The unique composition of Indian gut microbiome, gene catalogue, and associated fecal metabolome deciphered using multi-omics approaches

BACKGROUND

Metagenomic studies carried out in the past decade have led to an enhanced understanding of the gut microbiome in human health; however, the Indian gut microbiome has not been well explored. We analyzed the gut microbiome of 110 healthy individuals from two distinct locations (North-Central and Southern) in India using multi-omics approaches, including 16S rRNA gene amplicon sequencing, whole-genome shotgun metagenomic sequencing, and metabolomic profiling of fecal and serum samples.

RESULTS

The gene catalogue established in this study emphasizes the uniqueness of the Indian gut microbiome in comparison to other populations. The gut microbiome of the cohort from North-Central India, which was primarily consuming a plant-based diet, was found to be associated with Prevotella and also showed an enrichment of branched chain amino acid (BCAA) and lipopolysaccharide biosynthesis pathways. In contrast, the gut microbiome of the cohort from Southern India, which was consuming an omnivorous diet, showed associations with Bacteroides, Ruminococcus, and Faecalibacterium and had an enrichment of short chain fatty acid biosynthesis pathway and BCAA transporters. This corroborated well with the metabolomics results, which showed higher concentration of BCAAs in the serum metabolome of the North-Central cohort and an association with Prevotella. In contrast, the concentration of BCAAs was found to be higher in the fecal metabolome of the Southern-India cohort and showed a positive correlation with the higher abundance of BCAA transporters.

CONCLUSIONS

The study reveals the unique composition of the Indian gut microbiome, establishes the Indian gut microbial gene catalogue, and compares it with the gut microbiome of other populations. The functional associations revealed using metagenomic and metabolomic approaches provide novel insights on the gut-microbe-metabolic axis, which will be useful for future epidemiological and translational researches.

Typing of Neisseria gonorrhoeae isolates by phenotypic and genotypic techniques in New Delhi, India

BACKGROUND

The objective of this study is to investigate gonococcal isolates using phenotypic and genotypic methods.

METHODOLOGY

Sixty gonococcal isolates obtained were examined. Strains were divided into 9 resistant phenotypes: Chromosomally mediated penicillin-resistant Neisseria gonorrhoeae (CMRNGP), penicillinase-producing NG (PPNG), chromosomally mediated tetracycline-resistant NG (CMRNGT), TRNG, PPNG and TRNG, CMRNGPT, quinolone resistant NG (QRNG), Azithro R, and decreased susceptibility (DS) to ceftriaxone. These isolates were also subjected to auxotyping and NG-multi-antigen sequence typing (MAST).

RESULTS

Of 60 isolates, 32 (53.33%) PPNG and only one was CMRNGP; 16 (26.66%) were CMRNGT, while 18 (30%) were TRNG. Both PPNG and TRNG found in 13 (21.66%) and none were CMRNGPT. QRNG was seen in 93.33%, 5% Azithromycin R, and 6.66% were DS to ceftriaxone. Based on auxotyping, 24 (40%) nonrequiring, 16 (26.66%) were proline requiring, 13 (21.66%) arginine requiring while 7 (11.66%) belonged to others. The most common ST was 6058 (32.5%). The discriminatory indices of antibiogram, auxotyping and NG-MAST were 0.77, 0.72, and 0.95, respectively.

CONCLUSIONS

NG-MAST is the method of choice for epidemiological studies.

Effects of NSAIDs on the Dynamics and Phase Behavior of DODAB Bilayers

Despite well-known side effects, nonsteroidal anti-inflammatory drugs (NSAIDs) are one of the most prescribed drugs worldwide for their anti-inflammatory and antipyretic properties. Here, we report the effects of two NSAIDs, aspirin and indomethacin, on the thermotropic phase behavior and the dynamics of a dioctadecyldimethylammonium bromide (DODAB) lipid bilayer as studied using neutron scattering techniques. Elastic fixed window scans showed that the addition of aspirin and indomethacin affects the phase behavior of a DODAB bilayer in both heating and cooling cycles. Upon heating, there is a change in the coagel- to fluid-phase transition temperature from 327 K for pure DODAB bilayer to 321 and 323 K in the presence of aspirin and indomethacin, respectively. More strikingly, upon cooling, the addition of NSAIDs suppresses the formation of the intermediate gel phase observed in pure DODAB. The suppression of the gel phase on addition of the NSAIDs evidences the synchronous ordering of a lipid headgroup and chain. Analysis of quasi-elastic neutron scattering data showed that only localized internal motion exists in the coagel phase, whereas both internal and lateral motions exist in the fluid phase. The internal motion is described by a fractional uniaxial rotational diffusion model in the coagel phase and by a localized translation diffusion model in the fluid phase. In the coagel phase, the rotational diffusion coefficient of DODAB is found to be almost twice for the addition of the drugs, whereas the mobility fraction did not change for indomethacin but becomes twice for aspirin. In the fluid phase, the lateral motion, described well by a continuous diffusion model, is found to be slower by about ∼30% for indomethacin but almost no change for aspirin. For the internal motion, addition of aspirin leads to enhancement of the internal motion, whereas indomethacin did not show significant effect. This study shows that the effect of different NSAIDs on the dynamics of the lipid membrane is not the same; hence, one must consider these NSAIDs individually while studying their action mechanism on the cell membrane.

Genotype-Phenotype Correlations of Dystrophic Epidermolysis Bullosa in India: Experience from a Tertiary Care Centre

Recent advances in the field of genomics have seen the successful implementation of whole exome sequencing as a rapid and efficient diagnostic strategy in several genodermatoses. The aim of this study was to explore the potential of molecular studies in dystrophic epidermolysis bullosa (DEB) in India. Whole exome sequencing was performed using genomic DNA from each case of epidermolysis bullosa, followed by massively parallel sequencing. Resulting reads were mapped to the human reference genome hg19. Sanger sequencing subsequently confirmed the potentially pathogenic mutations. Whole exome sequencing of 18 patients with DEB from 17 unrelated Indian families revealed 20 distinct sequence variants in the COL7A1 gene including 2 widely prevalent mutations. Dominant inheritance was seen in 7 patients, while 11 patients showed a highly variable recessive DEB. This preliminary study using exome sequencing is clearly encouraging and will serve as the basis for future large-scale molecular studies to actively identify and understand DEB in the Indian population.

Modulation of Solvation and Molecular Recognition of a Lipid Bilayer under Dynamical Phase Transition

It is well accepted in contemporary biology that an ∼30 Å thick lipid bilayer film around living cells is a matter of life and death as the film typically delimits the environments that serve as a crucial margin. The dynamic organization of lipid molecules both across the lipid bilayer and in the lateral dimension are known to be crucial for cellular transport and molecular recognition by important biological macromolecules. Here, we study dilute (20 mM) Dioctadecyldimethylammonium bromide (DODAB) vesicles at different temperatures in aqueous dispersion with well-defined phases namely liquid crystalline, gel and subgel. The spectroscopic studies on two fluorescent probes 8-anilino-1-naphthalene sulfonic acid ammonium salt (ANS) and Coumarin 500 (C500), former in the head group region of the lipid-water interface and later located deeper in the lipid bilayer follow dynamics (solvation and fluidity) of their local environments in the vesicles. Binding of an anti-tuberculosis drug rifampicin has also been studied employing Förster resonance energy transfer (FRET) technique. The molecular insight concerning the effect of dynamical organization of the lipid molecules on the local dynamics of aqueous environments in different phases leading to molecular recognition becomes evident in our study.

Utility of Horizontal Sections of Scalp Biopsies in Differentiating between Androgenetic Alopecia and Alopecia Areata

BACKGROUND

Androgenetic alopecia (AGA) and alopecia areata (AA) are common causes of alopecia which can sometimes be difficult to differentiate clinically. Horizontal sections of scalp biopsies are used to study non-cicatricial alopecias due to the ability to perform both quantitative and morphometric analysis of hair follicles on them.

METHODS

It was a prospective, cross-sectional study conducted to assess the utility of horizontal sections to differentiate between the alopecias. Fifty-two cases were included: 20 cases of male AGA, 11 of female AGA and 21 cases of AA. After clinical examination and dermoscopy, a skin biopsy was taken and subjected to transverse sectioning. Histopathological assessment was done by two dermatopathologists blinded to clinical details.

RESULTS

Among the quantitative parameters, terminal:vellus hair ratio (3.08 in AGA and 1.83 in AA, p = 0.0091) and anagen:non-anagen hair ratio (9.25 in AGA and 3.56 in AA, p = 0.0021) were significantly lower in AA. In qualitative parameters, peribulbar inflammation was seen in 63% of AA cases (p = 0.0001). Pigment casts were seen in twice the number of AA (57%) than AGA (26%) cases. Broad avascular stelae and focal trichomalacia were seen in 9.5% of AA cases.

CONCLUSION

Besides peribulbar inflammation, we found a lower anagen:non-anagen hair ratio and presence of pigment casts in transverse sections of scalp biopsies favouring AA over AGA.

Nutritional characterization of apple as a function of genotype

Twenty two apple cultivars grown in Himachal Pradesh, India were harvested at commercial maturity and analysed for different physical (fruit weight, fruit dimensions, firmness, color) and nutritional attributes (ascorbic acid, antioxidant activity, total carotenoid, sugars, organic acids, phenolic compounds and minerals). Cultivar 'Oregon Spur II' was found to have maximum fruit size and weight while the least was observed for cultivar 'Starkrimson'. Quantitative differences were found in the nutritional profile among the cultivars with respect to all the above attributes. The ascorbic acid content ranged between 19.38 mg 100 g^-1 ('Well Spur') and 32.08 mg 100 g^-1 ('Starkrimson') while the antioxidant activity varied between 2.64 μmol Trolox equivalent g^-1 ('Granny Smith') and 13.20 μmol Trolox equivalent g^-1 ('Silver Spur'). The highest total carotenoid was found in 'Red Chief' (147.06 mg kg^-1) while in 'Early Red-I' the total carotenoid was only 29.03 mg kg^-1. HPLC analysis for individual sugars, organic acids and phenolic compounds was carried out. Fructose (average 50.79 g L^-1) was the most abundant sugar. Malic acid (average 6.03 mg L^-1) predominated among the individual organic acids. Potassium (average 795.14 mg 100 g^-1) and iron (average 2.04 µg g^-1) were the predominant macro and micro elements, respectively. Chlorogenic acid was the major constituent among phenolic compounds.

Deciphering interactions of ionic liquids with biomembrane

Ionic liquids (ILs) are a special class of low-temperature (typically < 100 °C) molten salts, which have huge upsurge interest in the field of chemical synthesis, catalysis, electrochemistry, pharmacology, and biotechnology, mainly due to their highly tunable nature and exceptional properties. However, practical uses of ILs are restricted mainly due to their adverse actions on organisms. Understanding interactions of ILs with biomembrane is prerequisite to assimilate the actions of these ionic compounds on the organism. Here, we review different biophysical methods to characterize interactions between ILs and phospholipid membrane, a model biomembrane. All these studies indicate that ILs interact profoundly with the lipid bilayer and modulate the structure, microscopic dynamics, and phase behavior of the membrane, which could be the fundamental cause of the observed toxicity of ILs. Effects of ILs on the membrane are found to be strongly dependent on the lipophilicity of the IL and are found to increase with the alkyl chain length of IL. This can be correlated with the observed higher toxicity of IL with the longer alkyl chain length. These informations would be useful to tune the toxicity of IL which is required in designing environment-friendly nontoxic solvents of the so-called green chemistry for various practical applications.

Effects of ionic liquids on the nanoscopic dynamics and phase behaviour of a phosphatidylcholine membrane

Ionic liquids (ILs) are potential candidates for new antimicrobials due to their tunable antibacterial and antifungal properties that are required to keep pace with the growing challenge of bacterial resistance. To a great extent their antimicrobial actions are related to the interactions of ILs with cell membranes. Here, we report the effects of ILs on the nanoscopic dynamics and phase behaviour of a dimyristoylphosphatidylcholine (DMPC) membrane, a model cell membrane, as studied using neutron scattering techniques. Two prototypical imidazolium-based ILs 1-butyl-3-methylimidazolium tetrafluoroborate (BMIM[BF4]) and 1-decyl-3-methylimidazolium tetrafluoroborate (DMIM[BF4]), which differ only in terms of the alkyl chain length of cations, have been used for the present study. Fixed Elastic Window Scan (FEWS) shows that the incorporation of ILs affects the phase behaviour of the phospholipid membrane significantly and the transition from a solid gel to a fluid phase shifts to lower temperature. This is found to be consistent with our differential scanning calorimetry measurements. DMIM[BF4], which has a longer alkyl chain cation, affects the phase behaviour more strongly in comparison to BMIM[BF4]. The pressure-area isotherms of the DMPC monolayer measured at the air-water interface show that in the presence of ILs, isotherms shift towards higher area-per lipid molecule. DMIM[BF4] is found to shift the isotherm to a greater extent compared to BMIM[BF4]. Quasielastic neutron scattering (QENS) data show that both ILs act as a plasticizer, which enhances the fluidity of the membrane. DMIM[BF4] is found to be a stronger plasticizing agent in comparison to BMIM[BF4] that has a cation with a shorter alkyl chain. The incorporation of DMIM[BF4] enhances not only the long range lateral motion but also the localised internal motion of the lipids. On the other hand, BMIM[BF4] acts weakly in comparison to DMIM[BF4] and mainly alters the localised internal motion of the lipids. Any subtle change in the dynamical properties of the membrane can profoundly affect the stability of the cell. Hence, the dominant effect of the IL with the longer chain length on the dynamics of the phospholipid membrane might be correlated with its cytotoxic activity. QENS data analysis has provided a quantitative description of the effects of the two imidazolium-based ILs on the dynamical and phase behaviour of the model cell membrane, which is essential for a detailed understanding of their action mechanism.

Buffalo heifers selected for lower residual feed intake have lower feed intake, better dietary nitrogen utilisation and reduced enteric methane production

This study was conducted to evaluate the utilisation of the residual feed intake (RFI) as a feed efficiency selection tool and its relationship with methane emissions. Eighteen Murrah buffalo (Bubalus bubalis) heifers were fed ad libitum with total mixed ration (TMR) for 120 days. Based on linear regression models involving dry matter intake (DMI), average daily gain (ADG) and mid-test metabolic body size (MBW^0.75 ), heifers were assigned into low and high RFI groups. The RFI varied from -0.09 to +0.12 kg DM/day with average RFI of -0.05 and 0.05 kg DM/day in low and high RFI heifers respectively. Low RFI heifers ate 11.6% less DM each day, yet average daily gain (ADG) and feed utilisation were comparable among low and high RFI groups. Low RFI heifers required significantly (p < .05) less metabolizable energy for maintenance (MEm) compared to high RFI heifers. Apparent nutrient digestibility showed non-significant difference (p > .05) among low and high RFI groups. Although the nitrogen balance was similar among heifers of low and high RFI groups, nitrogen metabolism was significantly higher (p > .05) in high RFI heifers. Comparison of data from heifers exhibiting the low (n = 9) and high (n = 9) RFI showed that the low RFI heifers have lower enteric methane production and methane losses than high RFI heifers. In conclusion, results of this study revealed that selection of more efficient buffalo heifers has multiple benefits, such as decreased feed intake and less emission of methane.

T helper type 1 polarizing γδ T cells and Scavenger receptors contribute to the pathogenesis of Pemphigus vulgaris

γδ T cells and Scavenger receptors are key parts of the innate immune machinery, playing significant roles in regulating immune homeostasis at the epithelial surface. The roles of these immune components are not yet characterized for the autoimmune skin disorder Pemphigus vulgaris (PV). Phenotyping and frequency of γδ T cells estimated by flow cytometry have shown increased frequency of γδ T cells (6·7% versus 4·4%) producing interferon- γ (IFN-γ; 35·2% versus 26·68%) in the circulation of patients compared with controls. Dual cytokine-secreting (IFN-γ and interleukin-4) γδ T cells indicate the plasticity of these cells. The γδ T cells of patients with PV have shown higher cytotoxic potential and the higher frequency of γδ T cells producing IFN-γ shows T helper type 1 polarization. The increased expression of Scavenger receptors expression (CD36 and CD163) could be contributing to the elevated inflammatory environment and immune imbalance in this disease. Targeting the inflammatory γδ T cells and Scavenger receptors may pave the way for novel therapeutics.

Association and expression of the antigen-processing gene PSMB8, coding for low-molecular-mass protease 7, with vitiligo in North India: case-control study

BACKGROUND

Vitiligo is a multifactorial, autoimmune, depigmenting disorder of the skin where aberrant presentation of autoantigens may have a role.

OBJECTIVES

To study the association of two antigen-processing genes, PSMB8 and PSMB9, with vitiligo.

METHODS

In total 1320 cases of vitiligo (1050 generalized and 270 localized) and 752 healthy controls were studied for the PSMB9 exon 3 G/A single-nucleotide polymorphism (SNP), PSMB8 exon 2 C/A SNP and PSMB8 intron 6 G/T SNP at site 37 360 using polymerase chain reaction (PCR)-restriction fragment length polymorphism. Real-time PCR was used for transcriptional expression of PSMB8 and cytokines. Expression of ubiquitinated proteins and phosphorylated-p38 (P-p38) was studied by Western blotting.

RESULTS

Significant increases in PSMB8 exon 2 allele A (P < 2.07 × 10^-6 , odds ratio 1·93) and genotypes AA (P < 1.03 × 10^-6 , odds ratio 2·51) and AC (P < 1.29 × 10^-6 , odds ratio 1·63) were observed in patients with vitiligo. Interferon-γ stimulation induced lower expression of PSMB8 in peripheral blood mononuclear cells of cases compared with controls, suggesting impaired antigen processing, which was confirmed by accumulation of ubiquitinated proteins in both lesional and nonlesional skin of patients with vitiligo. Expression of proinflammatory cytokines - interleukin (IL)-6, IL-1β and IL-8 - was higher in the lesional skin. P-p38 expression was variable but correlated with the amount of ubiquitinated proteins in the lesional and nonlesional skin, suggesting that the inflammatory cytokine responses in lesional skin could be a result of both P-p38-dependent and -independent pathways.

CONCLUSIONS

The PSMB8 exon 2 SNP is significantly associated with vitiligo. Accumulation of ubiquitinated proteins in skin of cases of vitiligo suggests their aberrant processing, which may promote the development of the disease.

Study of efficacy and safety of noncultured, extracted follicular outer root sheath cell suspension transplantation in the management of stable vitiligo

BACKGROUND

Noncultured, extracted follicular outer root sheath suspension (NC-EHF-ORS-CS) is a recently introduced technique for the treatment of stable vitiligo.

OBJECTIVE

To study the clinical efficacy of this technique and to determine the viability and cell composition of the suspension.

METHODS

Twenty-five patients with stable vitiligo were included in this prospective study. Fifty follicles were extracted from occipital scalp and were incubated with trypsin-ethylenediaminetetraacetic acid to separate outer root sheath cells. The cell suspension was filtered and centrifuged to obtain a cell pellet, which was resuspended and applied to the dermabraded recipient area. Cell viability of the suspension was assessed using trypan blue staining, and markers of keratinocyte stem cells (CD200) and melanocytes (S100) were evaluated using flow cytometry and immunocytochemistry, respectively.

RESULTS

At 6 months, the mean (±SD) repigmentation was 52 ± 25.1%, and >75% repigmentation was seen in 8/25 (32%) patients. Mean percentage cell viability of the suspension was 80 ± 17.2% with a mean concentration of CD200 + and S100 + cells being 7.91 ± 8.68% and 9.93 ± 1.22% (n = 3), respectively. Recipient site infection was seen in 4 of 25 (16%) patients and a color mismatch in 11 of 25 (44%) patients.

CONCLUSION

NC-EHF-ORS-CS is a useful minimally invasive therapy for vitiligo.

Atypical morphology of anogenital warts is not a marker of atypical histology or of infection to the high-risk human papillomavirus genotypes

BACKGROUND

The clinical morphology of anogenital warts may vary from flat, filiform, papular, or verrucous to giant condyloma acuminatum. Clinically atypical-looking genital warts may alarm the clinician because of their suspected malignant potential, which may cause anxiety, often leading to aggressive interventions.

OBJECTIVE

To study if clinically atypical-looking anogenital warts are more likely to be premalignant or malignant as compared to typical warts.

METHOD

Data of 41 (37 males, 4 females) patients with anogenital warts was retrospectively analyzed. After a detailed literature review and in-house discussions, criteria for anogenital warts with typical and atypical clinical morphology were defined. Clinical photographs were independently reviewed by three dermatologists, and human papillomavirus (HPV) genotyping results, histological evaluation, and immunohistochemical analysis for p53 expression were evaluated.

RESULTS

Fifteen (36.6%) anogenital warts were classified as atypical by at least two of three blinded dermatologists. The histological examination showed mitotic figures in 31/41 (75.6%) specimens, dysplasia in 14/41 (44.1%) specimens, and p53 positivity in 34/41 (82.9%) specimens. There was no significant difference in the high-risk HPV genotyping (P = 0.67), frequency of dysplastic changes on histology (P = 0.19), and immunohistochemistry with p53 (P = 0.08) between clinically typical and atypical-appearing anogenital warts. Similarly, no significant difference was found in the frequency of dysplastic changes (P = 0.67) or p53 expressions (P =0.41) based on the HPV genotypes.

CONCLUSIONS

The atypical clinical morphology of anogenital warts may not be a marker of increased malignant potential. High-risk HPV genotypes do not have a statistically significant association with dysplasia or positive immunohistochemistry with p53.

Nanoscopic dynamics of bicontinous microemulsions: effect of membrane associated protein

Bicontinous microemulsions (BμE) generally consist of nanodomains formed by surfactant in a mixture of water and oil at nearly equal proportions and are potential candidates for the solubilization and purification of membrane proteins. Here we present the first time report of nanoscopic dynamics of surfactant monolayers within BμEs formed by the anionic surfactant sodium dodecyl sulfate (SDS) measured on the nanosecond to picosecond time scale using quasielastic neutron scattering (QENS). BμEs investigated herein consisted of middle phases isolated from Winsor-III microemulsion systems that were formed by mixing aqueous and oil solutions under optimal conditions. QENS data indicates that surfactants undergo two distinct motions, namely (i) lateral motion along the surface of the oil nanodomains and (ii) localized internal motion. Lateral motion can be described using a continuous diffusion model, from which the lateral diffusion coefficient is obtained. Internal motion of surfactant is described using a model which assumes that a fraction of the surfactants' hydrogens undergoes localized translational diffusion that could be considered confined within a spherical volume. The effect of cytochrome c, an archetypal membrane-associated protein known to strongly partition near the surfactant head groups in BμEs (a trend supported by small-angle X-ray scattering [SAXS] analysis), on the dynamics of BμE has also been investigated. QENS results demonstrated that cytochrome c significantly hindered both the lateral and the internal motions of surfactant. The lateral motion was more strongly affected: a reduction of the lateral diffusion coefficient by 33% was measured. This change is mainly attributable to the strong association of cytochrome c with oppositely charged SDS. In contrast, analysis of SAXS data suggested that thermal fluctuations (for a longer length and slower time scale compared to QENS) were increased upon incorporation of cytochrome c. This study demonstrates the utility of QENS for evaluating dynamics of BμEs in nanoscopic region, and that proteins directly affect the microscopic dynamics, which is of relevance for evaluating release kinetics of encapsulated drugs from BμE delivery systems and the use of BμEs as biomembrane mimetic systems for investigating membrane protein-biomembrane interactions.

Effects of Hydrotropic Salt on the Nanoscopic Dynamics of DTAB Micelles

Effects of a hydrotropic salt, sodium salicylate (NaSal), on the dynamic behavior of cationic dodecyltrimethylammonium bromide (DTAB) micelles as studied using dynamic light scattering (DLS) and quasielastic neutron scattering (QENS) techniques are reported here. DLS study showed that the addition of NaSal leads to a decrease in the apparent diffusion coefficient of the whole micelle indicating micellar growth. QENS data analysis suggested that observed dynamics involves two distinct motions, lateral motion of the surfactant over the curved micellar surface and localized segmental motion of the surfactant. It is found that the addition of NaSal slows down the lateral motion of DTAB while the localized segmental motion of the DTAB chain is not affected much. An atomistic molecular dynamics (MD) simulation was performed to gain further insight into the underlying phenomena. MD simulation results are found to be consistent with the experimental observations. MD simulation revealed that location of the salicylate ions on the micellar surface and their strong electrostatic association with their oppositely charged surfactant headgroup are the major factors in slowing down the lateral motion of the DTAB molecule. In the present work, a quantitative description of the effects of NaSal on the nanoscopic dynamics of DTAB micelles and its correlation with the microstructure of the micelle is provided.