Distinct commensal bacteria associated with ingesta and mucosal epithelium in the gastrointestinal tracts of calves and chickens

Malmuthuge, Nilusha; Li, Meiju; Chen, Yanhong; Fries, Patrick; Griebel, Philip; Baurhoo, B.; Zhao, Xin; Guan, Le Luo

doi:10.1111/j.1574-6941.2011.01220.x

Cited by 67 publications

(68 citation statements)

References 42 publications

(52 reference statements)

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“…In addition, the species richness (Chao1 index) was also higher in the mucosaassociated communities of the jejunum, ileum, and cecum than in the respective digesta. The higher species richness observed for the mucosa-associated communities is in agreement with our previous study conducted with the same samples but using PCR-DGGE (9). The association of mucosal bacteria with the expression of TLR2 and TLR4 in the colons of mice (10) suggests that mucosaassociated bacteria may play an important role in stimulating host immune responses through pattern recognition receptors.…”

Section: Discussionsupporting

confidence: 79%

“…The distribution of OTUs obtained via pyrosequencing of mucosal tissue and digesta samples from the length of the GIT of 3-week-old preweaned calves in the present study was similar to that of bacterial phylotypes obtained via PCR-DGGE (PCR-denaturing gradient gel electrophoresis) profiling of the same samples in our previous study (9). The taxonomy analysis conducted in the present study was based on pooled samples from 8 animals.…”

Section: Discussionsupporting

confidence: 52%

“…This was a companion study conducted using samples collected from 3-week-old Holstein bull calves used in our previous study (9). One-week-old bull calves (n ϭ 8) were purchased from a commercial dairy farm and housed at the Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan.…”

Section: Methodsmentioning

confidence: 99%

“…These changes include the appearance of new species such as Ruminococcus flavefaciens and Fibrobacter species and the disappearance of Bifidobacterium, Enterobacteriaceae, Streptococcus, and Lactobacillus species (8), suggesting that both diet and gut development may drive changes in the bacterial composition during early life. A study comparing mucosa-and digesta-associated bacterial phylotypes in preweaned calves revealed a much greater richness in mucosa-associated bacterial phylotypes throughout the GIT than in those in the regional digesta (9). Moreover, mucosa-associated bacteria in the murine distal colon not only differed significantly from fecal bacteria but also correlated with Toll-like receptor 2 (TLR2) and TLR4 gene expression in colon epithelial cells (10).…”

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confidence: 99%

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Taxonomic Identification of Commensal Bacteria Associated with the Mucosa and Digesta throughout the Gastrointestinal Tracts of Preweaned Calves

Malmuthuge

Griebel

Guan

2014

Appl Environ Microbiol

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Bacterial colonization in the gastrointestinal tracts (GIT) of preweaned calves is very important, since it can influence early development and postweaning performance and health. This study investigated the composition of the bacteria along the GIT (rumen, jejunum, ileum, cecum, and colon) of preweaned bull calves (3 weeks old) using pyrosequencing to understand the segregation of bacteria between the mucosal surface and digesta. Phylogenetic analysis revealed that a total of 83 genera belonging to 13 phyla were distributed throughout the GIT of preweaned calves, with the Firmicutes, Bacteroidetes, and Proteobacteria predominating. Quantitative PCR (qPCR) analysis of selected abundant bacterial genera (Prevotella, Bacteroides, Lactobacillus, and Faecalibacterium) revealed that their prevalence was significantly different among the GIT regions and between mucosa-and digesta-associated communities. Rumens contained the most diverse bacterial population, consisting of 47 genera, including 16 rumen-specific genera, followed by the large intestine and then the small intestine. Bacterial species richness was higher at the mucosal surface than in the local digesta, with the exception of the rumen. The majority of bacteria found on the rumen epithelial surface and within the small intestine could not be identified due to a lack of known genus-level information. Thus, future studies will be required to fully characterize the microbiome during the development of the rumens and the mucosal immune systems of newborn calves. This is the first study to analyze in depth the bacterial composition of the GIT microbiome in preweaned calves, which extends previous findings regarding early rumen colonization and bacterial segregation between mucosa-and digesta-associated microbial communities.T he gastrointestinal tracts (GIT) of newborns contain a less diverse microbiome than those of adults, and progressive colonization over time increases this diversity (1). Based on the fecal microbiomes of infants, the pioneer gut bacteria are comprised of facultative anaerobes such as Staphylococcus, Streptococcus, Enterococcus, and Enterobacteriaceae spp. during the first few days of life (2). These species create the reduced environment that is required for obligate anaerobic gut microbes (3). Besides the facultative anaerobes, anaerobic Bifidobacterium species are also present at high levels in the guts of 1-week-old neonates (3). An increasing number of studies are investigating microbial establishment and the factors influencing this process in newborn livestock, such as dairy calves. A recent study reported a link between the prevalence of Faecalibacterium during the first week of life and body weight gain as well as diarrhea incidences in 4-week-old calves (4). This suggests a potential role for gut bacteria in both animal health and production. Evidence is also emerging that the initial acquisition of and continuous exposure to microbes result in a host-specific gut microbiome, which plays a vital role in the maturation of the mucosa...

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Section: Discussionsupporting

confidence: 79%

Section: Discussionsupporting

confidence: 52%

Section: Methodsmentioning

confidence: 99%

mentioning

confidence: 99%

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Taxonomic Identification of Commensal Bacteria Associated with the Mucosa and Digesta throughout the Gastrointestinal Tracts of Preweaned Calves

Malmuthuge

Griebel

Guan

2014

Appl Environ Microbiol

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199

220

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“…In our study, the effects of age on rumen epithelial bacterial diversity were compared using different groups of kids, which also accounted for the variation. Moreover, total epithelial bacterial populations for alfalfa hay-and oat-fed dairy calves (30), hay-fed sheep (31), and concentrate-and freshgrass-fed goat kids (this study) ranged from 4.4 ϫ 10 9 to 4.2 ϫ 10 10 , 4.4 ϫ 10 7 to 2.2 ϫ 10 8 , and 1.4 ϫ 10 8 to 4.4 ϫ 10 7 copy numbers per g of wet tissue, respectively. Besides the differences in model animals, diet, the DNA extraction method, and PCR primers and conditions, the host might also be an important determinant in regulating bacterial density.…”

Section: Figmentioning

confidence: 99%

Taxonomic Identification of Ruminal Epithelial Bacterial Diversity during Rumen Development in Goats

Jiao

Huang

Zhou

et al. 2015

Appl Environ Microbiol

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bUnderstanding of the colonization process of epithelial bacteria attached to the rumen tissue during rumen development is very limited. Ruminal epithelial bacterial colonization is of great significance for the relationship between the microbiota and the host and can influence the early development and health of the host. MiSeq sequencing of 16S rRNA genes and quantitative realtime PCR (qPCR) were applied to characterize ruminal epithelial bacterial diversity during rumen development in this study. Seventeen goat kids were selected to reflect the no-rumination (0 and 7 days), transition (28 and 42 days), and rumination (70 days) phases of animal development. Alpha diversity indices (operational taxonomic unit [OTU] numbers, Chao estimate, and Shannon index) increased (P < 0.01) with age, and principal coordinate analysis (PCoA) revealed that the samples clustered together according to age group. Phylogenetic analysis revealed that Proteobacteria, Firmicutes, and Bacteroidetes were detected as the dominant phyla regardless of the age group, and the abundance of Proteobacteria declined quadratically with age (P < 0.001), while the abundances of Bacteroidetes (P ‫؍‬ 0.088) and Firmicutes (P ‫؍‬ 0.009) increased with age. At the genus level, Escherichia (80.79%) dominated at day zero, while Prevotella, Butyrivibrio, and Campylobacter surged (linearly; P < 0.01) in abundance at 42 and 70 days. qPCR showed that the total copy number of epithelial bacteria increased linearly (P ‫؍‬ 0.013) with age. In addition, the abundances of the genera Butyrivibrio, Campylobacter, and Desulfobulbus were positively correlated with rumen weight, rumen papilla length, ruminal ammonia and total volatile fatty acid concentrations, and activities of carboxymethylcellulase (CMCase) and xylanase. Taking the data together, colonization by ruminal epithelial bacteria is age related (achieved at 2 months) and might participate in the anatomic and functional development of the rumen. R ecent years have witnessed growing interest in the diversity and function of ruminal epithelial bacteria. It has been demonstrated that ruminal epithelial bacteria are involved in oxygen scavenging, tissue recycling, and urea digestion (1). Furthermore, in steers, the ruminal epithelial bacterial communities of acidosisresistant and acidosis-susceptible groups were different during subacute ruminal acidosis development, and this difference could be recognized by the host TLRs (Toll-like receptors), which are associated with changes in the function of the rumen epithelial tissue barrier (2). Similarly, in the mouse colon, epithelial bacterial diversity correlated with TLR2 and TLR4 gene expression (3). These findings reveal that since epithelial bacteria are directly attached to the epithelial surface, their end products may play a direct or indirect role in host immune responses and tissue barrier function.Ruminal epithelial bacteria are distinctly different at the taxonomic level from bacteria associated with rumen contents (4, 5). By use of culture-based tech...

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Metagenomic assessment of the Cebus apella gut microbiota

Firrman

Liu

Tanes

et al. 2019

American J Primatol

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Cebus Apella (C. apella) is a species of Nonhuman Primate (NHP) used for biomedical research because it is phylogenetically similar and shares anatomical commonalities with humans. Here, the gut microbiota of three C. apella were examined in the different regions of the intestinal tract. Using metagenomics, the gut microbiota associated with the luminal content and mucus layer for each intestinal region was identified, and functionality was investigated by quantifying the levels of short chain fatty acids (SCFAs) produced. The results of this study show a high degree of similarity in the intestinal communities among C. apella subjects, with multiple shared characteristics. First, the communities in the lumen were more phylogenetically diverse and rich compared to the mucus layer communities throughout the entire intestinal tract. The small intestine communities in the lumen displayed a higher Shannon diversity index compared to the colon communities. Second, all the communities were dominated by aero-tolerant taxa such as Streptococcus, Enterococcus, Abiotrophia, and Lactobacillus, although there was preferential colonization of specific taxa observed. Finally, the primary SCFA produced throughout the intestinal tract was acetic acid, with some propionic acid and butyric acid detected in the colon regions. The small intestine microbiota produced significantly less SCFAs compared to the communities in the colon. Collectively, these data provide an in-depth report on the composition, distribution, and SCFA production of the gut microbiota along the intestinal tract of the C. apella NHP animal model. K E Y W O R D SCebus apella, gut microbiota, in vivo studies, intestinal tract, primate research, tufted capuchin

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Distinct commensal bacteria associated with ingesta and mucosal epithelium in the gastrointestinal tracts of calves and chickens

Cited by 67 publications

References 42 publications

Taxonomic Identification of Commensal Bacteria Associated with the Mucosa and Digesta throughout the Gastrointestinal Tracts of Preweaned Calves

Taxonomic Identification of Commensal Bacteria Associated with the Mucosa and Digesta throughout the Gastrointestinal Tracts of Preweaned Calves

Taxonomic Identification of Ruminal Epithelial Bacterial Diversity during Rumen Development in Goats

Metagenomic assessment of the Cebus apella gut microbiota

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