Tanu Saroha’s research while affiliated with Academy of Scientific and Innovative Research and other places

In this study, the safety of Bifidobacterium longum Bif10, Bifidobacterium breve Bif11, Lacticaseibacillus rhamnosus LAB3, and Lactiplantibacillus plantarum LAB39 was evaluated using in-vitro, genomics, and in-vivo approaches. In the in-vitro safety studies, mucin degradation, biogenic amine production and cytotoxicity on HEK-293 cells by these strains were evaluated. Whole genome sequencing and bioinformatics analysis were carried out to identify the genes responsible for mucin degradation, biogenic amine production, antibiotic resistance, and virulence factors. In-vivo safety was assessed after acute, subacute, and sub-chronic oral feeding with respective strains to the mice as per revised OECD guidelines. Histopathological examination, gut permeability, hematological, blood biochemistry, and oxidative stress were evaluated after sacrificing the animals. Further, the compatibility of the four strains was assessed and their synbiotic combination with isomaltooligosaccharides (IMOs) was evaluated for its potential in alleviating lipopolysaccharide (LPS) induced inflammation in murine macrophages. In-vitro studies indicated that the strains do not produce biogenic amines and were non-cytotoxic to HEK-293 cells. Whole genome analysis suggested a lack of transferable antibiotic-resistance genes or potentially lethal virulence factors and genes for biogenic amines. In vivo studies showed that the bacterial strains did not affect the health parameters related to blood or induce histological alterations in the vital organs. The four strains were compatible with each other and their synbiotic blend efficiently curtailed LPS-induced oxidative stress, inducible nitric oxide and proinflammatory cytokine production. Given these observations, Bif10, Bif11, LAB3, and LAB39 can be deemed safe and their synbiotic blend with IMOs could impart anti-inflammatory effects.

Introduction Burkholderia cepacia complex (Bcc) clonal complex (CC) 31, the predominant lineage causing devastating outbreaks globally, has been a growing concern of infections in non-cystic fibrosis (NCF) patients in India. B. cenocepacia is very challenging to treat owing to its virulence determinants and antibiotic resistance. Improving the management of these infections requires a better knowledge of their resistance patterns and mechanisms. Methods Whole-genome sequences of 35 CC31 isolates obtained from patient samples, were analyzed against available 210 CC31 genomes in the NCBI database to glean details of resistance, virulence, mobile elements, and phylogenetic markers to study genomic diversity and evolution of CC31 lineage in India. Results Genomic analysis revealed that 35 isolates belonging to CC31 were categorized into 11 sequence types (ST), of which five STs were reported exclusively from India. Phylogenetic analysis classified 245 CC31 isolates into eight distinct clades (I-VIII) and unveiled that NCF isolates are evolving independently from the global cystic fibrosis (CF) isolates forming a distinct clade. The detection rate of seven classes of antibiotic-related genes in 35 isolates was 35 (100%) for tetracyclines, aminoglycosides, and fluoroquinolones; 26 (74.2%) for sulphonamides and phenicols; 7 (20%) for beta-lactamases; and 1 (2.8%) for trimethoprim resistance genes. Additionally, 3 (8.5%) NCF isolates were resistant to disinfecting agents and antiseptics. Antimicrobial susceptibility testing revealed that majority of NCF isolates were resistant to chloramphenicol (77%) and levofloxacin (34%). NCF isolates have a comparable number of virulence genes to CF isolates. A well-studied pathogenicity island of B. cenocepacia, GI11 is present in ST628 and ST709 isolates from the Indian Bcc population. In contrast, genomic island GI15 (highly similar to the island found in B. pseudomallei strain EY1) is exclusively reported in ST839 and ST824 isolates from two different locations in India. Horizontal acquisition of lytic phage ST79 of pathogenic B. pseudomallei is demonstrated in ST628 isolates Bcc1463, Bcc29163, and BccR4654 amongst CC31 lineage. Discussion The study reveals a high diversity of CC31 lineages among B. cenocepacia isolates from India. The extensive information from this study will facilitate the development of rapid diagnostic and novel therapeutic approaches to manage B. cenocepacia infections.

A Gram-positive facultative anaerobe, non-spore forming, and non-motile bacterial strain M31 was isolated from faecal contaminated soil. The strain is previously reported to produce a novel antimicrobial lipopeptide and displayed probiotic properties. The strain M31 is catalase negative and fermented D-galactose, D-glucose, esculin, D-maltose, D-lactose, D-melibiose, D-raffinose, D-saccharose (weak reaction), D-xylose (weak reaction), D-ribose (weak reaction), and L-arabinose (weak reaction). The majority of fatty acids were C16:0 (53.9%), C18:0 (26.9%), and C19:0 cyclo ω8c (19.1%). The genome is 2 234 040 bp long with 38.81% GC content. The pairwise ortho average nucleotide identity and digital DNA-DNA hybridisation values of strain M31 with its closest relative species from Lm. reuteri clade and Lm. rudii is below the recommended cut-off of 95% and 70% respectively. Herein, we propose Limosilactobacillus walteri sp. nov. as a novel species of the genus Limosilactobacillus with M31 = MTCC 12838 = JCM 32759 = KCTC 25569.

Introduction: Burkholderia cepacia complex (Bcc) is a non-fermenting Gram-negative bacilli (NFGNB) cluster with high genome plasticity and large genome size. As a major nosocomial pathogen, it is known to cause bacteremia, infections in cystic fibrosis patients. One of the factors contributing to multidrug resistance, virulence, and fitness is through chromosomally encoded genetic elements. They carry advantageous genes benefitting the host, thus its crucial to understand their stability and transfer in population. In an earlier study, we have reported a novel genomic island BcenGI15 in a unique clone of Bcc, ST824, involved in a major sepsis outbreak of a pediatric ward in an Indian hospital. In the present study, we have carried out screening of this genomic island by polymerase chain reaction (PCR) in an extensive collection of Bcc isolates from a major tertiary care hospital in Northern part of India. Materials and methods: 90 isolates obtained from routine patient specimens over a period of 9 years revived from glycerol stock and identified as Burkholderia cenocepacia based on conventional biochemical tests, recA PCR-based restriction fragment length polymorphism (RFLP), and matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). Isolates were screened for genomic island BcenGI15 via PCR using attL gene primers. Island positive isolates were subjected to multilocus sequence typing (MLST) and antibiotic susceptibility testing. Results: The PCR in 16/90 (17.77%) isolates came positive for the presence of BcenGI15. Multi-locus sequence typing (MLST) revealed that all the positive isolates are clonal and belong to a dominant sequence type (ST) ST839. Conclusion: MLST data analysis suggested presence of BcenGI15 in two different STs (ST824, ST839) from hospitals in north and west part of India. This suggests probable movement and selection for this element in Indian population of Bcc isolates.

Xanthomonas is a major group of pathogenic bacteria infecting staple food crops like rice. Increasingly it is being recognized that non-pathogenic Xanthomonas (NPX) are also important members of a healthy plant microbiome. However, the vast majority of the species described in this genus are of pathogenic nature, and only a few NPX species have been reported till now. Genomic and taxonogenomic analysis of NPX is needed for the management of this important group of bacteria. In this study, two yellow-pigmented bacterial isolates were obtained from healthy rice seeds in Punjab, India. The isolates designated PPL560T and PPL568 were identified as members of the genus Xanthomonas based on biochemical tests and 16S rRNA gene sequence analysis retrieved from the whole-genome sequences. Isolates formed a distinct monophyletic lineage with Xanthomonas sontii and Xanthomonas sacchari as the closest relatives in the phylogenetic tree based on core gene content shared by the representative species of the genus Xanthomonas. Pairwise ortho Average Nucleotide Identity and digital DNA-DNA hybridization values calculated against other species of Xanthomonas were below their respective cut-offs. In planta studies revealed that PPL560T and PPL568 are non-pathogenic to rice plants upon leaf clip inoculation. The absence of type III secretion system-related genes and effectors further supported their non-pathogenic status. Herein, we propose Xanthomonas indica sp. nov. as novel species of the genus Xanthomonas with PPL560T = MTCC 13185 = CFBP 9039 = ICMP 24394 as its type strain and PPL568 as another constituent member.

Two yellow pigmented bacterial strains were isolated from healthy rice seeds. The strains designated as PPL560 T and PPL568 were identified as members of genus Xanthomonas based on analysis of biochemical and 16S rRNA gene sequence retrieved from whole genome sequence. Isolates formed a distinct monophyletic lineage with X. sontii and X. sacchari as the closest relatives in the phylogenetic tree based on core gene content shared by reported species in genus Xanthomonas . Pairwise ortho Average Nucleotide Identity and digital DNA-DNA hybridisation values calculated against other species of Xanthomonas were below their respective cut-offs. In planta studies revealed that PPL560 T and PPL568 are non-pathogenic to rice plants upon leaf clip inoculation. Absence of type III secretion system related genes and effectors further supported their non-pathogenic status. Herein, we propose Xanthomonas indica sp. nov. as novel species of genus Xanthomonas with PPL560 T =MTCC13185 as its type strain and PPL568 as another constituent member.

Staphylococcus haemolyticus is a species of coagulase-negative staphylococci that has primarily been studied as a human skin microbiome member and an emerging nosocomial pathogen. Here, we present the first complete genome of S. haemolyticus strains SE3.9, SE3.8 and SE2.14 reported as an endophyte of rice seed. Detailed investigation of the genome dynamics of strains from diverse origins revealed an expanded genome size in clinical isolates, and a role of many insertion sequence (IS) elements in strain diversification. Interestingly, several of the IS elements are also unique or enriched in a particular habitat. Comparative studies also revealed the potential movement of mobile elements from rice endophytic S. haemolyticus to strains from other pathogenic species such as Staphylococcus aureus . The study highlights the importance of ecological studies in the systematic understanding of genome plasticity and management of medically important Staphylococcus species.

Arsenic is highly toxic element to all forms of life and is a major environmental contaminant. Understanding acquisition, detoxification and adaptation mechanisms in bacteria that are associated with the host in arsenic-rich conditions can provide novel insights into the evolutionary dynamics of host–microbe–environment interactions. In the present study, we have investigated an arsenic-resistance mechanism acquired during the evolution of a particular lineage in the population of Xanthomonas oryzae pv. oryzae , which is a serious plant pathogen infecting rice. Our study revealed the horizontal acquisition of a novel chromosomal 12 kb ars cassette in X. oryzae pv. oryzae IXO1088 that confers high resistance to arsenate/arsenite. The ars cassette comprises several genes that constitute an operon induced in the presence of arsenate/arsenite. Transfer of the cloned ars cassette to X. oryzae pv. oryzae BXO512, which lacks the cassette, confers an arsenic-resistance phenotype. Furthermore, the transcriptional response of X. oryzae pv. oryzae IXO1088 under arsenate/arsenite exposure was analysed using RNA sequencing. Arsenic detoxification and efflux, oxidative stress, iron acquisition/storage, and damage repair are the main cellular responses to arsenic exposure. Our investigation has provided insights into the existence of a novel detoxification and adaptation mechanism within the X. oryzae pv. oryzae population to deal with high-arsenic conditions outside the rice plant.

Arsenic (As) is highly toxic element to all forms of life and is a major environmental contaminant. Understanding acquisition, detoxification, and adaptation mechanisms in bacteria that are associated with host in arsenic-rich conditions can provide novel insights into dynamics of host-microbe-microenvironment interactions. In the present study, we have investigated an arsenic resistance mechanism acquired during the evolution of a particular lineage in the population of Xanthomonas oryzae pv. oryzae ( Xoo) , which is a serious plant pathogen infecting rice. Our study revealed the horizontal acquisition of a novel chromosomal 12kb ars cassette in Xoo IXO1088 that confers high resistance to arsenate/arsenite. The ars cassette comprises several genes that constitute an operon induced in the presence of arsenate/arsenite. Transfer of cloned ars cassette to Xoo BXO512 lacking it confers arsenic resistance phenotype. Further, the transcriptional response of Xoo IXO1088 under arsenate/arsenite exposure was analyzed using RNA sequencing. Arsenic detoxification and efflux, oxidative stress, iron acquisition/storage, and damage repair are the main cellular responses to arsenic exposure. Our investigation has provided novel insights in to how a pathogenic bacterium is coping with arsenic-rich unique micro-environments like seen in rice growing in submerged water conditions. Impact statement Arsenic accumulation in rice is a serious and unique agronomic issue. Arsenic contaminated groundwater used for irrigation purposes is adding to the accumulation of arsenic in rice. Submerged conditions in the paddy fields further induce the prevalence of toxic inorganic arsenic species in the environment. Our genomics and transcriptomics-based study reveals how a rice pathogen is coping with the lethal concentrations of arsenic by acquiring a novel resistance cassette during diversification into lineages. Acquisition of such detoxification mechanisms can provide a selective advantage to the bacterial population in avoiding toxicity or enhancing virulence and to their on-going evolutionary events. While there are numerous studies on plant-pathogen-environment interactions, our study highlights the importance of systematic studies on the role of unique micro-environmental conditions on the evolution of host-adapted pathogens/microbes.