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8 protocols using bifidobacterium agar

1

Characterization of Gut Microbiota Composition

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The colon samples of 1 cm2 lengths (2 cm from the anus) was collected during autopsy for the bacteriological analysis of the mucosa-associated microbiota [51 (link)]. Selective diagnostic media (all produced by HiMedia Laboratories Pvt. Ltd., India): Bifidobacterium Agar, MRS agar, Endo agar, Mannitol Salt Agar, Iron Sulphite Agar, Simmons Citrate Agar, and Blood Agar Base (with aseptically added 5% sterile sheep's blood) were used for quantitative and qualitative analysis of microbiota composition. After inoculation, media were incubated in a thermostat at 37 °C for 24–48 h. Bacteria identification was performed using Bergey's Manual of determinative Bacteriology. The morphological and tinctorial characteristics of bacteria were assessed using reaction to plasma coagulation, DNA activity test, lysozyme and phosphatase production tests, oxidase test, carbohydrate fermentation tests, Voges-Proskauer's reaction, mobility test. Sensitivity to novobiocin was determined to differ S. aureus, S. epidermidis from S. saprophyticus. Lactose-negative E. coli were differentiated from opportunistic enterobacteria by detecting hydrogen sulphide formation. The results are presented as M ± m lg CFU/g and M ± m lg CFU/cm2.
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2

Probiotic and Omega-3 Supplementation Protocol

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VSL#3 (manufactured in India by Sun Pharmaceutical Ind. Ltd.) is a freeze-dried pharmaceutical probiotic preparation containing 112.5 × 109 CFU/capsule of three strains of bifidobacteria (Bifidobacterium longum, Bifidobacterium infantis, and Bifidobacterium breve), four strains of lactobacilli (Lactobacillus acidophilus, Lactobacillus paracasei, Lactobacillus delbrueckii subsp. bulgaricus, and Lactobacillus plantarum), and one strain of Streptococcus salivarius subsp. thermophilus. Identical-looking placebo capsules containing 40 mg microcrystalline cellulose were used for blinding. The capsules were stored at 2 to 8°C prior to distribution and the subjects were instructed to refrigerate the capsules. Bacterial viability was confirmed at the Department of Microbiology and Immunology, National Institute of Nutrition (ICMR), Hyderabad, by plating serial dilutions of bacterial suspensions onto Bifidobacterium Agar, Lactobacillus MRS Agar (HiMedia, India), and Streptococcus thermophilus Agar (HiMedia Laboratories Pvt. Ltd., India) followed by incubation in an anaerobic jar with anaerobic gas pack (HiMedia, India) at 37°C for 48 hours. The omega-3 capsule contained 180 mg EPA and 120 mg DHA per capsule (Dr. Reddy's Laboratories Ltd. Hyderabad, India).
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3

Anaerobic Gut Microbiome Analysis

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Coliform, anaerobes, Lactobacillus, and Bifidobacterium from the caecum were inoculated and incubated for 3 days on MacConkey agar (Oxoid), GAM agar (Nissui), Rogosa agar (Nissui), and Bifidobacterium agar (Himedia, India) at 37°C by the GasPak method described previously [21 (link)].
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4

Enumeration of Gut Microbiota Composition

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Fecal samples were obtained from the subjects at the beginning of the trial and after 45 days, for stool culture. The specimens were collected in sterile plastic containers and were immediately preserved at 4°C and were analysed on the same day or within 2 days. Fecal samples were homogenized using PBS and serially diluted. Plates were incubated in triplicate using selective media for enumeration of total aerobes (Nutrient agar, HiMedia India), total anaerobes (Schaedler agar, HiMedia India), coliforms (Violet Red Bile Agar, HiMedia India), E. coli (Eosin Methylene blue Agar, HiMedia India), bacteroides (Bacteroides Bile Esculin Agar Base, HiMedia India), bifidobacteria (Bifidobacterium Agar, HiMedia), lactic acid bacteria (Lactobacillus MRS Agar, HiMedia India), and Streptococcus thermophilus (Streptococcus thermophilus Agar, HiMedia India). Plates were incubated aerobically or anaerobically as appropriate and the colonies were counted after 48 hours.
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5

Quantifying Gut Bacterial Diversity

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The total bacterial count, Bacillus, and Bifidobacterium counts were determined using Nutrient Agar, Bacillus Medium, and Bifidobacterium Agar plates (Himedia, India), respectively. The method followed the standard protocol of tube dilution and plate counting described earlier (Wayne, 2011 ). Bacterial loads were expressed in cfu/gm of the whole gut sample and compared among the groups.
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6

Isolation and Enumeration of Probiotic Bacteria

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De Man, Rogosa and Sharpe Agar or MRS agar (HIMedia, India), Eosin Methylene Blue Agar or EMB agar (HIMedia, India), M17 agar (HIMedia, India) and Bifidobacterium agar (HIMedia, India) were used in the isolation and selective enumeration of Lactobacillus species, E. coli, Streptococcus sp. and Bifidobacterium, respectively.
Lactic acid bacteria used in this research was L. plantarum TISTR082 and enteric strain used were E. coli TISTR073 were purchased from the Thailand Institute of Scientific and Technological Research (TISTR), Pathumthani Province, Thailand. Commercial culture of probiotics (L. acidophilus, L. casei, S. thermophiles and B. animalis) was purchased from Sacco, Italy.
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7

Fecal Sample Analysis in Animal Studies

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For three consecutive days, that is, on days 26, 27 and 28 of treatment, faecal samples were collected and stored at -20°C. For analysis, the samples were diluted in deionised water (1 mg/ml) and faecal pH was measured using a digital potentiometer (Q400AS; Quimis) (34) . A separate portion of faecal sample was dried in an oven (320-SE; Fanem) at 105°C for 24 h to determine faecal moisture (27, 35) .
Another portion of faecal samples collected from caecum was diluted (1:9) in sterile peptone water and inoculated (20 µl), using the microdrop technique (36) , on selective agar for counting Lactobacillus spp. (de Man, Rogosa and Sharpe (MRS); HiMedia), Bifidobacterium spp. (Bifidobacterium agar; HiMedia) and Enterobacteriaceae (MacConkey agar; HiMedia). Agar plates for counting Lactobacillus spp. and Bifidobacterium spp. were incubated under anaerobic conditions (Anaerobic System Anaerogen; Oxoid Ltd) and agar plates for counting Enterobacteriaceae were incubated under aerobic conditions, all at 37°C for 24-48 h. At the end of the incubation period, characteristic colonies on the selective media were counted, and the results were expressed as log of colony-forming units per g of faeces (log 10 CFU/g) (37) . Total lipid in faeces and liver was determined by cold extraction (38) .
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8

Gut Microbiome Analysis of Dams and Offspring

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Faecal samples were collected on the three consecutive days before euthanasia for quantification of excreted fat or counting of the faecal microbiota population in both dams and offspring on the 30th and 90th days. Part of the faecal samples from dams and pups was used to quantify total lipids by cold extraction using a previously described procedure (29) . The other part of the faecal samples was homogenised in peptone water (100 mg/ml) and serially diluted in the same diluent. In all, 20 µl aliquots of the respective dilutions were inoculated using a microdrop technique (30) in Bifidobacterium agar (HiMedia) to count Bifidobacterium spp.; agar Man, Rogosa and Sharpe (HiMedia) to count Lactobacillus spp.; agar MacConkey (HiMedia) to count Enterobacteriaceae and agar Bacteroides Bile Esculina (Acumedia) to count Bacteroides spp. (Acumedia). Incubation was performed under anaerobic conditions (Anaerobic System Anaerogen; Oxoid Ltd) for counting Bifidobacterium spp., Lactobacillus spp. and Bacteroides spp. and under aerobic conditions for counting Enterobacteriaceae. After an incubation period of 24-48 h, the number of colonies on each selective medium was counted, and the results were expressed as log colony-forming units/g (15) .
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