Fecal microbial composition associated with variation in feed efficiency in pigs depends on diet and sex1

Verschuren, L.M.G.; Calus, M.P.L.; Jansman, A.J.M.; Bergsma, R.; Knol, E.F.; Gilbert, Hélène; Zemb, Olivier

doi:10.1093/jas/sky060

Cited by 52 publications

(40 citation statements)

References 43 publications

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“…Barley has been described as favoring Firmicutes and Ruminococcaceae members such as Dialister or Megasphaera [15]; however, we could not find such changes in our study, probably due to the complexity of our diets and the interactions with other ingredients. It is worth to mention, additionally, that greatest divergences on gut microbiota ecosystems between corn-and barley-based diets have been detected at greater differences on cereal proportions and after longer times of administration than in our trial [55].…”

Section: Discussionmentioning

confidence: 54%

Applicability of an Unmedicated Feeding Program Aimed to Reduce the Use of Antimicrobials in Nursery Piglets: Impact on Performance and Fecal Microbiota

López-Colom

Estellé

Bonet

et al. 2020

Animals

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This study aimed to assess the impact of two different feeding programs, including or not antimicrobials, on gut microbiota development at early ages in commercial pigs. For this, 21-day-old weaned piglets were distributed into 12 pens (6 replicates with 26 pigs each) and fed ad libitum until fattening with: standard commercial formula with antibiotics and zinc oxide (2400 ppm) (AB), and alternative unmedicated feed formula (UN). Subsequently, the animals were moved to the fattening unit (F) receiving a common diet. Pigs were weighed, and feed consumption and diarrhea scores registered. Feces were collected on days 9 (pre-starter), 40 (starter) and 72 (fattening) post-weaning and microbial DNA extracted for 16S rDNA sequencing. Piglets fed UN diets had a worse feed efficiency (p < 0.05) than AB during nursery; however, UN pigs spent less time scouring after weaning (p = 0.098). The structure of fecal community evolved with the age of the animals (p = 0.001), and diet also showed to have a role, particularly in the starter period when UN microbiomes clustered apart from AB, resembling the ecosystems found in the fattening animals. Fibrolytic genera (Fibrobacter, Butyrivibrio, Christellansellaceae) were enriched in UN piglets whereas Lactobacillus characterized AB piglets (adjusted p < 0.05). Overall, this alternative feeding program could anticipate the gut development of piglets despite a lower feed efficiency compared to standard medicalized programs.

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Section: Discussionmentioning

confidence: 54%

Applicability of an Unmedicated Feeding Program Aimed to Reduce the Use of Antimicrobials in Nursery Piglets: Impact on Performance and Fecal Microbiota

López-Colom

Estellé

Bonet

et al. 2020

Animals

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“…Step 6: Amplify the variable regions of the 16S rRNA gene with compatible primers and sequence with the Illumina chemistry. Here, we used the 343F and 784R primers and the pipeline described previously (Verschuren et al, 2018). Briefly, the V3V4 region was amplified from purified genomic DNA (gDNA) with the primers F343 and R784 using 30 amplification cycles with an annealing temperature of 65° to produce a 510 bp amplicon, although the exact length varies depending on the organisms.…”

Section: Dna Extraction 16s Sequencing Data Storage and Productimentioning

confidence: 99%

Absolute quantitation of microbes using 16S rRNA gene metabarcoding: A rapid normalization of relative abundances by quantitative PCR targeting a 16S rRNA gene spike‐in standard

et al. 2020

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Metabarcoding of the 16S rRNA gene is commonly used to characterize microbial communities, by estimating the relative abundance of microbes. Here, we present a method to retrieve the concentrations of the 16S rRNA gene per gram of any environmental sample using a synthetic standard in minuscule amounts (100 ppm to 1% of the 16S rRNA sequences) that is added to the sample before DNA extraction and quantified by two quantitative polymerase chain reaction (qPCR) reactions. This allows normalizing by the initial microbial density, taking into account the DNA recovery yield. We quantified the internal standard and the total load of 16S rRNA genes by qPCR. The qPCR for the latter uses the exact same primers as those used for Illumina sequencing of the V3‐V4 hypervariable regions of the 16S rRNA gene to increase accuracy. We are able to calculate the absolute concentration of the species per gram of sample, taking into account the DNA recovery yield. This is crucial for an accurate estimate as the yield varied between 40% and 84%. This method avoids sacrificing a high proportion of the sequencing effort to quantify the internal standard. If sacrificing a part of the sequencing effort to the internal standard is acceptable, we however recommend that the internal standard accounts for 30% of the environmental 16S rRNA genes to avoid the PCR bias associated with rare phylotypes. The method proposed here was tested on a feces sample but can be applied more broadly on any environmental sample. This method offers a real improvement of metabarcoding of microbial communities since it makes the method quantitative with limited efforts.

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“…Microbial DNA was extracted using beat-beating with the Zymo kit from 50 mg of feces sample according to a method described previously [ 14 ]. The V3-V4 region of the 16S rRNA gene was amplified using F460 and R460 primers (F460: , R460: ) and 30 cycles of PCR with an annealing temperature of 65°C.…”

Section: Methodsmentioning

confidence: 99%

“…Dietary fiber content seems to be a major driver of gut microbiota composition [ 13 ]. Numerous studies have already focused on the relationship between dietary fiber and pig gut microbiota [ 8 , 14 , 15 ]: addition of resistant starch increases total bacterial counts and stimulates healthy gut-associated butyrate-producing Faecalibacterium prausnitzii growth in the colon [ 15 ] even though the impact of repeated changes in fiber content in the pig diets has not been evaluated yet.…”

Section: Introductionmentioning

confidence: 99%

Effect of dietary fiber content on nutrient digestibility and fecal microbiota composition in growing-finishing pigs

et al. 2018

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Microbial population in the gastrointestinal tract plays a central role in health and nutrient digestion. The objective of the present study was to investigate the relationships between microbiota and apparent digestibility coefficients with respect to age and diet. Pigs from Large-White, Duroc or Pietrain breeds were raised under the same housing conditions and fed alternately a low-fiber (LF) and a high-fiber diet (HF) during 4 successive 3-week periods. Data collection for digestibility measurements was achieved during the last week of each period. At the end of each period, fecal microbiota was collected for 16S rRNA gene sequencing. The microbiota remained stable across periods whereas digestibility of energy, crude proteins and cell wall components increased. The microbiota was resilient to diet effect and pigs fed the LF diet were discriminated to those fed the HF diet using 31 predicting OTUs with a mean classification error-rate of 3.9%. Clostridiaceae and Turicibacter were negatively correlated whereas Lactobacillus was positively correlated with protein and energy digestibility coefficients in the LF group. In addition, Lachnospiraceae and Prevotella were negatively correlated with cell wall component digestibility. In contrast, no significant correlation was found between microbiota composition and digestibility coefficients when pigs were fed the HF diet. Interestingly, it was also no longer possible to distinguish animals from different breeds once the animals were fed a HF diet, so that the microbiota could only trace the breed origin in the first period and in the LF group. In our experimental conditions, 3 weeks of adaptation to a new diet seems to be sufficient to observe resilience in growing pigs’ microbiota. We demonstrated that fecal microbiota can be used to classify pigs according to their dietary treatment. Some bacteria are favorable or unfavorable to digestibility. This suggests that manipulations of bacterial populations can improve digestibility and feed efficiency.

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Fecal microbial composition associated with variation in feed efficiency in pigs depends on diet and sex1

Cited by 52 publications

References 43 publications

Applicability of an Unmedicated Feeding Program Aimed to Reduce the Use of Antimicrobials in Nursery Piglets: Impact on Performance and Fecal Microbiota

Applicability of an Unmedicated Feeding Program Aimed to Reduce the Use of Antimicrobials in Nursery Piglets: Impact on Performance and Fecal Microbiota

Absolute quantitation of microbes using 16S rRNA gene metabarcoding: A rapid normalization of relative abundances by quantitative PCR targeting a 16S rRNA gene spike‐in standard

Effect of dietary fiber content on nutrient digestibility and fecal microbiota composition in growing-finishing pigs

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