Disease-causing microorganisms pose a constant threat to public health and global economics due to the incessant evolution of known pathogens and the emergence of novel ones. Between 1940 and 2010 almost 160 new infectious diseases caused by bacteria have been identified. Patho-mechanism of most of the disease-causing microorganisms can be demonstrated. However, the evolutionary origin of virulence is not well-deciphered. The virulence factors attributing to disease symptoms may originate from complex interaction of the pathogen with host, abiotic, and biotic components of the environment as well as other related or unrelated microorganisms. The presence of virulence factors in soil and freshwater environments has been reported in several studies employing PCR and traditional microbial culture-based techniques. However, a much elaborate investigation encompassing multiple environmental microbiomes is essential for an in-depth understanding of –

(i) the importance of virulence gene cognate for microbial persistence in non-human environments and

(ii) the contribution of these environments in the evolution of microbial pathogens.

So, microbial metagenomics is now being implemented to target the environmental gene pool of pathogenic traits. Microbial metagenomics is the culture-independent sequence and function-based analysis of the heterogeneous microbial genomes of a microbial community from their natural habitats, through the application of contemporary high-throughput genomic techniques. Metagenomics has radically transformed in the approach of the researchers to explore the community structure, composition, and distribution of populations of microorganisms from a diverse form of environments, from the mundane to the extreme and human to non-human together with the identification of genes that encode a function of interest. Landmarks in metagenomic studies have extended from outcomes with significant biotechnological impact to surprising revelations of high biomedical relevance, unraveling hidden molecular components, and connections between microbial communities and complex diseases. Metagenomic research was successfully initiated with Sanger sequencing technology.  Now the advent of next-generation sequencing (NGS) technologies with several updated sequencing platforms capable of simultaneous sequencing of millions of DNA fragments and therefore the generation of abundant data have revolutionized our understanding of microbiomes in our surroundings in the following ways:

a) Comparison and correlation of sequencing data obtained help in the identification of a novel protein family with implications in virulence such as its overexpression in disease conditions, its association with virulence phenotypes, its prevalence in a pathogenicity island, or its overrepresentation within genomes of pathogenic or host-associated species.

b) Several virulence factors display homologies to host proteins, allowing them to interfere with host functions. Identification of genes encoding such “mimicry” proteins in bacterial genomes is another promising approach for virulence factor detection.

c) Comparison of DNA signatures of isolated microorganisms with those that probe the biology of that environment in which they inhabit may lead to the identification of environment-exclusive gene clusters encoding for new protein families that impeccably correlated with pathogenicity regimes.

Application of all these approaches revealed the presence of dynamic interactions and genetic exchange occurring between bacterial members of the same or other species and also between bacteria and their viruses. By the process of horizontal gene transfer mediated by transmission of phage DNA or plasmid such novel genes get transferred in bacterial population rendering them pathogenic. Transmission of these unique genes influences the population dynamics of bacteria making them ecologically fit. At the same time, they encode exotoxins or lytic enzymes that impart virulence property in recipient microorganisms.

Several metagenome-wide association studies (MGWAS) revealed that multiple complex diseases like Crohn’s disease, rheumatoid arthritis, obesity, type 1 and type 2 diabetes, and atherosclerosis are associated with the gut microbiome. These observations have led to the identification of microbiome-based signatures that are of biomedical relevance for use in diagnostics, prognostics, and treatment of patients.    One such MGWASled to the identification of more than 20 microbial gene markers including those from Fusobacteriumnucleatum and Peptostreptococcus stomatis specific for colorectal cancer. Thereafter a panel of four such gene markers was shortlisted and validated as a non-invasive signature biomarker for early detection of colorectal cancer in patient cohorts from China, France, Austria, and Denmark. A similar MGWAS with 2045 individuals from four countries Spain, Belgium, UK, and Germany led to the identification of a microbial signature of eight groups of microorganisms that could be used to discriminate between two inflammatory bowel diseases with similar prognosis- Crohn’s disease and ulcerative colitis. Likewise, unique gut microbiome signatures can be used for the diagnosis of advanced fibrosis in individuals with non-alcoholic fatty liver and also distinguish between type 2 diabetic and non-diabetic individuals.

Environmental disruption is driven by global climate change, urbanization and other human interventions may wreak havoc with the biodiversity. Loss of biodiversity facilitates the microbial ecosystem in the evolution and transmission of infectious diseases that affect plants, animals, and humans. The use of metagenomics to assess the microbial landscape before and after human activities provides an approach to examine the influence of such changes. For instance, the decline of biodiversity associated with the reduction in natural forests and their inhabitants were reported to be a major cause of the spread of Lyme disease in the United States. Also, the increasing proximity of humans to wild and domesticated animals along with human population growth has been related to the emergence of the Nipah virus in Malaysia, as well as the worldwide increase in food-borne illnesses.

Diseases of viral origin have largely contributed to many epidemics and pandemics taking a toll on human life globally. The evolution of viral virulence can be better understood within a phylogenomic outline if relevant data are available and strong links are formed between genomics, phylogenetic, epidemiology, and experimental studies of virus virulence and fitness. Therefore, a concurrent combination of clinical and epidemiological metadata with that of the sequencing of virus genomes from clinical samples is essential. We should also emphasize the significance of gathering concurrent and historical data from probable reservoir species as these may provide a more complete insight into virulence evolution and determining the full range of microorganisms that infect a particular species, as well as their interactions which can successfully be achieved by metagenomic studies. Similar studies are now being effectively carried out worldwide to elucidate the role of the viral evolution of SARS-CoV2 in the severity and progression of the current pandemic of COVID19.

For analysis of genome and metagenome along with the characterization of epidemiology and clinical attributes of diseases caused by microorganisms require in-depth knowledge of Microbiology. Proficiency in this subject will enable the characterization of virulence factors of novel pathogens which will facilitate understanding of patho-mechanism of the disease and subsequent disease management.