Different alpha diversity indices for each sample of university farm data estimated using QIIME for primer pair P2 data. OTUs were clustered at >â97% similarity. (XLSX 12 kb

A Jung

A Psifidi

AK Smilde

B Chengat Prakashbabu

BA Degnan

BB Oakley

BP Willing

D Arndt

D Grace

D Mariat

D Stanley

DH Parks

DW Pitta

E Amit-Romach

ER Davenport

F Meyer

G Arora

J Ding

J Lu

J Salanitro

J Tremblay

J Zhang

JC Oliveros

JK Goodrich

JL Danzeisen

KT Ramasamy

L Beckmann

L Bjerrum

L Mancabelli

L Wang

L Zhao

M Albertsen

M Spitzer

MAM Shaufi

MJ Sergeant

MP Cox

N Segata

NO Kaakoush

O Polansky

P Wigley

PB Eckburg

PJ Turnbaugh

PK Rout

R Baelmans

R Blekhman

RE Ley

S Haunshi

S Hessenberger

S Humphrey

S Saxena

S Wei

V Ahir

WA Awad

XY Zhu

Ř Hammer

Microbiome

Crossref

Microbial diversity and community composition of caecal microbiota in commercial and indigenous Indian chickens determined using 16s rDNA amplicon sequencing

Pandit, R J

Hinsu, A T

Patel, N V

Koringa, P G

Jakhesara, S J

Thakkar, J R

Shah, T M

Limon, G

Psifidi, A

Guitian, J

Hume, D A

Tomley, F M

Rank, D N

Raman, M

Tirumurugaan, K G

Blake, D P

Joshi, C G

RVC Repository (Royal Veterinary College)

Background: The caecal microbiota plays a key role in chicken health and performance, influencing digestion and absorption of nutrients, and contributing to defence against colonisation by invading pathogens. Measures of productivity and resistance to pathogen colonisation are directly influenced by chicken genotype, but host driven variation in microbiome structure is also likely to exert a considerable indirect influence. Methods: Here, we define the caecal microbiome of indigenous Indian Aseel and Kadaknath chicken breeds and compare them with the global commercial broiler Cobb400 and Ross 308 lines using 16S rDNA V3-V4 hypervariable amplicon sequencing. Results: Each caecal microbiome was dominated by the genera Bacteroides, unclassified bacteria, unclassified Clostridiales, Clostridium, Alistipes, Faecalibacterium, Eubacterium and Blautia. Geographic location (a measure recognised to include variation in environmental and climatic factors, but also likely to feature varied management practices) and chicken line/breed were both found to exert significant impacts (p < 0.05) on caecal microbiome composition. Linear discriminant analysis effect size (LEfSe) revealed 42 breed-specific biomarkers in the chicken lines reared under controlled conditions at two different locations. Conclusion: Chicken breed-specific variation in bacterial occurrence, correlation between genera and clustering of operational taxonomic units indicate scope for quantitative genetic analysis and the possibility of selective breeding of chickens for defined enteric microbiota

Pandit, Ramesh J.

Hinsu, Ankit T.

Patel, Namrata V.

Koringa, Prakash G.

Jakhesara, Subhash J.

Thakkar, Jalpa R.

Shah, Tejas M.

Limon, Georgina

Psifidi, Androniki

Guitian, Javier

Hume, David A.

Tomley, Fiona M.

Rank, Dharamshibhai N.

Raman, M.

Tirumurugaan, K. G.

Blake, Damer P.

Joshi, Chaitanya G.

University of Queensland eSpace

Pairwise comparison of P values by ANOSIM analysis based on Bray-Curtis Index using PAST. The P value was corrected with sequential Bonfferoni correction method. (XLSX 9 kb

Ramesh Pandit (5444858)

Ankit Hinsu (5444867)

Namrata Patel (5444861)

Prakash Koringa (5444846)

Subhash Jakhesara (5444849)

Jalpa Thakkar (5444843)

Tejas Shah (825803)

Georgina Limon (5444855)

Androniki Psifidi (357421)

Javier Guitian (160212)

David Hume (3460133)

Fiona Tomley (203471)

Dharamshibhai Rank (5444852)

M. Raman (2016148)

K. Tirumurugaan (5444864)

Damer Blake (230189)

Chaitanya Joshi (653787)

The Francis Crick Institute

Additional file 10: of Microbial diversity and community composition of caecal microbiota in commercial and indigenous Indian chickens determined using 16s rDNA amplicon sequencing

BACKGROUND: The caecal microbiota plays a key role in chicken health and performance, influencing digestion and absorption of nutrients, and contributing to defence against colonisation by invading pathogens. Measures of productivity and resistance to pathogen colonisation are directly influenced by chicken genotype, but host driven variation in microbiome structure is also likely to exert a considerable indirect influence.METHODS: Here, we define the caecal microbiome of indigenous Indian Aseel and Kadaknath chicken breeds and compare them with the global commercial broiler Cobb400 and Ross 308 lines using 16S rDNA V3-V4 hypervariable amplicon sequencing.RESULTS: Each caecal microbiome was dominated by the genera Bacteroides, unclassified bacteria, unclassified Clostridiales, Clostridium, Alistipes, Faecalibacterium, Eubacterium and Blautia. Geographic location (a measure recognised to include variation in environmental and climatic factors, but also likely to feature varied management practices) and chicken line/breed were both found to exert significant impacts (p &lt; 0.05) on caecal microbiome composition. Linear discriminant analysis effect size (LEfSe) revealed 42 breed-specific biomarkers in the chicken lines reared under controlled conditions at two different locations.CONCLUSION: Chicken breed-specific variation in bacterial occurrence, correlation between genera and clustering of operational taxonomic units indicate scope for quantitative genetic analysis and the possibility of selective breeding of chickens for defined enteric microbiota.</p

Pandit, Ramesh J

Hinsu, Ankit T

Patel, Namrata V

Koringa, Prakash G

Jakhesara, Subhash J

Thakkar, Jalpa R

Shah, Tejas M

Hume, David A

Tomley, Fiona M

Rank, Dharamshibhai N

Blake, Damer P

Joshi, Chaitanya G

Edinburgh Research Explorer

English

Sample wise details of the sequencing reads uploaded to MG-RAST for taxonomy assignment. TPC, TPA and TPK for Ross 300, Aseel and Kadaknath, respectively at Tamil Nadu location similarly APC, APA and APK for Cobb400, Aseel and Kadaknath, respectively at Anand location. (XLSX 13 kb

Additional file 3: of Microbial diversity and community composition of caecal microbiota in commercial and indigenous Indian chickens determined using 16s rDNA amplicon sequencing

Abstract Background The caecal microbiota plays a key role in chicken health and performance, influencing digestion and absorption of nutrients, and contributing to defence against colonisation by invading pathogens. Measures of productivity and resistance to pathogen colonisation are directly influenced by chicken genotype, but host driven variation in microbiome structure is also likely to exert a considerable indirect influence. Methods Here, we define the caecal microbiome of indigenous Indian Aseel and Kadaknath chicken breeds and compare them with the global commercial broiler Cobb400 and Ross 308 lines using 16S rDNA V3-V4 hypervariable amplicon sequencing. Results Each caecal microbiome was dominated by the genera Bacteroides, unclassified bacteria, unclassified Clostridiales, Clostridium, Alistipes, Faecalibacterium, Eubacterium and Blautia. Geographic location (a measure recognised to include variation in environmental and climatic factors, but also likely to feature varied management practices) and chicken line/breed were both found to exert significant impacts (p < 0.05) on caecal microbiome composition. Linear discriminant analysis effect size (LEfSe) revealed 42 breed-specific biomarkers in the chicken lines reared under controlled conditions at two different locations. Conclusion Chicken breed-specific variation in bacterial occurrence, correlation between genera and clustering of operational taxonomic units indicate scope for quantitative genetic analysis and the possibility of selective breeding of chickens for defined enteric microbiota

Ramesh J. Pandit

Ankit T. Hinsu

Namrata V. Patel

Prakash G. Koringa

Subhash J. Jakhesara

Jalpa R. Thakkar

Tejas M. Shah

Georgina Limon

Androniki Psifidi

Javier Guitian

David A. Hume

Fiona M. Tomley

Dharamshibhai N. Rank

M. Raman

K. G. Tirumurugaan

Damer P. Blake

Chaitanya G. Joshi

Directory of Open Access Journals

RVC Research Online

Additional file 12: of Microbial diversity and community composition of caecal microbiota in commercial and indigenous Indian chickens determined using 16s rDNA amplicon sequencing

https://rvc-repository.worktribe.com/preview/1386780/11629.pdf

Microbial diversity and community composition of caecal microbiota in commercial and indigenous Indian chickens determined using 16s rDNA amplicon sequencing

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Crossref

RVC Repository (Royal Veterinary College)

University of Queensland eSpace

The Francis Crick Institute

Edinburgh Research Explorer

Edinburgh Research Explorer

The Francis Crick Institute

Directory of Open Access Journals

RVC Research Online

The Francis Crick Institute