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The Role of Microbes in the Our Life

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Human xenobiotic metabolism generally converts non polar compounds into hydrophilic, high molecular weight compounds so that they can be more readily excreted. The process occurs in hepatic circulation as follows: In phase I, enzymes such as Cytochrome P450 oxidases, introduce a functional electrophilic centre (such as –OH,-SH, -NH2, etc.) into the xenobiotic molecule. This process is known as oxidative metabolism. The creation of such reactive centre allows phase II enzymes {such as Glutathione S-transferases (GSTs) etc.} to introduce a hydrophilic moiety (such as glutathione etc.) into the molecule resulting in the production of its water-soluble form; a process referred to as conjugate metabolism. Finally, in phase III, the conjugated xenobiotics may be further processed, before being recognized by efflux transporters and pumped out of cells. If due to any reason any of the steps in the metabolic pathway is dysregulated then the ultimate ending will be GENOTOXIC RISK.


Over past few decades gut’s microbiota has been linked to several conditions- depression to obesity. In this microbiome revolutionary era though late but cancer has got the spot light. Earlier only provocative connections were dealt with: linkage of Helicobacter pylori to gastric cancer is one such example. In some cases, the bacterium activates inflammatory response by disrupting the mucus layer and thereby creates a tumour supporting environment. Besides, some increases the resistivity of anticancer drugs. The discovery of cancer immunotherapies had increased the dimensions for microbiome. Now, microorganisms are studied closely to find out their interactive role with the treatment and how it can be harnessed.

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The chemotherapeutic drug irinotecan (also called CPT-11) is one of three first-line chemotherapy drugs used to treat colorectal cancer that has spread, or metastasized, to other parts of the body. CPT-11 is modified by carboxylesterases in host tissues into active form SN-38, an inhibitor of topoisomerase I in tumor cells. SN-38 is conjugated into SN-38-G by hepatic UDP-glucuronosyltransferases prior of being secreted into intestine. However, the nontoxic SN-38-G could be converted to SN-38 by the β-glucuronidase of gut bacteria leading to the severe intestinal side effect of diarrhea.


In 2013 team led by Laurence Zitvogel showed that gut microbiome influences the cancer treatment by activating immune response [48]. They found that chemotherapy drug ‘cyclophosphamide’ damaged the mucus layer lining of intestine which in turn allowed some gut bacteria to travel to the lymph node and spleen, where specific immune cells were activated. Various researchers’ teams then examined whether gut bacteria influence the response of checkpoint inhibitors, antibodies to cell surface molecules such as CTLA4 and PD1. In 2015 again Zitvogel and her team showed mice failed to respond to CTLA4 blockade in microbe free environment but showed better response in the presence of bacterium Bacteroides fragilis. Sivan et al discovered that oral administration of Bifidobacterium controlled to the same extent as programmed cell death protein 1 ligand 1 (PD-L-1)- specific antibody therapy, whereas combined treatment nearly abolished the tumor growth.

The underlying phenomenon behind this success is the augmentation of dendritic cell function leading to enhanced CD8+T cell priming and accumulation of the same in the tumour microenvironment. In another study conducted by Routy et al., it was found that antibiotic consumption led to poor response to immunotherapeutic PD1. On analysing samples from lung and kidney cancer patients it was found that the nonrespondance was due to low levels of Akkermansia muciniphila. On oral administration of the respective microbe the efficacy of PD-1 was restored back in an interleukin-12 dependent manner by increasing the availability of CCR9+ CXCR3+CD4+T lymphocytes into mouse tumor beds. Thus, manipulation of of microbiota will add new dimensions to cancer immunotherapy.


The GI microbiota is considered to be less diverse than that of soil microbes but that doesnot reduce its potential to metabolise environmental chemicals. The xenobiotic-metabolising enzymes of the GI microbiota are as follows

  • The reductive cleavage of azo (N=N) bonds is performed by bacterial azoreductases.
  • Bacterial nitroreductases reduce nitro (–NO2) functional groups to the corresponding amines.
  • Endogenous sulfate esters are hydrolysed in the GI tract by sulfatases of bacterial origin.
  • Glutathione conjugates of xenobiotics are degraded by mammalian enzyme (γ-glutamyl transpeptidase and carboxypeptidase), resulting in the formation of cysteine conjugates which reaches the GI tract and converts them to their corresponding thiol by ß-lyase activity.
  • ß-glucuronidases are present throughout the GI tract and play a role in the hydrolysis of xenobiotic glucuronides.

Gut microbes are capable of metabolizing many chemicsls such as hydrocarbons, nitro toluenes, pesticides, polychlorobiphenyls, melanine, artificial sweetners etc. in our review we will mainly concentrate on hydrocarbons. Polycyclic Aromatic Hydrocarbon (PAHs) is one of the most widespread organic pollutants generated by the incomplete combustion of carbon-containing fuels. Its toxicity is structure dependent; some have been classified as oestrogenic and some as human carcinogens. Exposure to PAHs has been associated with higher risks of lung and bladder cancer. Estrogenecity was evaluated of four colonic digests of PAHs (naphthalene, phenanthrene, pyrene and benzo(a)pyrene) before and after digestion by a typical human microbiota in vitro. This indicates that the microorganisms present in the human colon can bioactivate PAHs, by converting them to oestrogenic molecules. Besides, rat and human gut microbiota could regenerate benzo(a)pyrene its hepatic conjugate thus reversing the endogenous detoxification process.

Besides, human gut microbes references are also available from fish and wax worm gut microbes of being involved in hydrocarbon degradation. Janina Š. and Liongina M., on investigating the gut microbe of – the Baltic cod (Gadus morhua), plaice (Platichthys flesus) and the Baltic herring (Clupea harengus) – from the Baltic Sea by molecular method and phenotypic examination found that the abundance of hydrocarbon-degrading bacteria in the intestinal tract of fish varied from 2.40×104 to 1.08×105 cfu g–1 between fish species and was still high and the prevalent bacteria were: Aeromonas, Pseudomonas/Shewanella. Jun Yang et al isolated E. asburiae strain YT1 and Bacillus sp. Strain YP1 from the enrichment of wax worm gut as potential PE-degraders within limited incubation period.


Clustered regularly interspaced short palindromic repeats (CRISPR) loci, along with their associated cas genes constitute a defense system against propagation of phages and plasmids. During the defense mechanism, initially, bacteria incorporate fragments of phage or plasmid genomes as novel spacers, which are then transcribed into small RNAs. These RNAs together with the Cas protein complex guide the way to interfere with phage replication by sequence homology. This has enabled successful implementation of the CRISPRi not only in prokaryotic system but also in eukaryotic system] and thus enabled the scientists in constructing synthetic genetic circuits and has enhanced the study of natural biological networks. In a study conducted by Adi et al, CRISPR spacers were directly extracted from the raw sequencing reads and then used as probes to search for phage genomic segments within the assembled sequences of the metagenomes. This allowed them to

  1. Identify and characterize a large catalog of phages and mobile elements that infect bacteria in the human gut;
  2. Identify, for a subset of these phages and their bacterial hosts; and
  3. Perform a subject-wide analysis of phage–bacteria coexistence, by correlating patterns of phage abundance with patterns of bacterial abundance and resistance.

Mark et al. developed a synthetic biology toolbox for engineering a prominent member of the human gut microbiome, Bacteroides thetaiotaomicron, to accurately detect and precisely respond to gut-localized signals. CRISPRi technology was used by them to regulate the knockdown of recombinant and endogenous gene expression, to alter the metabolic capacity of B. thetaiotaomicron, a prevalent and stable resident of the human gut, and its resistance to antimicrobial peptides. The successful achievement of the objectives by Mark et al has created a blueprint for engineering Bacteroides for surveillance of or therapeutic delivery to the gut microbiome. Utilization of this blueprint will help to understand the underlying mechanism of various diseases like obesity, diabetes, colon cancer and inflammatory bowel disease caused due to changing composition of human gut microbiome and will enable therapeutical treatment of gut dysbioses.

Food industry is also not lagging behind in utilizing gene editing system, CRISPR-cas. Probiotic is one of the most promising aspects of food industry. Intake of probiotics helps to colonize gut by the beneficial bacterial strain by competing with the bad strain for nutrients. The exponential growth of the probiotc industry depends on the efficacy of the the strain. Thus genetic modification of the strain with desirable gene has positive impact on food industry. CRIPSR-Cas was applied in L. reuteri, one dairy starter culture for developing the customized probiotic.

The utilization of CRISPR is beyond expectation. Scientists are engrossing themselves to harness even the last drop of the advantage that the system can provide. As per the Merck news released on 16th of May 2018, the two year collaboration of Merck with Washington University in St. Louis, Missouri, USA will utilize Merck’s CRISPR genome-editing technology in research studies by Dr. Jeffrey Gordon of Washington University School of Medicine. The research aims to determine the differences between gut bacterial communities in healthy and malnourished children, and to identify what features of healthy intestinal bacteria are critical for supporting healthy growth and their involvement in muscle and bone growth, maturation of our immune systems and metabolic health.


Researchers are targeting to develop strategies to engineer bacteria to perform specific functions such as secreting a therapeutic molecule (mostly peptides and small proteins) and detecting a particular signal, such as small molecules derived from other bacteria, food, or cancerous or inflamed tissues. CRISPR-cas technology can be fruitfully utilized to insert gene of interest in desirable vector to create the molecular weapon to combat the detrimental invaders such as infectious microbe. Development of proper strain like super bug can help us to quickly manage the problems related with hydrocarbon toxicity. In our current ongoing studies we are trying to evaluate the hydrocarbon-utilization ability of gut bacteria at different dilutions.

During the course of evaluation we have found positive result for 10-4 dilution plate against 0.2% naphthalene. A control plate was also kept containing only PCA-Naphthalene plate to nullify any error based on contamination. Using colony characterization and 16S rDNA sequencing, the sequence of the isolate was obtained and the isolate was confirmed to be Escherichia ferugusonii. Sequence obtained was subjected to a similarity search BLAST on the National Centre for Biotechnology Information (NCBI) database and submitted into GenBank. Similarly, analysing various other strains will open new roads and further aidance of CRISPR-cas gene editing technique will help us in creating molecular weapons to triumph over the limitations in the field of- health care, agriculture, food industry, bioremediation etc.


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