Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, India
© Copyright 2018. Korean Association for the Study of Intestinal Diseases. All rights reserved.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
FINANCIAL SUPPORT
This study was supported by Department of Biotechnology (DBT), Government of India (BT/PR6119/GBD/27/370/2012) and Jaypee University of Information Technology (JUIT), Solan, India.
CONFLICT OF INTEREST
No potential conflict of interest relevant to this article was reported.
AUTHOR CONTRIBUTION
SA, RM, and GG planned the study, SA executed the experiment, SA, RM and GG drafted the manuscript.
Observation time |
LAB |
Bifidobacteria |
||||
---|---|---|---|---|---|---|
Richness (S) | Shannon diversity index (H) | Evenness (E) | Richness (S) | Shannon diversity index (H) | Evenness (E) | |
1st month | 15a | 1.160b | 0.428 | 10c | 0.975c | 0.423 |
2nd month | 8c | 0.895c | 0.430 | 11c | 1.023a | 0.426 |
3rd month | 9c | 0.946a | 0.430 | 11c | 1.029a | 0.429 |
4th month | 21b | 1.318d | 0.433 | 20a | 1.293b | 0.431 |
Primers | Target | Conditions | Product size | Reference |
---|---|---|---|---|
PRBA338fGC | Total bacteria | 5’-94°C | 236 bp | 12 |
P518r | 1’-95°C, 1’-53°C, 2’-72°C (30X) | |||
10’-72°C | ||||
SGLAB0159F | Lactic acid bacteria | 7’-95°C | 550 bp | 13 |
SGLAB0667R | 1’-94°C, 1’-56°C, 2’-72°C (30X) | |||
10’-72°C | ||||
Bif164-F | Bifidobacteria | 5’-95°C | 523 bp | 14 |
Bif662-R | 1’-95°C, 1’-66°C, 1’-72°C (30X) | |||
5’-72°C |
Representative sequence (accession number) | Closest homologue |
|
---|---|---|
Taxonomic name (accession number) | Homology (%) | |
Lactic acid producing bacteria | ||
Enterococcus sp. isolate gel band G7 (KU891046) | Enterococcus sulfureus (NR_113928) | 100 |
Enterococcus sp. gel band G8 (KU891047) | Enterococcus gallinarum (NR_104559) | 100 |
Streptococcus sp. isolate DGGE gel band G11 (KU891048) | Streptococcus thermophilus (NR_074827) | 99 |
Streptococcus sp. isolate DGGE gel band G28 (KU877515) | Streptococcus salivarius (NR_102816) | 95 |
Lactobacillus sp. isolate DGGE gel band G13 (KU877519) | Lactobacillus ruminis (NR_102839) | 98 |
Streptococcus sp. isolate DGGE gel band G12 (KU877520) | Streptococcus vestibularis (NR_042777) | 88 |
Lactobacillus sp. isolate DGGE gel band G10 (KU877521) | Lactobacillus salivarius (NR_074589.1) | 98 |
Enterococcus sp. isolate DGGE gel band G9 (KU877522) | Enterococcus hermanniensis (NR_042897) | 98 |
Enterococcus sp. isolate DGGE gel band G6 (KU877523) | Enterococcus sulfureus (NR_113928) | 99 |
Enterococcus sp. isolate DGGE gel band G4 (KU877525) | Enterococcus faecium (NR_042054) | 85 |
Enterococcus sp. isolate DGGE gel band G3 (KU877526) | Lactobacillus ceti (NR_042539) | 85 |
Bifidobacteria | ||
Bifidobacterium sp. isolate DGGE gel band G44 (KU877499) | Bifidobacterium breve (NR_102863) | 100 |
Bifidobacterium sp. isolate DGGE gel band G43 (KU877500) | Bifidobacterium breve (NR_102863) | 100 |
Bifidobacterium sp. isolate DGGE gel band G42 (KU877501) | Bifidobacterium breve (NR_102863) | 100 |
Bifidobacterium sp. isolate DGGE gel band G41 (KU877502) | Bifidobacterium choerinum (NR_037116) | 98 |
Bifidobacterium sp. isolate DGGE gel band G40 (KU877503) | Bifidobacterium choerinum (NR_037116) | 98 |
Bifidobacterium sp. isolate DGGE gel band G39 (KU877504) | Bifidobacterium animalis subsp. animalis (NR_119007) | 92 |
Bifidobacterium sp. isolate DGGE gel band G38 (KU877505) | Bifidobacterium choerinum (NR_037116) | 98 |
Bifidobacterium sp. isolate DGGE gel band G37 (KU877506) | Bifidobacterium choerinum (NR_037116) | 98 |
Bifidobacterium sp. isolate DGGE gel band G36 (KU877507) | Bifidobacterium choerinum (NR_037116) | 97 |
Bifidobacterium sp. isolate DGGE gel band G35 (KU877508) | Bifidobacterium pseudolongum subsp. globosum (NR_043441) | 98 |
Bifidobacterium sp. isolate DGGE gel band G34 (KU877509) | Bifidobacterium choerinum (NR_043438) | 98 |
Bifidobacterium sp. isolate DGGE gel band G29 (KU877514) | Bifidobacterium breve (NR_102863) | 100 |
Bifidobacterium sp. isolate DGGE gel band G26 (KU877517) | Bifidobacterium breve (NR_102863) | 99 |
Observation time | LAB |
Bifidobacteria |
||||
---|---|---|---|---|---|---|
Richness (S) | Shannon diversity index (H) | Evenness (E) | Richness (S) | Shannon diversity index (H) | Evenness (E) | |
1st month | 15 |
1.160 |
0.428 | 10 |
0.975 |
0.423 |
2nd month | 8 |
0.895 |
0.430 | 11 |
1.023 |
0.426 |
3rd month | 9 |
0.946 |
0.430 | 11 |
1.029 |
0.429 |
4th month | 21 |
1.318 |
0.433 | 20 |
1.293 |
0.431 |
DGGE, denaturing gradient gel electrophoresis.
Means in the column with same superscript letter are not significantly different as measured by two-sided Tukey’s – LAB, lactic acid bacteria; DGGE, denaturing gradient gel electrophoresis.