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Accessing Dietary Effects on the Rumen Microbiome: Different Sequencing Methods Tell Different Stories.

ABSTRACT: The current study employed both amplicon and shotgun sequencing to examine and compare the rumen microbiome in Angus bulls fed with either a backgrounding diet (BCK) or finishing diet (HG), to assess if both methods produce comparable results. Rumen digesta samples from 16 bulls were subjected for microbial profiling. Distinctive microbial profiles were revealed by the two methods, indicating that choice of sequencing approach may be a critical facet in studies of the rumen microbiome. Shotgun-sequencing identified the presence of 303 bacterial genera and 171 archaeal species, several of which exhibited differential abundance. Amplicon-sequencing identified 48 bacterial genera, 4 archaeal species, and 9 protozoal species. Among them, 20 bacterial genera and 5 protozoal species were differentially abundant between the two diets. Overall, amplicon-sequencing showed a more drastic diet-derived effect on the ruminal microbial profile compared to shotgun-sequencing. While both methods detected dietary differences at various taxonomic levels, few consistent patterns were evident. Opposite results were seen for the phyla Firmicutes and Bacteroidetes, and the genus Selenomonas. This study showcases the importance of sequencing platform choice and suggests a need for integrative methods that allow robust comparisons of microbial data drawn from various omic approaches, allowing for comprehensive comparisons across studies.

SUBMITTER: Zhou M

PROVIDER: S-EPMC8310016 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Over one third of crops are animal pollinated, with insects being the largest group. In some crops, including strawberries, fruit yield, weight, quality, aesthetics and shelf life increase with insect pollination. Many crops are protected from extreme weather in polytunnels, but the impacts of polytunnels on insects are poorly understood. Polytunnels could reduce pollination services, especially if insects have access issues. Here we examine the distribution and activity of honeybees and non-honeybee wild insects on a commercial fruit farm. We evaluated whether insect distributions are impacted by flower type (strawberry; raspberry; weed), or distance from polytunnel edges. We compared passive pan-trapping and active quadrat observations to establish their suitability for monitoring insect distribution and behaviour on a farm. To understand the relative value of honeybees compared to other insects for strawberry pollination, the primary crop at the site, we enhanced our observations with video data analysed using insect tracking software to document the time spent by insects on flowers. The results show honeybees strongly prefer raspberry and weed flowers over strawberry flowers and that location within the polytunnel impacts insect distributions. Consistent with recent studies, we also show that pan-traps are ineffective to sample honeybee numbers. While the pan-traps and quadrat observations tend to suggest that investment in managed honeybees for strawberry pollination might be ineffective due to consistent low numbers within the crop, the camera data provides contrary evidence. Although honeybees were relatively scarce among strawberry crops, camera data shows they spent more time visiting flowers than other insects. Our results demonstrate that a commercial fruit farm is a complex ecosystem influencing pollinator diversity and abundance through a range of factors. We show that monitoring methods may differ in their valuation of relative contributions of insects to crop pollination.

Project description:The standardization of collection and processing methods for rumen samples is crucial to reduce the level of errors that may affect the analysis and interpretation of the data. The aim of this study was to compare two processing methods and their impacts on the microbial community composition analysis, from material that was either immediately frozen or samples that were stored as cell pellets after removing the supernatant prior to freezing. Eight rumen-fistulated Brahman steers received chloroform as an antimethanogenic compound for 21 days. Rumen fluid samples (60 mL per animal) were collected using a probe covered with two layers of cheesecloth at 3 h post feeding at day 0 prior-treatment (control period) and day 21 of treatment. One sub-set of samples were placed in dry ice and stored at -80°C (Method 1) for subsequent DNA extraction, while a second subset of samples was centrifuged, the supernatant removed and the microbial pellet and rumen contents placed in dry ice and stored at -80°C (Method 2) prior to DNA extractions. Phylogenetic based methods (Illumina Miseq) targeting the 16S rRNA gene were used to characterize the bacterial and archaeal communities from both collection methods for the control and treatment periods. The results from this study showed that the chloroform treatment was significantly different for all beta diversity measures regardless of the processing method used. Significant differences in the relative abundances of some bacteria and archaea, such as Elusimicrobia, Fibrobacteres, Lentisphaerae, Spirochaetes, and Verrucomicrobia and Methanomassiliicoccaceae, were observed at higher levels in the Method 2. These microbial populations are known to have fragile cell wall structures and are susceptible to cell lysis. Regardless of the processing method used, both identified the key microbial groups and can be used to compare the relative shifts in the rumen microbiome between treatments. However, immediately freezing samples might alter the abundance of material from species that are more readily lysed and will not be suitable for studies that aim to assign absolute abundance values to these species within the rumen.

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Accessing Dietary Effects on the Rumen Microbiome: Different Sequencing Methods Tell Different Stories.

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