A systematic assessment of automated ribosomal intergenic spacer analysis (ARISA) as a tool for estimating bacterial richness

Kovacs, Amir; Yacoby, Keren; Gophna, Uri

doi:10.1016/j.resmic.2010.01.006

Cited by 72 publications

(57 citation statements)

References 9 publications

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“…The labeled fragments were separated on the capillary sequencer along with a custom-made ROX-labeled 250-to 1150-bp standard (BioVentures Inc., Murfreesboro, TN, USA). Raw data generated by the genetic analyzer were initially analyzed using GeneMarker software (SoftGenetics LLC, State College, PA, USA) according to Kovacs et al (2010). After performing accurate size calling using the program, all data were exported to Excel (Microsoft Corp., Redmond, WA, USA) for further analysis.…”

Section: Structural and Chemical Analyses And In Vitro Digestibilitymentioning

confidence: 99%

Effect of wheat hay particle size and replacement of wheat hay with wheat silage on rumen pH, rumination and digestibility in ruminally cannulated non-lactating cows

Shaani

Nikbachat

Yosef

et al. 2017

Animal

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This study examined the effects on intake, diurnal rumen pH changes, rumination and digestibility of feeding ruminally cannulated non-lactating cows in a Latin square design (four cows × four periods) with four total mixed rations (TMRs) typical for lactating cows. TMRs were based on: long wheat hay or short wheat hay, wheat silage or wheat silage + 1.5% NaHCO 3 buffer, as the sole roughage source (30% of TMR dry matter (DM)). The level of physically effective NDF remaining above the 8 mm screen (peNDF) was similar in the long hay and silage-based TMRs (9.45% to 9.64% of DM) and lower in the short hay TMR (7.47% of DM). The four TMRs were offered individually at 95% of ad libitum intake to avoid orts within 24 h. Cows fed long hay consumed less DM than the short hay and silage groups (9.6 v. 10.5 and 10.8 kg/day, respectively) and sorted against large hay particles at 12 h post-feeding. Under the limitations of this study (non-lactating cows fed at restricted intake) short hay TMR prevented sorting within 12 h post-feeding, encouraged rumination per kg peNDF ingested, and had higher average rumen pH (6.24), whereas preventing sub acute ruminal acidosis (SARA, defined as pH < 5.8 for at least 5 h/day). In contrast, the long hay and silage-based groups were under SARA. In vitro methane production of rumen fluid was higher in the hay-fed cows than in their silage-fed counterparts, and in all treatments lower at 1 h pre-feeding than at 6 h post-feeding. In vivo DM and NDF digestibility were similar for the short hay and silage TMRs, and higher than those of the long hay TMR. Under the conditions of this study, addition of 1.5% buffer to the wheat silage TMR had no effect on intake, rumen pH, creation of SARA and digestibility.

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Section: Structural and Chemical Analyses And In Vitro Digestibilitymentioning

confidence: 99%

Effect of wheat hay particle size and replacement of wheat hay with wheat silage on rumen pH, rumination and digestibility in ruminally cannulated non-lactating cows

Shaani

Nikbachat

Yosef

et al. 2017

Animal

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“…In order to contribute to the faecal model statement, the present work compared the equine faecal bacterial community to those of the caecum and the right ventral colon by using a fingerprint profiles analysis: the Automated Ribosomal Intergenic Spacer Analysis (ARISA). As underlined by Kovacs et al (2010) ARISA has become a very useful tool for comparing community structure across multiple samples based on profile patterns. Additionally, this fingerprint technique has a high-resolution, is highly reproducible and is very robust for discriminating between microbial communities based on the length polymorphism of the intergenic spacer (IGS) between the small (16S) and large (23S) subunit rRNA genes in the ribosomal RNA (rrn) operon (Ranjard et al, 2001).…”

Section: Introductionmentioning

confidence: 99%

Comparison of the bacterial community structure within the equine hindgut and faeces using Automated Ribosomal Intergenic Spacer Analysis (ARISA)

Sadet-Bourgeteau

Philippeau

Dequiedt

et al. 2014

Animal

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The horse's hindgut bacterial ecosystem has often been studied using faecal samples. However few studies compared both bacterial ecosystems and the validity of using faecal samples may be questionable. Hence, the present study aimed to compare the structure of the equine bacterial community in the hindgut (caecum, right ventral colon) and faeces using a fingerprint technique known as Automated Ribosomal Intergenic Spacer Analysis (ARISA). Two DNA extraction methods were also assessed. Intestinal contents and faeces were sampled 3 h after the morning meal on four adult fistulated horses fed meadow hay and pelleted concentrate. Irrespective of the intestinal segment, Principal Component Analysis of ARISA profiles showed a strong individual effect ( P < 0.0001). However, across the study, faecal bacterial community structure significantly ( P < 0.001) differed from those of the caecum and colon, while there was no difference between the two hindgut communities. The use of a QIAamp ® DNA Stool Mini kit increased the quality of DNA extracted irrespective of sample type. The differences observed between faecal and hindgut bacterial communities challenge the use of faeces as a representative for hindgut activity. Further investigations are necessary to compare bacterial activity between the hindgut and faeces in order to understand the validity of using faecal samples.

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“…Fingerprinting techniques provide information on general changes in the phytoplankton community (Knefelkamp, 2009;Wolf et al, 2013), although they are not suitable for an absolute assessment of biodiversity (Bent et al, 2007). The ARISA (automated ribosomal intergenic spacer analysis) approach used in this study has been often applied for prokaryotic communities (e.g., Danovaro et al, 2006;Kovacs et al, 2010), but has also been used for eukaryotes (Fechner et al, 2010;Wolf et al, 2013). In contrast, DNA-microarrays can provide taxon-specific information about the phytoplankton community in a sample (Kochzius et al, 2007;Metfies and Medlin, 2005).…”

Section: Discussionmentioning

confidence: 99%

Analysis of phytoplankton distribution and community structure in the German Bight with respect to the different size classes

Wollschläger

Wiltshire

Petersen

et al. 2015

Journal of Sea Research

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Investigation of phytoplankton biodiversity, ecology, and biogeography is crucial for understanding marine ecosystems. Research is often carried out on the basis of microscopic observations, but due to the limitations of this approach regarding detection and identification of picophytoplankton (0.2-2 μm) and nanophytoplankton (2-20 μm), these investigations are mainly focused on the microphytoplankton (20-200 μm). In the last decades, various methods based on optical and molecular biological approaches have evolved which enable a more rapid and convenient analysis of phytoplankton samples and a more detailed assessment of small phytoplankton. In this study, a selection of these methods (in situ fluorescence, flow cytometry, genetic fingerprinting, and DNA microarray) was placed in complement to light microscopy and HPLC-based pigment analysis to investigate both biomass distribution and community structure of phytoplankton. As far as possible, the size classes were analyzed separately. Investigations were carried out on six cruises in the German Bight in 2010 and 2011 to analyze both spatial and seasonal variability. Microphytoplankton was identified as the major contributor to biomass in all seasons, followed by the nanophytoplankton. Generally, biomass distribution was patchy, but the overall contribution of small phytoplankton was higher in offshore areas and also in areas exhibiting higher turbidity. Regarding temporal development of the community, differences between the small phytoplankton community and the microphytoplankton were found. The latter exhibited a seasonal pattern regarding number of taxa present, alphaand beta-diversity, and community structure, while for the nano-and especially the picophytoplankton, a general shift in the community between both years was observable without seasonality. Although the reason for this shift remains unclear, the results imply a different response of large and small phytoplankton to environmental influences.

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A systematic assessment of automated ribosomal intergenic spacer analysis (ARISA) as a tool for estimating bacterial richness

Cited by 72 publications

References 9 publications

Effect of wheat hay particle size and replacement of wheat hay with wheat silage on rumen pH, rumination and digestibility in ruminally cannulated non-lactating cows

Effect of wheat hay particle size and replacement of wheat hay with wheat silage on rumen pH, rumination and digestibility in ruminally cannulated non-lactating cows

Comparison of the bacterial community structure within the equine hindgut and faeces using Automated Ribosomal Intergenic Spacer Analysis (ARISA)

Analysis of phytoplankton distribution and community structure in the German Bight with respect to the different size classes

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