome-research.html

30. Singh, R., Chandrashekharappa, S., Bodduluri, S.R. et al. Enhancement of the gut barrier integrity by a microbial metabolite through the Nrf2 pathway. Nat Commun 10, 89 (2019).

31. Ngangyola Tuikhar, Santosh Keisam, Rajendra Kumar Labala, Imrat, Padma Ramakrishnan, Moirangthem Cha Arunkumar, Giasuddin Ahmed, Elena Biagi, Kumaraswamy Jeyaram,Comparative analysis of the gut microbiota in centenarians and young adults shows a common signature across genotypically non-related populations,Mechanisms of Ageing and Development,Volume 179,2019,