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Article ; Online: Comprehensive bacterial-metabolite profiles of Hawaijar, Bekang, and Akhone: a comparative study on traditional fermented soybeans of north-east India.

Das, Sushmita / Bhattacharjee, Maloyjo Joyraj / Mukherjee, Ashis K / Khan, Mojibur Rohman

World journal of microbiology & biotechnology

2023 Volume 39, Issue 11, Page(s) 315

Abstract: Preparation of traditionally fermented soybeans varies across ethnicities with distinct tastes, flavour, and nutritional values. The fermented soybean varieties Hawaijar, Bekang, and Akhone of north-east India are associated with diverse ethnic groups ... ...

Abstract	Preparation of traditionally fermented soybeans varies across ethnicities with distinct tastes, flavour, and nutritional values. The fermented soybean varieties Hawaijar, Bekang, and Akhone of north-east India are associated with diverse ethnic groups from Manipur, Mizoram, and Nagaland, respectively. These varieties differ in substrate and traditional practice that exerts differential bacterial-metabolite profile, which needs an in-depth analysis i. Culture-dependent and independent techniques investigated the bacterial diversity of the fermented soybean varieties. Gas chromatography and mass spectroscopy (GC-MS) studied these varieties' metabolite profiles. The common dominant bacterial genera detected in Hawaijar, Bekang, and Akhone were Bacillus, Ignatzschinaria, and Corynebacterium, with the presence of Brevibacillus and Staphylococcus exclusively in Hawaijar and Oceanobacillus in Bekang and Akhone. The metabolite analysis identified a higher abundance of essential amino acids, amino and nucleotide sugars, and vitamins in Hawaijar, short-chain fatty acids in Bekang, polyunsaturated fatty acids in Akhone and Hawaijar, and prebiotics in Akhone. The bacteria-metabolite correlation analysis predicted four distinct bacterial clusters associated with the differential synthesis of the functional metabolites. While B. subtilis is ubiquitous, cluster-1 comprised B. thermoamylovorans/B. amyloliquefaciens, cluster-2 comprised B. tropicus, cluster-3 comprised B. megaterium/B. borstelensis, and cluster-4 comprised B. rugosus. To the best of our knowledge, this is the first comparative study on traditional fermented soybean varieties of north-east India linking bacterial-metabolite profiles which may help in designing starters for desired functionalities in the future.
MeSH term(s)	Humans ; Animals ; Glycine max ; India ; Ethnicity ; Brevibacillus ; Coleoptera ; Fermented Foods
Language	English
Publishing date	2023-09-22
Publishing country	Germany
Document type	Journal Article
ZDB-ID	1499109-3
ISSN	1573-0972 ; 0959-3993
ISSN (online)	1573-0972
ISSN	0959-3993
DOI	10.1007/s11274-023-03773-3
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Article ; Online: Recent advances in understanding of multifaceted changes in the vaginal microenvironment: implications in vaginal health and therapeutics.

Das, Sushmita / Bhattacharjee, Maloyjo Joyraj / Mukherjee, Ashis K / Khan, Mojibur Rohman

Critical reviews in microbiology

2022 Volume 49, Issue 2, Page(s) 256–282

Abstract: The vagina endures multifaceted changes from neonatal to menopausal phases due to hormonal flux, metabolite deposition, and microbial colonization. These features have important implications in women's health. Several pre-factors show dynamic ... ...

Abstract	The vagina endures multifaceted changes from neonatal to menopausal phases due to hormonal flux, metabolite deposition, and microbial colonization. These features have important implications in women's health. Several pre-factors show dynamic characteristics according to the phases that shift the vaginal microbiota from anaerobes to aerobes which is a hallmark of healthy vaginal environment. These factors include oestrogen levels, glycogen deposition, and vaginal microstructure. In the adult phase,
MeSH term(s)	Adult ; Infant, Newborn ; Female ; Humans ; Dysbiosis/microbiology ; Vagina/microbiology ; Lactobacillus/metabolism ; Women's Health ; Bacteria ; Probiotics ; Vaginosis, Bacterial/microbiology
Language	English
Publishing date	2022-03-21
Publishing country	England
Document type	Review ; Journal Article
ZDB-ID	1053620-6
ISSN	1549-7828 ; 1040-841X
ISSN (online)	1549-7828
ISSN	1040-841X
DOI	10.1080/1040841X.2022.2049696
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Article ; Online: Comparative pangenomic analysis of predominant human vaginal lactobacilli strains towards population-specific adaptation: understanding the role in sustaining a balanced and healthy vaginal microenvironment.

Bhattacharya, Anupam / Das, Sushmita / Bhattacharjee, Maloyjo Joyraj / Mukherjee, Ashis K / Khan, Mojibur Rohman

BMC genomics

2023 Volume 24, Issue 1, Page(s) 565

Abstract: The vaginal microenvironment of healthy women has a predominance of Lactobacillus crispatus, L. iners, L. gasseri, and L. jensenii. The genomic repertoire of the strains of each of the species associated with the key attributes thereby regulating a ... ...

Abstract	The vaginal microenvironment of healthy women has a predominance of Lactobacillus crispatus, L. iners, L. gasseri, and L. jensenii. The genomic repertoire of the strains of each of the species associated with the key attributes thereby regulating a healthy vaginal environment needs a substantial understanding.We studied all available human strains of the four lactobacilli across different countries, isolated from vaginal and urinal sources through phylogenetic and pangenomic approaches. The findings showed that L. iners has the highest retention of core genes, and L. crispatus has more gene gain in the evolutionary stratum. Interestingly, L. gasseri and L. jensenii demonstrated major population-specific gene-cluster gain/loss associated with bacteriocin synthesis, iron chelating, adherence, zinc and ATP binding proteins, and hydrolase activity. Gene ontology enrichment analysis revealed that L. crispatus strains showed greater enrichment of functions related to plasma membrane integrity, biosurfactant, hydrogen peroxide synthesis, and iron sequestration as an ancestral derived core function, while bacteriocin and organic acid biosynthesis are strain-specific accessory enriched functions. L. jensenii showed greater enrichment of functions related to adherence, aggregation, and exopolysaccharide synthesis. Notably, the key functionalities are heterogeneously enriched in some specific strains of L. iners and L. gasseri.This study shed light on the genomic features and their variability that provides advantageous attributes to predominant vaginal Lactobacillus species maintaining vaginal homeostasis. These findings evoke the need to consider region-specific candidate strains of Lactobacillus to formulate prophylactic measures against vaginal dysbiosis for women's health.
MeSH term(s)	Humans ; Female ; Lactobacillus/genetics ; Phylogeny ; Bacteriocins/genetics ; Biological Evolution ; Cell Membrane
Chemical Substances	Bacteriocins
Language	English
Publishing date	2023-09-22
Publishing country	England
Document type	Journal Article
ZDB-ID	2041499-7
ISSN	1471-2164 ; 1471-2164
ISSN (online)	1471-2164
ISSN	1471-2164
DOI	10.1186/s12864-023-09665-y
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Article ; Online: Recent advances in understanding of multifaceted changes in the vaginal microenvironment: implications in vaginal health and therapeutics

Das, Sushmita / Bhattacharjee, Maloyjo Joyraj / Mukherjee, Ashis K. / Khan, Mojibur Rohman

Critical Reviews in Microbiology. 2023 Mar. 4, v. 49, no. 2 p.256-282

2023

Abstract: The vagina endures multifaceted changes from neonatal to menopausal phases due to hormonal flux, metabolite deposition, and microbial colonization. These features have important implications in women’s health. Several pre-factors show dynamic ... ...

Abstract	The vagina endures multifaceted changes from neonatal to menopausal phases due to hormonal flux, metabolite deposition, and microbial colonization. These features have important implications in women’s health. Several pre-factors show dynamic characteristics according to the phases that shift the vaginal microbiota from anaerobes to aerobes which is a hallmark of healthy vaginal environment. These factors include oestrogen levels, glycogen deposition, and vaginal microstructure. In the adult phase, Lactobacillus is highly dominant and regulates pH, adherence, aggregation, immune modulation, synthesis of bacteriocins, and biosurfactants (BSs) which are antagonistic to pathogens. Maternal factors are protective by favouring the colonization of lactobacilli in the vagina in the neonatal phase, which diminishes with age. The dominance of lactobacilli and dysbiosis in the adult phase depends on intrinsic and extrinsic factors in women, which vary between ethnicities. Recent developments in probiotics used against vaginal microbiome dysbiosis have shown great promise in restoring the normal microbiota including preventing the loss of beneficial bacteria. However, further in-depth studies are warranted to ensure long-term protection by probiotics. This review highlights various aspects of the vaginal microenvironment in different phases of growth and diverse ethnicities. Furthermore, it discusses future trends for formulating more effective population-specific probiotics and implications of paraprobiotics and postbiotics as effective therapeutics.
Keywords	Lactobacillus ; adults ; anaerobes ; bacteriocins ; biosurfactants ; dysbiosis ; estrogens ; glycogen ; immunomodulation ; menopause ; metabolites ; microbial colonization ; microbiome ; microstructure ; pH ; probiotics ; therapeutics ; vagina ; paraprobiotics ; postbiotics
Language	English
Dates of publication	2023-0304
Size	p. 256-282.
Publishing place	Taylor & Francis
Document type	Article ; Online
ZDB-ID	1053620-6
ISSN	1549-7828 ; 1040-841X
ISSN (online)	1549-7828
ISSN	1040-841X
DOI	10.1080/1040841X.2022.2049696
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Article ; Online: Genome analysis of SARS-CoV-2 isolates from a population reveals the rapid selective sweep of a haplotype carrying many pre-existing and new mutations.

Bhattacharjee, Maloyjo Joyraj / Bhattacharya, Anupam / Kashyap, Bhaswati / Taw, Manash Jyoti / Li, Wen-Hsiung / Mukherjee, Ashis K / Khan, Mojibur Rohman

Virology journal

2023 Volume 20, Issue 1, Page(s) 201

Abstract: To understand the mechanism underlying the evolution of SARS-CoV-2 in a population, we sequenced 92 viral genomes from Assam, India. Analysis of these and database sequences revealed a complete selective sweep of a haplotype in Assam carrying 13 pre- ... ...

Abstract	To understand the mechanism underlying the evolution of SARS-CoV-2 in a population, we sequenced 92 viral genomes from Assam, India. Analysis of these and database sequences revealed a complete selective sweep of a haplotype in Assam carrying 13 pre-existing variants, including a high leap in frequency of a variant on ORF8, which is involved in immune evasion. A comparative study between sequences of same lineage and similar time frames in and outside Assam showed that 10 of the 13 pre-existing variants had a frequency ranging from 96 to 99%, and the remaining 3 had a low frequency outside Assam. Using a phylogenetic approach to infer sequential occurrences of variants we found that the variant Phe120del on ORF8, which had a low frequency (1.75%) outside Assam, is at the base of the phylogenetic tree of variants and became totally fixed (100%) in Assam population. Based on this observation, we inferred that the variant on ORF8 had a selective advantage, so it carried the haplotype to reach the100% frequency. The haplotype also carried 32 pre-existing variants at a frequency from 1.00 to 80.00% outside Assam. Those of these variants that are more closely linked to the S-protein locus, which often carries advantageous mutations and is tightly linked to the ORF8 locus, retained higher frequencies, while the less tightly linked variants showed lower frequencies, likely due to recombination among co- circulating variants in Assam. The ratios of non-synonymous substitutions to synonymous substitutions suggested that some genes such as those coding for the S-protein and non-structural proteins underwent positive selection while others were subject to purifying selection during their evolution in Assam. Furthermore, we observed negative correlation of the Ct value of qRT-PCR of the patients with abundant ORF6 transcripts, suggesting that ORF6 can be used as a marker for estimating viral titer. In conclusion, our in-depth analysis of SARS-CoV-2 genomes in a regional population reveals the mechanism and dynamics of viral evolution.
MeSH term(s)	Humans ; Haplotypes ; SARS-CoV-2/genetics ; Phylogeny ; COVID-19/epidemiology ; Mutation
Language	English
Publishing date	2023-09-01
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2160640-7
ISSN	1743-422X ; 1743-422X
ISSN (online)	1743-422X
ISSN	1743-422X
DOI	10.1186/s12985-023-02139-3
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Article ; Online: Many human RNA viruses show extraordinarily stringent selective constraints on protein evolution.

Lin, Jinn-Jy / Bhattacharjee, Maloyjo Joyraj / Yu, Chun-Ping / Tseng, Yan Yuan / Li, Wen-Hsiung

Proceedings of the National Academy of Sciences of the United States of America

2019 Volume 116, Issue 38, Page(s) 19009–19018

Abstract: How negative selection, positive selection, and population size contribute to the large variation in nucleotide substitution rates among RNA viruses remains unclear. Here, we studied the ratios of nonsynonymous-to-synonymous substitution rates ( ...

Abstract	How negative selection, positive selection, and population size contribute to the large variation in nucleotide substitution rates among RNA viruses remains unclear. Here, we studied the ratios of nonsynonymous-to-synonymous substitution rates (
MeSH term(s)	Animals ; Evolution, Molecular ; Genome, Viral ; Humans ; Mammals ; Mutation Rate ; RNA Virus Infections/virology ; RNA Viruses/genetics ; Selection, Genetic ; Viral Proteins/genetics
Chemical Substances	Viral Proteins
Keywords	covid19
Language	English
Publishing date	2019-09-04
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.1907626116
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Article ; Online: Identifying Primate ACE2 Variants That Confer Resistance to SARS-CoV-2.

Bhattacharjee, Maloyjo Joyraj / Lin, Jinn-Jy / Chang, Chih-Yao / Chiou, Yu-Ting / Li, Tian-Neng / Tai, Chia-Wei / Shiu, Tz-Fan / Chen, Chi-An / Chou, Chia-Yi / Chakraborty, Paromita / Tseng, Yan Yuan / Wang, Lily Hui-Ching / Li, Wen-Hsiung

Molecular biology and evolution

2021 Volume 38, Issue 7, Page(s) 2715–2731

Abstract: SARS-CoV-2 infects humans through the binding of viral S-protein (spike protein) to human angiotensin I converting enzyme 2 (ACE2). The structure of the ACE2-S-protein complex has been deciphered and we focused on the 27 ACE2 residues that bind to S- ... ...

Abstract	SARS-CoV-2 infects humans through the binding of viral S-protein (spike protein) to human angiotensin I converting enzyme 2 (ACE2). The structure of the ACE2-S-protein complex has been deciphered and we focused on the 27 ACE2 residues that bind to S-protein. From human sequence databases, we identified nine ACE2 variants at ACE2-S-protein binding sites. We used both experimental assays and protein structure analysis to evaluate the effect of each variant on the binding affinity of ACE2 to S-protein. We found one variant causing complete binding disruption, two and three variants, respectively, strongly and mildly reducing the binding affinity, and two variants strongly enhancing the binding affinity. We then collected the ACE2 gene sequences from 57 nonhuman primates. Among the 6 apes and 20 Old World monkeys (OWMs) studied, we found no new variants. In contrast, all 11 New World monkeys (NWMs) studied share four variants each causing a strong reduction in binding affinity, the Philippine tarsier also possesses three such variants, and 18 of the 19 prosimian species studied share one variant causing a strong reduction in binding affinity. Moreover, one OWM and three prosimian variants increased binding affinity by >50%. Based on these findings, we proposed that the common ancestor of primates was strongly resistant to and that of NWMs was completely resistant to SARS-CoV-2 and so is the Philippine tarsier, whereas apes and OWMs, like most humans, are susceptible. This study increases our understanding of the differences in susceptibility to SARS-CoV-2 infection among primates.
MeSH term(s)	Animals ; COVID-19/genetics ; COVID-19/immunology ; Chlorocebus aethiops ; Disease Resistance/genetics ; Humans ; Macaca mulatta ; Peptidyl-Dipeptidase A/genetics ; Peptidyl-Dipeptidase A/immunology ; SARS-CoV-2/genetics ; SARS-CoV-2/immunology
Chemical Substances	ACE protein, human (EC 3.4.15.1) ; Peptidyl-Dipeptidase A (EC 3.4.15.1)
Language	English
Publishing date	2021-03-05
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	998579-7
ISSN	1537-1719 ; 0737-4038
ISSN (online)	1537-1719
ISSN	0737-4038
DOI	10.1093/molbev/msab060
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Article ; Online: Contrasting diversity of vaginal lactobacilli among the females of Northeast India.

Das Purkayastha, Sumi / Bhattacharya, Mrinal Kanti / Prasad, Himanshu Kishore / Upadhyaya, Hrishikesh / Lala, Suparna Das / Pal, Kunal / Das, Meenakshi / Sharma, Gauri Dutt / Bhattacharjee, Maloyjo Joyraj

BMC microbiology

2019 Volume 19, Issue 1, Page(s) 198

Abstract: Background: Lactobacilli are gatekeepers of vaginal ecosystem impeding growth of pathogenic microbes and their diversity varies across populations worldwide. The present study investigated diversity of human vaginal microbiota among females of Northeast ...

Abstract	Background: Lactobacilli are gatekeepers of vaginal ecosystem impeding growth of pathogenic microbes and their diversity varies across populations worldwide. The present study investigated diversity of human vaginal microbiota among females of Northeast India, who are distinct in dietary habits, lifestyle, and genomic composition from rest of India. Results: Altogether, 154 bacterial isolates were obtained from vaginal swab samples of 40 pregnant and 29 non-pregnant females. The samples were sequenced for 16 s rRNA gene and analysed for identification using a dual approach of homology search and maximum likelihood based clustering. Molecular identification based on 16S rRNA gene sequence confirmed the isolates belonging to 31 species. Lactobacilli constituted 37.7% of the bacterial isolates with 10 species and other Lactic Acid Bacteria (39.61%) represented another 10 species, some of which are opportunistic pathogens. The remaining of the communities are mostly dominated by species of Staphylococcus (14.28%) and rarely by Propionibacterium avidum (3.90%), Bacillus subtilis, Escherchia coli, Janthinobacterium lividum, and Kocuria kristinae (each 0.64%). Interestingly Lactobacillus mucosae and Enterococcus faecalis, which are globally uncommon vaginal microbes is found dominant among women of Northeast India. This tentatively reflects adaptability of particular Lactobacillus species, in distinct population, to better compete for receptors and nutrients in vaginal epithelium than other species. Further, intrageneric 16S rRNA gene exchange was observed among Enterococcus, Staphylococcus, and two species of Lactobacillus, and deep intraspecies divergence among L. mucosae, which pinpointed possibility of emergence of new strains with evolved functionality. Lactobacilli percentage decreased from young pregnant to aged non-pregnant women with maximum colonization in trimester II. Conclusion: The study highlighted importance of assessment of vaginal microbiota, Lactobacillus in particular, across different population to gain more insight on female health.
MeSH term(s)	Adolescent ; Adult ; Bacteria/classification ; Bacteria/genetics ; Bacteria/isolation & purification ; Biodiversity ; Female ; Humans ; India ; Lactobacillus/classification ; Lactobacillus/genetics ; Lactobacillus/isolation & purification ; Microbiota ; Phylogeny ; Pregnancy ; Vagina/microbiology ; Young Adult
Language	English
Publishing date	2019-08-27
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1471-2180
ISSN (online)	1471-2180
DOI	10.1186/s12866-019-1568-6
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Article ; Online: Regulatory Divergence among Beta-Keratin Genes during Bird Evolution.

Bhattacharjee, Maloyjo Joyraj / Yu, Chun-Ping / Lin, Jinn-Jy / Ng, Chen Siang / Wang, Tzi-Yuan / Lin, Hsin-Hung / Li, Wen-Hsiung

Molecular biology and evolution

2016 Volume 33, Issue 11, Page(s) 2769–2780

Abstract: Feathers, which are mainly composed of α- and β-keratins, are highly diversified, largely owing to duplication and diversification of β-keratin genes during bird evolution. However, little is known about the regulatory changes that contributed to the ... ...

Abstract	Feathers, which are mainly composed of α- and β-keratins, are highly diversified, largely owing to duplication and diversification of β-keratin genes during bird evolution. However, little is known about the regulatory changes that contributed to the expressional diversification of β-keratin genes. To address this issue, we studied transcriptomes from five different parts of chicken contour and flight feathers. From these transcriptomes we inferred β-keratin enriched co-expression modules of genes and predicted transcription factors (TFs) of β-keratin genes. In total, we predicted 262 TF-target gene relationships in which 56 TFs regulate 91 β-keratin genes; we validated 14 of them by in vitro tests. A dual criterion of TF enrichment and "TF-target gene" expression correlation identified 26 TFs as the major regulators of β-keratin genes. According to our predictions, the ancestral scale and claw β-keratin genes have common and unique regulators, whereas most feather β-keratin genes show chromosome-wise regulation, distinct from scale and claw β-keratin genes. Thus, after expansion from the β-keratin gene on Chr7 to other chromosomes, which still shares a TF with scale and claw β-keratin genes, most feather β-keratin genes have recruited distinct or chromosome-specific regulators. Moreover, our data showed correlated gene expression profiles, positive or negative, between predicted TFs and their target genes over the five studied feather regions. Therefore, regulatory divergences among feather β-keratin genes have contributed to structural differences among different parts of feathers. Our study sheds light on how feather β-keratin genes have diverged in regulation from scale and claw β-keratin genes and among themselves.
MeSH term(s)	Animals ; Biological Evolution ; Chickens/genetics ; Evolution, Molecular ; Feathers/metabolism ; Feathers/physiology ; Gene Expression Regulation/genetics ; Genetic Variation ; Multigene Family ; Sequence Analysis, DNA/methods ; Transcription Factors/genetics ; Transcription Factors/metabolism ; Transcriptome ; beta-Keratins/genetics ; beta-Keratins/metabolism
Chemical Substances	Transcription Factors ; beta-Keratins
Language	English
Publishing date	2016-11
Publishing country	United States
Document type	Journal Article
ZDB-ID	998579-7
ISSN	1537-1719 ; 0737-4038
ISSN (online)	1537-1719
ISSN	0737-4038
DOI	10.1093/molbev/msw165
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