Table 1.
Common and/or unique trends observed between gut microbiome of Indian and global populations in noncommunicable and communicable diseases
| Phenotype | Country | Sample size | Age group | Sequenced region | Sequencing platform | High | Low | References |
|---|---|---|---|---|---|---|---|---|
| Malnutrition | Indonesia | Healthy = 53, Stunted = 78 | 3–5 years | V3–V4 | Illumina Miseq | p–Bacillota | p–Bacteroidota, g–Prevotella 9 | Surono et al. (2021) |
| Mexico | Healthy = 12, Undernourished = 12, Obese = 12 | 9–11 years | V3–V4 | Illumina Miseq | p–Pseudomonadota | alpha diversity, p–Bacteroidota | Méndez–Salazar et al. (2018) | |
| Bangladesh | Healthy = 7, Malnourished = 7 | 2–3 years | V5–V6 | 454 parallel sequencing | p–Pseudomonadota, g–Klebsiella, Escherichia, Neisseria | p–Bacteroidota | Monira et al. (2011) | |
| Bangladesh | Cases and controls = 68 | 6–31 months | V1–V3 | Illumina Miseq | p–Pseudomonadota, g–Escherichia/Shigella | g–Prevotella | Perin et al. (2020) | |
| India | Stunted, wasted, and underweight = 41 | 18–12 months | V3–V4 | llumina HiSeq2500 | g–Prevotella 9, Bifidobacterium, Escherichia–Shigella | Shivakumar et al. (2021) | ||
| India | Control = 10, Stunted = 10 | Birth to 2 years | V4 | Illumina MiSeq | g–Desulfovibrio, o–Campylobacterales | s–Bifidobacterium longum, Lactobacillus mucosae | Dinh et al. (2016) | |
| India | Undernourished = 53 | 10–18 months | V3–V4 | Illumina MiSeq | p–Pseudomonadota, o–Aeromonadales, g–Enterococcus, g– Anaerococcus, g–Vibrio | Huey et al. (2020) | ||
| Obesity | Finland | Normal–weight women = 36, Overweight women = 18 | ~30 years | fluorescent in situ hybridisation coupled with flow cytometry (FCM–FISH) and by quantitative real–time polymerase chain reaction (qPCR) | g–Bacteroides, g–Staphylococcus | g–Bifidobacterium | Collado et al. (2008) | |
| European countries (Cyprus, Estonia, Germany, Hungary, and Sweden) | 70 subjects (2 time points), Time point 0: Normal = 70, Time point 1: Normal = 34, Obese = 36 | 2–9 years | V3–V4 | Illumina MiSeq | p–Pseudomonadota, f–Bacteroidaceae | diversity, f–Clostridiaceae, f–Ruminococcaceae, f–Prevotellaceae | Rampelli et al. (2018) | |
| Germany | Normal weight = 30, Overweight = 35, Obese = 33 | 14–74 years | qPCR to detect a group of commensals | p–Bacteroidota, g–Bacteroides | g–Bifidobacterium, s–Ruminococcus flavefaciens | Schwiertz et al. (2010) | ||
| India | 20 (5 lean, 5 normal, 5 obese, 5 surgically treated obese) | 21–62 years | 900 bases amplicon | BigDye™ Terminator Cycle Sequencing Ready Reaction Kit v3.1 in an automated 3730 DNA analyser | g–Bacteroides | Ppatil et al. (2012) | ||
| India | Normal = 13, Obese = 15 | 11–14 years | 16S rRNA | qPCR | s–F. prausnitzii | Balamurugan et al. (2010) | ||
| India | Normal = 10, Obese = 10 | NA | V3 | Denaturing Gradient Gel Electrophoresis analysed in Gel Compar II version 6.6 software (Sequencing platform was not mentioned) | s–Collinsella aerofaciens, g–Dialister, g– Eubacterium, g–Mitsuokella, g–Victivallis | Diversity | Bahadur et al. (2021) | |
| Type 2 diabetes | West Africa | Controls = 193, Cases = 98 | 57 years (mean) | V4 | Illumina MiSeq | s–Desulfovibrio piger, g–Prevotella, g–Peptostreptococcus, g–Eubacterium | f–Clostridiaceae, f–Peptostreptococcaceaea | Doumatey et al. (2020) |
| China | Normal glucose tolerance = 97, Prediabetese patients = 80, Newly diagnosed treatment naive T2D patient = 77 | 62.53 years (mean) | WGS | Combinatorial probe–anchor synthesis (cPAS)–based BGISEQ–500 sequencing | s–Dialister invisus, s–Roseburia hominis | Zhong et al. (2019) | ||
| Denmark and India | Indian non–diabetics = 137, Danish non–diabetics = 138, Indian T2D patients = 157, Danish diabetic patients = 141 | 35–74 years | V1–V5 | 454 GS FLX+ pyrosequencer platform | f–Lachnospiraceae | g–Subdoligranulum and Butyricicoccus | Alvarez–Silva et al. (2021) | |
| Meta–analysis (Denmark, Sweden, China) | Danish non–diabetic = 277, Swedish non–diabetic = 92, Chinese non–diabetic = 185, Danish T2D = 75, T1D = 31, Swedish T2D = 52, Chinese T2D = 71 | 35–75 years | WGS + 16S rRNA | Illumina shotgun sequencing | metformin untreated: s–Roseburia spp., Subdoligranulum spp | Forslund et al. (2015) | ||
| China | Non–diabetic = 185, Diabetic = 183 | 13–86 years | WGS | Illumin aHiSeq 2000 | s–Bacteroides caccae, Clostridium hathewayi, Clostridium ramosum, Clostridium symbiosum, Eggerthella lenta, and Escherichia coli | s–Clostridiales sp. SS3/4, Eubacterium rectale, Faecalibacterium prausnitzii, Roseburia intestinalis, and Roseburia inulinivorans | Wang et al. (2012) | |
| India | Healthy = 19, New diabetic patients = 14, Known diabetic patients = 16 | 49.37 years (mean) | V3 | Ion Torrent | g–Lactobacillus, p–Bacillota | s–P. copri, s–Faecalibacterium prausnitzii, f–Ruminococcaceae, Lachnospiraceae | Bhute et al. (2017) | |
| India | Healthy = 9, T1D = 8, T2D = 10, T3cD = 17 | 18–60 years (Healthy), patient’s age was not mentioned | V3–V4 | Illumina MiSeq | Diversity, g–Fecalibacterium, Eubacterium, and Ruminococcus | Talukdar et al. (2021) | ||
| India | Healthy = 30, T2D and no diabetic retinopathy (DR) = 25, T2D + DR = 28 | 54.86 years (mean) | V3–V4 | Illumina HiSeq | g–Escherichia, Enterobacter, Methanobrevibacter, and Treponema | g–Roseburia, Lachnospira, Sutterella, Coprococcus, Phascolarctobacterium, Haemophilus, Blautia, Comamonas, Anaerostipes, and Turicibacter | Das et al. (2021) | |
| Colorectal cancer | China | Healthy = 56, Patients = 46 | 40–77 years | V3 | 454 pyrosequencing | s–Bacteroides fragilis, g–Escherichia/Shigella, Klebsiella, Streptococcus, Enterococcus, Peptostreptococcus, Eggerthella, Fusobacterium | s–Bacteroides uniformis, Roseburia spp. and Eubacterium spp. | T. Wang et al. (2012) |
| China | Healthy = 130, Patients = 130 | 59.1 years (mean) | V3–V4 | Illumina MiSeq | s–Peptostreptococcus stomatis, Fusobacterium nucleatum, etc. | s–Roseburia faecis, Ruminococcus lactaris, Eubacterium desmolans, Streptococcus salivarius, etc. | Zhang et al. (2018) | |
| China | Patients = 23 (tumour tissue and surrounding healthy tissue) (early and late stages) | 49–70 years | V4 | Illumina MiSeq | late stage: g–Akkermansia, Fusobacterium, Peptostreptococcus, Streptococcus, and Ruminococcus | Pan et al. (2020) | ||
| USA | Healthy = 52, Patients = 52 | 61 years (mean) | WGS | Illumina HiSeq 2000/2500 | g–Fusobacterium, Porphyromonas | Vogtmann et al. (2016) | ||
| India | Healthy = 30, Patients = 30 | Not mentioned | WGS | Illumina NextSeq 500 | Diversity, g–Bacteroides, s–Flavonifractor plautii | Gupta et al. (2019a) | ||
| India | Patients = 5 (healthy tissue = 5, tumour tissue = 5) | 40–83 years | V3–V4 | Ion 520 OT2 | s–Bacteroides massiliensis, Alistipes sp. Alistipes onderdonkii, Bifidobacterium pseudocatenulatum, Corynebacterium appendicis, and Acidiphilium sp. | s–Bacillus sp., Veillonella atypica, etc. | Hasan et al. (2022) | |
| Inflammatory bowel diseases | USA | Non–IBD = 27, UC = 38, CD = 67 | 27.5 years (mean) | WGS | Illumina HiSeq2500 | s–E. coli, Ruminococcus torques and Ruminococcus gnavus | Faecalibacterium prausnitzii, and Roseburia hominis | Lloyd–Price et al. (2019) |
| USA and Netherlands | Non–IBD = 34, UC = 53, CD = 68 | >18 years | WGS | Illumina HiSeq2500 | g–Unclassified Roseburia | s–Roseburia hominis, Dorea formicigenerans and Ruminococcus obeum | Franzosa et al. (2019) | |
| China | Healthy = 30, IBD patients = 18 | 37 years (mean) | V3–V4 | Illumina MiSeq | p–Pseudomonadota, Fusobacteriota, g–Escherichia_Shigella | s–Eubacterium coprostanoligenes, Eubacterium hallii group | T. Wang et al. (2022) | |
| India | Health control = 17, CD = 20, UC = 22 | 33.6 years (mean) | 16S rRNA gene sequences specific to C. leptum group | Not mentioned | s–Faecalibacterium prausnitzii, C. leptum group | Kabeerdoss et al. (2013) | ||
| India | Control individuals (haemorrhoid patients only) = 14, UC patients (severe: n = 12, moderate: n = 6, remission: n = 8) = 26 | 36 years (mean) | Clostridium cluster population targeted by 16S rRNA gene | Not mentioned | s–Faecalibacterium prausnitzii, R. intestinalis, a member of the C. coccoides group, reduced SCFA | Kumari et al. (2013) | ||
| India | Control = 65, UC = 72, CD = 12 | 38 years (mean) | Real–time analysis using 16S rRNA | g–Eubacterium, Peptostreptococcus | g–Lactobacillus, Ruminococcus, and Bifidobacterium, C. leptum group | Verma et al. (2010) | ||
| Gut inflammation and damage to the brain function | ||||||||
| ASD | Italy | Healthy control = 14, ASD patients = 11 | 35 months (mean) | V3–V4 | Illumina Miseq | p–Bacteroidota, Proteobacteria, s–F. prausnitzii, B. uniformis and B. vulgatus and P. distasonis, f–Enterobacteriaceae and Pasteurellaceae | p–Actinomycetota, s–Bifidobacterium longum and Eggerthella lenta | Coretti et al. (2018) |
| China | Healthy control = 48, ASD patients = 48 | 2–7 years | V3–V4 | Illumina Miseq | s–P. copri, Bacteroides coprocola, B. vulgatus, Eubacterium eligens, Roseburia faecis | s–A. muciniphila, Dialister invisus, Escherichia coli, B. fragilis, Haemophilus parainfluenzae, Flavonifractor plautii | Zou et al. (2020) | |
| China | Healthy Control = 18, ASD patients = 71 | 3–6 years | V1–V2 | Illumina Miseq | Eisenbergiella, Klebsiella, Faecalibacterium, and Blautia | Escherichia, Shigella, Veillonella, Akkermansia, Provindencia, Dialister, Bifidobacterium, Streptococcus | Ye et al. (2021) | |
| India | Family–matched healthy = 24, ASD children = 30 | 3–16 years | V3 | Illumin NextSeq500 | p–Bacillota, g–Lactobacillus (f–Lactobacillaceae), Bifidobacterium (f–Bifidobacteraceae), Megasphaera, and Mitsuokella (f–Veillonellaceae) | f–Prevotellaceae, g–Faecalibacterium and Roseburia | Pulikkan et al. (2018) | |
| PD | China | Healthy control = 114, ASD patients = 106 (early stage = 48, advanced stage = 58) | 67.6 years (mean) | V3–V4 | Illumina Miseq | In advanced PD patients: p–Desulfobacterota, f–Lachnospiraceae, Desulfovibrionaceae, g–Parasutterella | In advanced PD patients: g–Subdoligranulum | Zhang et al. (2022) |
| Luxembourg | Healthy control = 162, PD patients = 147 | 66.3 years (mean) | V3–V4 | Illumina Miseq | Akkermansia muciniphila, Biolophila, Christensenella, Lactobacillus, Christensenella, and Lactobacillus | Turicibacter | Baldini et al. (2020) | |
| Germany | Healthy control = 25, PD patients = 34 | V4–V5 | Ion Torrent PGM | Clostridiales family XI, Peptoniphilus | Faecalibacterium and Fusicatenibacter | Weis et al. (2019) | ||
| Alzheimer’s disease | Italy | No brain amyloidosis and no cognitive impairment = 10, cognitively impaired patients with amyloidosis = 40, cognitively impaired patients with NO brain amyloidosis = 33 | 69.6 years (mean) | Selected bacterial DNA quantification using the Microbial DNA qPCR Assay Kit | Escherichia/Shigella | E. rectale | Cattaneo et al. (2017) | |
| USA | Non–demented individuals = 25, Dementia due to AD = 25 | 70.3 years (mean) | V4 | Illumina Miseq | p–Bacteroidota, g–Bacteroides, Blautia, Phascolarctobacterium, Alistipes, Bilophila | alpha diversity, –p Bacillota, Actinomycetota, g–Bifidobacterium, Adlercreutzia, SMB53, Dialister, Clostridium, Turicibacter, and cc115 | Vogt et al. (2017) | |
| Diarrhoea | Bangladesh | Time–series metagenomic study with 7 patients, 50 healthy children, 12 healthy adult males | NA | V4 | Illumina Miseq | s–R. obeum restricts V. cholerae colonisation | Hsiao et al. (2014) | |
| Bangladesh | Patients’ household members who shared a cooking pot were defined as contacts (n = 27), cholera cohort 1 = 13, cholera cohort 2 = 10 | ≥6 months | 16S rRNA gene (V4) and WGS sequencing | Illumina HiSeq | Microbial succession follows secretory diarrheal illness in humans | David et al. (2015) | ||
| India | Healthy control = 0, Patients = 20 | 8 months to 56 years | V3–V4, WGS of 5 samples | Illumina MiSeq | p–Bacillota, Presence of s–V. cholerae, Helicobacter pylori, Eschericia sp. | p–Bacteroidota, significantly negative correlation between f–Enterobacteriaceae and Lachnospiraceae and Enterobacteriaceae and Ruminococcaceae | De et al. (2020) | |
| India | 46 children during an episode of acute diarrhoea, immediately after recovery from diarrhoea, and 3 months after recovery | 3 months to 5 years | 16srRNA gene (rDNA) sequences of specific bacterial group | qPCR | Bacteroides–Prevotella–Porphyromonas group, s–Eubacterium rectale, Faecalibacterium prauznitzii significantly less abundant during or immediately after diarrhoea than during normal health | Balamurugan et al. (2008) | ||
| India | Healthy infant = 1, diarrhoea infected infants = 3 | 3–18 months | V3 | Illumina MiSeq | p–Pseudomonadota, g–Klebsiella, Haemophilus, Rothia, Granulicatella, Chelonobacter and Vibrio species were identified as key pathogenic lineages in diarrheal samples | p–Bacillota, Bacteroidota | Thakur et al. (2018) | |
| India | 105 Central Indian participants comprising 35 rural (12 with diarrhoea) and 70 urban (46 with diarrhoea) | 38.8 years (mean) | WGS | Illumina | Rural habitants have g–Prevotella–dominant microbiome compared with the urban population. Urbanisation is associated with functional enrichment of genes involved in xenobiotic and lipid metabolism, have a much higher burden of AMR overall. | Monaghan et al. (2020) | ||
| Amoebiasis | Bangladesh | Uninfected = 85, Infected = 307 | Birth to 2 years | qPCR | Prevotella copri | Gilchrist et al. (2016) | ||
| Japan | Asymptomatic infection = 13, Symptomatic infection = 51 | 43 years (mean) | V3–V4 | Illumina Miseq | f–Streptococcaceae | f–Ruminococcaceae, Coriobacteriaceae, and Clostridiaceae, s–Collinsella aerofaciens | Yanagawa et al. (2021) | |
| India | Healthy = 22, chronic/acute diarrheal patients = 550 | 21–40 years | 16S rRNA | qPCR | g–Bifidobacterium | g–Bacteroides, Eubacterium, C. leptum subgroup, C. coccoides, Lactobacillus | Verma et al. (2012) | |
| India | Healthy = 29, E. histolytica positive patients = 14 | 15–69 years | V1–V5 | Illumina HiSeq 2500 | g–Escherichia, Klebsiella, and Ruminococcus | g–Prevotella, Sutterella, and Collinsella | Iyer et al. (2023) | |