Effective Recovery of Bacterial DNA and Percent-Guanine-Plus-Cytosine-Based Analysis of Community Structure in the Gastrointestinal Tract of Broiler Chickens

Apajalahti, Juha H. A.; Särkilahti, Laura K.; Mäki, Brita R. E.; Heikkinen, Jouni; Nurminen, Päivi; Holben, William E.

doi:10.1128/aem.64.10.4084-4088.1998

Cited by 177 publications

(71 citation statements)

References 31 publications

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“…Analysis of %G+C base pro¢les might give an indication of di¡erences in bacterial community structure at the community level. Such analyses have been used to demonstrate di¡erences in bacterial communities of aquatic and terrestrial environments [34], of compartments in an activated sludge system [35] and of compartments in the gastrointestinal tract of chickens [36]. In terrestrial environments, the bacterial communities of two pristine forest soils have been shown to di¡er in %G+C base pro¢les [20].…”

Section: Discussionmentioning

confidence: 99%

Analysis of bacterial communities in heavy metal-contaminated soils at different levels of resolution

Sandaa¹

1999

FEMS Microbiology Ecology

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The impact of heavy metal contamination on soil bacterial communities was studied in soils amended for many years with sewage sludge contaminated with heavy metals to varying extents. At the broad level of resolution, DNA reassociation analysis indicated a dramatic decrease in bacterial diversity from 16 000 bacterial genomes (g soil [wet wt]) 31 in the non-contaminated soil to 6400 bacterial genomes (g soil [wet wt]) 31 in soil with low metal amendments and only 2000 bacterial genomes (g soil [wet wt]) 31 in soil with high metal amendments. No differences between bacterial communities of these soils, however, were displayed in the %G+C profiles analysed by thermal denaturation. At a coarse level of characterisation, in situ hybridisation analysing larger phylogenetic groups of bacteria revealed a general decrease in the percentage of cells detected with probes ARCH915, BET42a, GAM42a, SRB385, CF319a, LGCb and HGC69a with increasing metal amendment. Only cells detected with probe ALF1b increased significantly from 3.1 þ 0.8% of the cells detected by the domain-specific probe EUB338 in the non-contaminated soil to 6.5 þ 1.3% in soil with high metal amendments. These shifts in populations of larger phylogenetic groups were largely confirmed by dot blot analysis of 16S and 23S rDNA clone libraries from bacteria in soil with low metal and high metal amendments, respectively. For a fine-level characterisation, 72 clones of 16S rDNA libraries were identified by comparative sequence analysis. A few sequences could not be assigned to the major taxa described. Most of the sequences were assigned to the Gram-positive bacteria with a high DNA G+C content (45%) and the K-subdivision of Proteobacteria (24%). However, only minor differences were seen between bacterial communities from the low and high metal soils. In the soil with high metal amendment, more sequences clustered to the K-subdivision of Proteobacteria, while in the low metal soil, more sequences clustered to the Gram-positive bacteria with a high DNA G+C content. ß

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Section: Discussionmentioning

confidence: 99%

Analysis of bacterial communities in heavy metal-contaminated soils at different levels of resolution

Sandaa¹

1999

FEMS Microbiology Ecology

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“…With regard to the adherent bacteria sample, a sample of 2 mL was vortexed thoroughly after 6 mL of PW was added. Bacterial cells were recovered from each sample using a differential centrifugation technique modified from Apajalahti, Särkilahti, Mäki, Heikkinen, Nurminen and Holben (1998). In brief, the liquid mixture was centrifugated at 200 g for 15 min at 4 °C.…”

Section: Methodsmentioning

confidence: 99%

Microbiota of yellow grouper (Epinephelus awoora Temminck & Schlegel, 1842) fed two different diets

Feng

Luo

et al. 2010

Aquaculture Research

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The rapidly growing yellow grouper industry has experienced relatively severe bacterial disease problems in China. The proliferation of pathogens in ¢sh can be suppressed by commensal microbiota. In this background, we used nested polymerase chain reactiondenaturing gradient gel electrophoresis (PCR-DGGE) and sequence analysis to investigate microbiota in the skin, gills and intestines, including adherent bacteria and non-adherent bacteria in yellow grouper fed with natural diet and complete feed. A total of 21 bacterial species were identi¢ed using phylogenetic analysis. The g-Proteobacteria group (81.0%, 17 species) dominated the bacterial communities in yellow grouper completely. Others belonged to Firmicutes (9.5%, two species), Actinobacteria (4.75%, one species) and Verrucomicrobia (4.75%, one species). The higher similarities (above 91%) of the DGGE band patterns in skin, gill and intestinal-non-adherent bacteria between two groups of ¢sh indicated that existed more stable microbial communities existed in these speci¢cally ecological niches in yellow grouper. However, considerable di¡erences existed between two intestinal-adherent bacteria (IAB) samples; that is, compared with natural diet fed yellow grouper, higher bacterial apparent species richness and possibly less abundance existed in IAB in ¢sh fed with complete diets, probably indicating that the community structures in IAB were a¡ected easily and signi¢cantly by diet.

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“…Equal amounts of ileal or caecal digesta from the ten birds within each treatment at each sampling were combined for preparation of bacterial samples that were subsequently used for DNA extraction. Bacterial samples from ileal digesta were prepared by a washing procedure as described by Apajalahti et al (1998), whereas caecal digesta was used directly for DNA extraction. Samples for DNA extraction were frozen in liquid nitrogen and stored at )70°C.…”

Section: Chicken Maintenance and Sample Collectionmentioning

confidence: 99%

Effects of zinc bacitracin, bird age and access to range on bacterial microbiota in the ileum and caeca of broiler chickens

et al. 2008

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Aims: Determining the effects of zinc bacitracin, bird age and access to range on bacterial microbiota in the ileum and caeca of broilers. Methods and Results: 16S rRNA gene‐based polymerase chain reaction‐based denaturing gradient gel electrophoresis (PCR–DGGE) profiling, DNA sequencing and real‐time quantitative PCR techniques were used. The richness of both ileal and caecal microbiota increased with chicken age. The microbiota from those birds of the same age demonstrated relatively similar PCR–DGGE profiles and tended to form closely related clusters in the relatedness analyses. Dietary treatment with bacitracin (50 mg kg−1) and access to range did not change the richness but altered the composition of the microbiota. The impact of bacitracin was particularly obvious in 3‐day‐old chicks. Lactobacilli were abundant in the caecal microbiota of 3‐day‐old chicks regardless of the dietary treatment with bacitracin. The access to range enriched Bifidobacterium in both the ileum and caeca. Conclusions: Bacitracin, bird age and access to range all influenced bacterial microbiota in the ileum and caeca of broilers, with bird age having the greatest apparent effect. Significance and Impact of the Study: Providing useful information for the development of antibiotic replacement therapy for poultry production.

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Effective Recovery of Bacterial DNA and Percent-Guanine-Plus-Cytosine-Based Analysis of Community Structure in the Gastrointestinal Tract of Broiler Chickens

Cited by 177 publications

References 31 publications

Analysis of bacterial communities in heavy metal-contaminated soils at different levels of resolution

Analysis of bacterial communities in heavy metal-contaminated soils at different levels of resolution

Microbiota of yellow grouper (Epinephelus awoora Temminck & Schlegel, 1842) fed two different diets

Effects of zinc bacitracin, bird age and access to range on bacterial microbiota in the ileum and caeca of broiler chickens

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