1Symposium on ‘Our Second genome,’ Annual meeting of Indian Academy of Sciences, Bhopal, 5-Nov-2016

Gut microbiome and health

Sharmila Mande, Ph.DChief Scientist & HeadBio-Sciences R&DTCS ResearchPune

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Outline

Gut microbiome

Challenges in analyzing microbiome data

What constitutes healthy gut microbiome?

Children and adult guts

Gut microbiome and response to antibiotics and drugs

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Gut microbiome

•Digestion of food•Produce vitamins (B and K)•Bio-availibity of drugs•Resistance to antibiotics•…..

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Gut microbiome and diseases/disorders

“All Disease Begins in the Gut” Hippocrates, Father of Medicine

A healthy and balanced gut microbiome is key to ensuring proper digestive functioning

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Analyzing microbiome data

What microbes are there and what are their relative proportions?

What functional genes do they have?

How do they function?

Majority of microbesare unknown!

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Estimating taxa diversity: Challenge

Segregating reads into species-specific bins / OTUs

Known Sequence DB..................................

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Unknown microbes

-Phyla-Class-Order-Family-Genus-Species

What microbes are there and what are their relative proportions?

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Analyzing microbiome data : Challenges

What functional genes do they have?

Contig assembly Functional characterization

Habitat-specific sequences

Key microbial groups,

interactions

How do they function?

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TCS’ end-to-end Metagenomics Analysis PlatformData Pre-processing Contig Assembly

Remove adaptors and primers;Filter out low-quality sequences

Remove host contamination Assemble reads into contigs and scaffolds

Estimate Taxonomic Diversity

Analyse WGS dataset Analyse 16S dataset

Characterize in Functional Terms

Assign sequences to functional categories (COG, KEGG, PFAM & FIGFAM)

Characterize in Functional Terms

Identify relatedness among metagenomes;Identify habitat specific sequences

Identify key microbial groupsand their interactions

In-house scripts EuDetect, CS-SCORE MetaCAA Grid-Assembly

i-rDNAC16S

SOrt-ITEMS; DiScRIBinATE; ProVIDE; SPHINX; INDUS; TWARIT; BinPairs

COGNIZER; Vikodak

HabiSign Igloo-Plot; Community Analyzer

Compress & Archive Datasets/ Results

Compression algorithms for Fasta and Fastq data formats

Data archival strategies

DELIMINATE; FQC; BIND Multi-level data compression strategy

Platform hosts

22 published algorithms

Patented algorithms:35 (10 granted)

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Gut microbiome: Diversity across various life stages

Front Cell Infect Microbiol. 2012; 2: 104 (2012)

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What constitutes the healthy gut microbiota?

2011

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Infection of the intestinal epithelium by gastrointestinal pathogensVicious cycle of infection and malnutrition

Infection adversely affects nutritional status Malnutrition can predispose to infection.

Presence of pathogens normally absent in the intestines of healthy subjects.

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Birbhum district of West Bengal which is typical ofrural and agricultural setting

Nutritional status and Gut microbiome

2014

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What constitutes the healthy human gut microbiota?

Computational Analysis of Metagenomic data

Quantifying the nutritional status of each child

as nutritional Z-scores

Profiling the taxonomic groups in each

sequenced microbiome

Profiling the functional groups in each

sequenced microbiom

Correlating the abundance of taxonomic/functional groups with the nutritional status of children

Nutritional Z-scoresHeight for age (stunted growth- chronic malnutrition)Weight for age (underweight)Weight for height (Wasting or thinness- acute malnutrition)

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Correlating abundance of Taxonomic Groups with Nutritional Status

G1

G4

Taxonomic markers positively or negatively influencing nutritional status

Healthy markers :Probiotic and/or anti-inflammatory genera

Roseburia, Mitsuokella, Faecalibacterium

Energy harvesters from dietary fiber

Butyrvibrio, Roseburia, Faecalibacterium

CommensalsEubacterium, Dialister

Malnourishment markers :Potential Pathogenic genera

Escherichia, Enterobacter, Shigella, Streptococcus, Veillonella

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Genera Co-occurrence network: Apparently healthy

G4

G1

G4

G1

G1

G4 members (Enterobacter and Streptococcus) associating with commensals/G1 members

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Borderline

Apparently healthy

G4 members associating with each other

G1

G1

G4

G1

G4

G4

G4

G4

G4

G1

G1

G1

G1

G4

G1

G1

G1 G1

G1

G1

G1

Variation of Microbial community with Nutritional status

Variation of Microbial community with decrease in nutritional status

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BorderlineG4

G4

G4

G4

G4

G1

G1

G1 G1

G1

G1

G1

Changes in genera co-occurrence networks with decrease in nutritional status

Severely Malnourished

G4

G4

G4

G4

G1

G1

G1

G1

G1

G1

G1

G4 members Enterobacter joining with other G4 members

Members from three hubs join to form one single hub

Two distinct hubs (or ‘armies’) of genera created, one dominated by G1 members and the other by G4 members

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Gut microbiome & Health status

170 severely malnourished children170 childchild

Food supplements

Increase in beneficial bacteria

ood supplements

18181818188818Prospects for development of probiotics and nutraceuticals

Ready-to-Use Therapeutic Food (RUTF)

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Depends on various factors –

• Life style• Ethnicity• Drug usage• Antibiotic usage• ……

How about Adult Gut microbiome?

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Dec. 2015193 individuals 15 ethnic groups 4 geographies :

Assam, Telangana, Sikkim Manipur

Gut microbiome of adult Indian tribes

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15 ethnic groups 4 geographies

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2013

Gut microbiome & response to Antibiotics and drugs

2016

23Increase in exposure to wide range of drugs/xenobiotics with age probably leads to an increase in the xenobiotic metabolizing potential of the gut microbiome.

2016

Abundance of xenobiotic enzymes produced by gut microbiome varies with age and geography

• 397 individuals from 8 nationalities

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2013

• 275 individuals from 8 nationalities

• Global trend of genes conferring resistance to 240 antibiotics

• Abundance of AR genes (total no. of detected AR genes)

• Diversity of AR (No. of antibiotics against which AR genes detected)

Gut microbiome & Antibiotic resistance

255

Genes conferring resistance to ~ 53 antibiotics detected

267 out of 275 263 out of 275

Global trend of antibiotic resistance genes in gut microflora

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Higher in ChineseHigher in American

Higher in Spanish

cephalosporin fosmidomycin

chloramphenicollincosamide, streptogramin B macrolide

F3H8F5

26Higher abundances but lower diversity of AR genes in Chinese

• Chinese have higher number of genes conferring resistance to the same antibiotic• 35 AR genes (out of 157) found only in the Chinese gut metagenomes

Country specific resistance patterns

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Resistotype 1:243 individuals

(Few Chinese + rest of the world)

Resistotype 2: All Chinese

Resistotype 1 resolved into three sub-clusters

Preferred in US individuals(60% of US)

Individuals could be grouped into four clusters based on the resistance profiles in their gut microbiomes

Two clusters represented groups of gut microbiomes having similar abundances of various AR genes

Preferred in Europeanand Japanese populations

Resistotypes: Individuals with similar resistance profiles

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Novel drug targets

Personalized therapeutics

Probiotics and Nutraceuticals

New diagnostic-biomarkers

Alter gut microbiome(we cannot really change our genome)

Analyze gut microbiome : predisposition to diseases/disorders?

Potential for curing chronic diseases using microbiome information

New era of Translational Medicine

AnlyticsPlatform

PharmaAcademia

Hospitals

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CollaboratorsTCS

Acknowledgements

E-mail : sharmila.mande@tcs.comhttp://www.tcs.com/about/research/researchers/Pages/Sharmila-Mande.aspx

NICED(Kolkata) & THSTI, (Gurgaon)

Dr. G.B. Nair

IASST (Guwahati)Dr. Mojibur KhanDr. R. Talukdar

MDRF (Chennai)Dr. V. Mohan

Copenhagen UniversityDr. Oluf Pedersen

Hinduja Hospital (Mumbai)Dr. Philip Abraham

IGIB, DelhiDr. Rajesh Gokhale

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Thank you

TCS Research, Pune