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Associative patterns among anaerobic fungi, methanogenic archaea, and bacterial communities in response to changes in diet and age in the rumen of dairy cows.

Kumar S, Indugu N, Vecchiarelli B, Pitta DW - Front Microbiol (2015)

Bottom Line: Among ARF, several lineages were unclassified, however, phylum Neocallimastigomycota showed the presence of three known genera.Abundance of Cyllamyces and Caecomyces shifted with diet, whereas Orpinomyces was influenced by both diet and age.Methanobrevibacter constituted the most dominant archaeal genus across all samples.

View Article: PubMed Central - PubMed

Affiliation: Agriculture Systems and Microbial Genomics Laboratory, Department of Clinical Studies, New Bolton Center, School of Veterinary Medicine, University of Pennsylvania, Kennett Square, PA USA.

ABSTRACT
The rumen microbiome represents a complex microbial genetic web where bacteria, anaerobic rumen fungi (ARF), protozoa and archaea work in harmony contributing to the health and productivity of ruminants. We hypothesized that the rumen microbiome shifts as the dairy cow advances in lactations and these microbial changes may contribute to differences in productivity between primiparous (first lactation) and multiparous (≥second lactation) cows. To this end, we investigated shifts in the ruminal ARF and methanogenic communities in both primiparous (n = 5) and multiparous (n = 5) cows as they transitioned from a high forage to a high grain diet upon initiation of lactation. A total of 20 rumen samples were extracted for genomic DNA, amplified using archaeal and fungal specific primers, sequenced on a 454 platform and analyzed using QIIME. Community comparisons (Bray-Curtis index) revealed the effect of diet (P < 0.01) on ARF composition, while archaeal communities differed between primiparous and multiparous cows (P < 0.05). Among ARF, several lineages were unclassified, however, phylum Neocallimastigomycota showed the presence of three known genera. Abundance of Cyllamyces and Caecomyces shifted with diet, whereas Orpinomyces was influenced by both diet and age. Methanobrevibacter constituted the most dominant archaeal genus across all samples. Co-occurrence analysis incorporating taxa from bacteria, ARF and archaea revealed syntrophic interactions both within and between microbial domains in response to change in diet as well as age of dairy cows. Notably, these interactions were numerous and complex in multiparous cows, supporting our hypothesis that the rumen microbiome also matures with age to sustain the growing metabolic needs of the host. This study provides a broader picture of the ARF and methanogenic populations in the rumen of dairy cows and their co-occurrence implicates specific relationships between different microbial domains in response to diet and age.

No MeSH data available.


Phylogenetic composition of (A) anaerobic fungi and (B) Methanogenic Archaea based on study group and diet. Sample identifiers are same as used in Figure 1.
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Figure 3: Phylogenetic composition of (A) anaerobic fungi and (B) Methanogenic Archaea based on study group and diet. Sample identifiers are same as used in Figure 1.

Mentions: In the family Neocallimastigaceae we identified three known major genera (Caeocomyces, Cyllamyces, and Orpinomyces) in addition to the large contribution (40–75%) of unclassified members (Figure 3A). In primiparous cows, Caecomyces and Cyllamyces together constituted 25% of the total identified anaerobic fungi in cows fed the D1 diet. In the D2 diet the proportion of Cyllamyces remained unchanged; however, Caeocomyces was completely replaced by Orpinomyces and other unclassified genera. Multiparous cows were similar to primiparous cows on D1 diets except for the presence of Orpinomyces (~5%). However, on the D2 diet, the proportion of the genus Cyllamyces increased substantially (45%) at the expense of Caecomyces, Orpinomyces, and unclassified Neocallimastigaceae taxa. Among archaea, the phylum Euryarchaeota included Vadin CA11 (0.01–0.07%), along with the genera Methanobrevibacter and Methanosphaera which together constituted >98% of the archaeal abundance. In both diets (D1 and D2) and study groups (primiparous and multiparous), Methanobrevibacter was the most dominant genus accounting for nearly 94–98% abundance. Although genus Methanosphaera was present in both groups, its abundance was slightly higher (4.5%) in primiparous than in multiparous cows (3.0%), in particular those on the D2 diet (Figure 3B).


Associative patterns among anaerobic fungi, methanogenic archaea, and bacterial communities in response to changes in diet and age in the rumen of dairy cows.

Kumar S, Indugu N, Vecchiarelli B, Pitta DW - Front Microbiol (2015)

Phylogenetic composition of (A) anaerobic fungi and (B) Methanogenic Archaea based on study group and diet. Sample identifiers are same as used in Figure 1.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4521595&req=5

Figure 3: Phylogenetic composition of (A) anaerobic fungi and (B) Methanogenic Archaea based on study group and diet. Sample identifiers are same as used in Figure 1.
Mentions: In the family Neocallimastigaceae we identified three known major genera (Caeocomyces, Cyllamyces, and Orpinomyces) in addition to the large contribution (40–75%) of unclassified members (Figure 3A). In primiparous cows, Caecomyces and Cyllamyces together constituted 25% of the total identified anaerobic fungi in cows fed the D1 diet. In the D2 diet the proportion of Cyllamyces remained unchanged; however, Caeocomyces was completely replaced by Orpinomyces and other unclassified genera. Multiparous cows were similar to primiparous cows on D1 diets except for the presence of Orpinomyces (~5%). However, on the D2 diet, the proportion of the genus Cyllamyces increased substantially (45%) at the expense of Caecomyces, Orpinomyces, and unclassified Neocallimastigaceae taxa. Among archaea, the phylum Euryarchaeota included Vadin CA11 (0.01–0.07%), along with the genera Methanobrevibacter and Methanosphaera which together constituted >98% of the archaeal abundance. In both diets (D1 and D2) and study groups (primiparous and multiparous), Methanobrevibacter was the most dominant genus accounting for nearly 94–98% abundance. Although genus Methanosphaera was present in both groups, its abundance was slightly higher (4.5%) in primiparous than in multiparous cows (3.0%), in particular those on the D2 diet (Figure 3B).

Bottom Line: Among ARF, several lineages were unclassified, however, phylum Neocallimastigomycota showed the presence of three known genera.Abundance of Cyllamyces and Caecomyces shifted with diet, whereas Orpinomyces was influenced by both diet and age.Methanobrevibacter constituted the most dominant archaeal genus across all samples.

View Article: PubMed Central - PubMed

Affiliation: Agriculture Systems and Microbial Genomics Laboratory, Department of Clinical Studies, New Bolton Center, School of Veterinary Medicine, University of Pennsylvania, Kennett Square, PA USA.

ABSTRACT
The rumen microbiome represents a complex microbial genetic web where bacteria, anaerobic rumen fungi (ARF), protozoa and archaea work in harmony contributing to the health and productivity of ruminants. We hypothesized that the rumen microbiome shifts as the dairy cow advances in lactations and these microbial changes may contribute to differences in productivity between primiparous (first lactation) and multiparous (≥second lactation) cows. To this end, we investigated shifts in the ruminal ARF and methanogenic communities in both primiparous (n = 5) and multiparous (n = 5) cows as they transitioned from a high forage to a high grain diet upon initiation of lactation. A total of 20 rumen samples were extracted for genomic DNA, amplified using archaeal and fungal specific primers, sequenced on a 454 platform and analyzed using QIIME. Community comparisons (Bray-Curtis index) revealed the effect of diet (P < 0.01) on ARF composition, while archaeal communities differed between primiparous and multiparous cows (P < 0.05). Among ARF, several lineages were unclassified, however, phylum Neocallimastigomycota showed the presence of three known genera. Abundance of Cyllamyces and Caecomyces shifted with diet, whereas Orpinomyces was influenced by both diet and age. Methanobrevibacter constituted the most dominant archaeal genus across all samples. Co-occurrence analysis incorporating taxa from bacteria, ARF and archaea revealed syntrophic interactions both within and between microbial domains in response to change in diet as well as age of dairy cows. Notably, these interactions were numerous and complex in multiparous cows, supporting our hypothesis that the rumen microbiome also matures with age to sustain the growing metabolic needs of the host. This study provides a broader picture of the ARF and methanogenic populations in the rumen of dairy cows and their co-occurrence implicates specific relationships between different microbial domains in response to diet and age.

No MeSH data available.