Tumor tissue-specific bacterial biomarker panel for colorectal cancer: Bacteroides massiliensis, Alistipes species, Alistipes onderdonkii, Bifidobacterium pseudocatenulatum, Corynebacterium appendicis.

Human microbiome studies have shown diversity to exist among different ethnic populations. However, studies pertaining to the microbial composition of CRC among the Indian population have not been well explored. We aimed to decipher the microbial signature in tumor tissues from North Indian CRC patients. Next-generation sequencing of tumor and adjacent tissue-derived bacterial 16S rRNA V3-V4 hypervariable regions was performed to investigate the abundance of specific microbes. The expression profile analysis deciphered a decreased diversity among the tumor-associated microbial communities. At the phyla level, Proteobacteria was differentially expressed in CRC tissues than adjacent normal. Further, DeSeq2 normalization identified 4 out of 79 distinct species (p < 0.005) only in CRC, Bacteroides massiliensis, Alistipes onderdonkii, Bifidobacterium pseudocatenulatum, and Corynebacterium appendicis. Thus, the findings suggest that microbial signatures can be used as putative biomarkers in diagnosis, prognosis and treatment management of CRC.

"MINES" method for genomic DNA extraction from deep biosphere biofilms.

Successful and efficient extraction of high quality, high molecular weight genomic DNA from the environmental samples is an essential primary step to understand the genetic, metabolic and evolutionary characteristics of the microbial communities. Deep mine biofilm samples that contain high amounts of mucoid exopolysaccharide often pose difficulties to obtaining refined community DNA. To circumvent this hindrance, we report our "MINES" method which we developed for optimal biofilm DNA recovery suitable for all types of high-resolution downstream applications. The method is also suitable for samples collected from landfill compost, kitchen digest (KD), and for Gram-positive Geobacillus sp. strain WSUCF1 and Gram-negative E. coli DH5α strains. In one form of the method, use of a gentle preprocessing technique to loosen the mucoid layer, combined with a multi-lytic polyzyme treatment to maximize yields from all cell types in the biofilm sample, yielded >1 µg of high molecular weight DNA (16-20 kb) per gram of the biofilm sample, with an A260/280 and A260/230 ratio of about 2. Furthermore, amplification of 16S rRNA genes as well as restriction digestion with BamHI and HindIII suggest that the newly developed method can minimize any inhibitory effects of contaminants. Results indicate that it is an appropriate methodology for the extraction of total genomic DNA for functional metagenomic studies and may be applicable to other environmental samples from which DNA extraction is challenging. IMPORTANCE: Our present knowledge of microorganisms and their enzymes from deep mine subsurfaces is based largely on laboratory studies of pure microbial cultures. These methods tend only to hit nearly 1% of the entire microbial community. In this regard, metagenomics, has emerged as a strategic approach to explore unculturable microbes through the sequencing and analysis of DNA extracted from the environmental samples. This research paper discusses our "MINES" method for genomic DNA extraction from deep biosphere biofilm samples.

Study of CD4+CD8+ double positive T-lymphocyte phenotype and function in Indian patients infected with HIV-1.

CD4+CD8+ double positive T cells represent a minor peripheral blood lymphocyte population. CD4+ expression on CD8+ T cells is induced following cellular activation, and as chronic HIV-1 infection is associated with generalized immune activation, double positive T cells studies have become necessary to understand the immunopathology of human immunodeficiency virus (HIV). The frequency of double positive T cells in persons infected with HIV was studied in comparison to uninfected controls. Further, the expression of CD38, HLA-DR, and programmed death (PD)-1 on these cells were ascertained. HIV-1 specific double positive T cells were also studied for their cytokine secretory ability and phenotype. A significantly higher double positive cell population was observed in the patients with advanced HIV disease (CD4+ T cell counts below 200 cells/µl), as compared to patients with CD4+ T cell counts above 500 cells/µl. Double positive T cells from patients with symptomatic HIV disease had a significantly increased activation and exhaustion levels, compared to asymptomatic subjects and to single positive T cells from the same subjects. HIV-1 specific double positive T cells showed further increase in CD38 and PD-1 expression levels. The proportion of CD38 and PD-1 expressing total and HIV-1 specific double positive T cells correlated positively with HIV-1 plasma viremia and negatively with CD4+ T cell counts. HIV infection results in a marked increase of double positive T cell population, and this cell population shows higher level of activation and exhaustion (increased PD-1 expression) compared to the single positive CD4+ and CD8+ T cells.

Usefulness of hemoglobin and albumin as prognostic markers for highly active antiretroviral therapy for HIV-1 infection.

BACKGROUND: Usefulness of hemoglobin and albumin as prognostic markers for highly active anti-retroviral therapy for HIV-1 infection. INTRODUCTION: Anemia and hypoalbuminemia are common complications in human immunodeficiency virus (HIV) infection. We aimed to investigate the changes in hemoglobin and albumin levels in response to highly active antiretroviral therapy (HAART). Further, we evaluated the appropriateness of using hemoglobin and albumin as HIV disease progression markers. MATERIALS AND METHODS: A prospective longitudinal study of 122 subjects was carried out. Pre-treatment, one year, and two year post-treatment hemoglobin, and albumin levels were correlated with respective CD4+ T cell counts. The sensitivity, specificity, and positive predictive value of each marker against CD4+ T cell counts were calculated in order to establish the appropriateness of use of these parameters as surrogate disease progression and prognostic markers. RESULTS: Mean hemoglobin and albumin levels pre-, one, and two year post HAART were 9.7 g/dL, 12.1 g/dL, and 13.1 g/dL, respectively, P = 0.001; albumin: 3.7 gm%, 4.4 gm%, and 4.7 gm%, respectively, P = 0.001. There was a positive correlation between hemoglobin, albumin, and CD4+ T cell count at pre-treatment, one year, and two year post-treatment visit. Both albumin and hemoglobin had high sensitivity when compared to CD4+ T cell counts. CONCLUSIONS: Hemoglobin and albumin levels were found to increase after initiation of HAART. Hemoglobin and albumin were seen to be a strong prognostic marker of HIV disease progression at pre-, one, and two year post-treatment. Therefore, hemoglobin and albumin may be used together along with CD4 + T cell counts in HIV management, particularly in resource-poor settings.

Polyfunctional analysis of Gag and Nef specific CD8+ T-cell responses in HIV-1 infected Indian individuals.

Polyfunctional CD8+ T-cells have been described as most competent in controlling viral replication. We studied the impact of antigen persistence on the polyfunctional immune responses of CD8+ T-lymphocytes to HIV Gag and Nef peptides and polyclonal stimuli in 40 ART naïve HIV infected individuals and analyzed the alterations in T-cell functionality in early and late stages of infection. Significantly elevated level of global response and polyfunctional profile of CD8+ T-cells were observed to polyclonal stimulation, than HIV specific antigens in chronically infected individuals. However no key differences were observed in CD8+ T-cell functional profile in any of the 15 unique subsets for Gag and Nef specific antigens. The subjects in early stage of infection (defined as a gap of 6 months or less between seroconversion and enrolment and with no apparent clinical symptoms) had a higher degree of response functionality (4+ or 3+ different functions simultaneously) than in the late stage infection (defined as time duration since seroconversion greater than 6 months). The data suggest that persistence of antigen during chronic infection leads to functional impairment of HIV specific responses.

Late presenters to HIV care and treatment, identification of associated risk factors in HIV-1 infected Indian population.

BACKGROUND: Timely access to antiretroviral therapy is a key to controlling HIV infection. Late diagnosis and presentation to care diminish the benefits of antiretrovirals and increase risk of transmission. We aimed to identify late presenters in patients sent for first CD4 T cell count after HIV diagnosis, for therapy initiation evaluation. Further we aimed at identifying patient factors associated with higher risk of late presentation. METHODS: Retrospective data collection and analysis was done for 3680 subjects visiting the laboratory for CD4 T cell counts between 2001 and 2007. We segregated the patients on basis of their CD4 T cell counts after first HIV diagnosis. Factors associated with risk of late presentation to CD4 T cell counts after HIV diagnosis were identified using univariate analysis, and the strength of association of individual factor was assessed by calculation of odds ratios. RESULTS: Of 3680 subjects, 2936 (83.37%) were defined as late presenters. Late testing varied among age groups, transmission categories, and gender. Males were twice as likely to present late as compared to females. We found significant positive association of heterosexual transmission route (p < 0.001), and older age groups of 45 years and above (p = 0.0004) to late presentation. Female sex, children below 14 years of age and sexual contact with HIV positive spouse were associated with significantly lower risks to presenting late. Intravenous drug users were also associated with lower risks of late presentation, in comparison to heterosexual transmission route. CONCLUSIONS: The study identifies HIV infected population groups at a higher risk of late presentation to care and treatment. The risk factors identified to be associated with late presentation should be utilised in formulating targeted public health interventions in order to improve early HIV diagnosis.