The Effect of a High-Grain Diet on the Rumen Microbiome of Goats with a Special Focus on Anaerobic Fungi

Fliegerová, K.; Podmirseg, Sabine Marie; Vinzelj, Julia; Grilli, Diego; Kvasnová, Simona; Schierová, Dagmar; Sechovcová, Hana; Mrázek, Jakub; Siddi, Giuliana; Arenas, Graciela Nora; Moniello, Giuseppe

doi:10.3390/microorganisms9010157

Cited by 17 publications

(12 citation statements)

References 95 publications

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“…In the current study, all sequences were clustered into three genera with validly published names and an unknown genus, and nine species with validly published names and two unknown species. Moreover, we found that Methanobacter was the most dominant genus in goat rumen, which is consistent with the previously reported results in buffaloes (Kala et al, 2020 ), goats (Fliegerova et al, 2021 ), sheep (McLoughlin et al, 2020 ), and beef cattle (Paul et al, 2017 ). The most dominant archaeal species was Methanobrevibacter sp.…”

Section: Discussionsupporting

confidence: 92%

Effect of dietary peNDF levels on digestibility and rumen fermentation, and microbial community in growing goats

Zhou

Xue

et al. 2022

Front. Microbiol.

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Physically effective neutral detergent fiber (peNDF) is a concept that accounts for the particle length of NDF in diets, sustaining the normal chewing behavior and rumen fermentation of ruminants. Specifically, peNDF>1.18 is the commonest one that is calculated from NDF and the percentage of feed dry matter left on the 1.18, 8.00, and 19.00 mm sieves. This study aimed to investigate the effects of different levels of peNDF>1.18 on the rumen microbiome and its correlation with nutrient digestibility and rumen fermentation in goats. A total of 30 Lezhi black goats were randomized and blocked to five dietary treatments (n = 6). All the diets were identical in composition but varied in hay lengths, leading to the different peNDF>1.18 content of the diets: 32.97, 29.93, 28.14, 26.48, and 24.75%. The results revealed that the nutrient digestibility increased when dietary peNDF>1.18 levels decreased from 32.97% to 28.14%, with the highest digestibility at 28.14% peNDF>1.18 treatment, after which nutrient digestibility decreased with the decreasing of dietary peNDF levels. Ruminal NH3-N concentrations in the 29.93% and 28.14% groups were higher than that in the 24.75% group (p < 0.05). Ruminal microbial protein concentration was the highest in the 32.97% group (p < 0.05). Daily CH4 production in the 32.97% and 24.75% peNDF>1.18 treatments was lower than that in the 26.48% group (p < 0.05) and no differences were observed among other groups. The relative abundance of rumen fungi at the phylum and genus levels and archaea at the species were affected by dietary peNDF>1.18 content. In conclusion, decreasing dietary peNDF>1.18 levels within a certain range can improve nutrient digestibility and change the rumen microbial community structure of goats. Dietary peNDF>1.18 level should be 28.14% (roughage length around 1 cm) among the five levels for 4 months Lezhi black goats with the purpose of optimal nutrient digestibility.

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Section: Discussionsupporting

confidence: 92%

Effect of dietary peNDF levels on digestibility and rumen fermentation, and microbial community in growing goats

Zhou

Xue

et al. 2022

Front. Microbiol.

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“…These inconsistencies on phylum level might be due to differences in primers used for sequencing. Nowadays, both the ITS region and LSU (28S rRNA gene; D1/D2) region have been recommended as the universal DNA barcode marker for fungi [ 11 ]. However, a sufficient reference database is lacking for LSU taxonomic marker genes so far [ 5 ].…”

Section: Discussionmentioning

confidence: 99%

“…The fungal ribosomal RNA (rRNA) operon-based analysis has facilitated the understanding of the diversity and phylogenetic relationships of gut fungi in natural ecosystems [ 9 ]. The internal transcribed spacer (ITS) region is usually recommended as the DNA barcode marker for gut fungi [ 10 , 11 ]. In addition, the 28S ribosomal large subunit (28S rRNA gene (LSU); D1/D2 region) might render higher coverage of early diverging lineages of fungi, such as Neocallimastigomycota , Chytridiomycota , and Mucoromycota [ 11 ].…”

Section: Introductionmentioning

confidence: 99%

“…The internal transcribed spacer (ITS) region is usually recommended as the DNA barcode marker for gut fungi [ 10 , 11 ]. In addition, the 28S ribosomal large subunit (28S rRNA gene (LSU); D1/D2 region) might render higher coverage of early diverging lineages of fungi, such as Neocallimastigomycota , Chytridiomycota , and Mucoromycota [ 11 ]. However, there is still a big challenge of how to relate LSU taxonomic sequences to the clades that until now only contained “unculturable representatives” derived ITS1 sequences [ 5 , 12 ].…”

Section: Introductionmentioning

confidence: 99%

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The Fibrolytic Enzyme Profiles and the Composition of Fungal Communities in Donkey Cecum-Colon Ecosystem

Zhang¹,

Wang²,

Huang³

et al. 2022

Animals

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The fibrolytic enzymes and the hindgut fungi in donkey cecum-colon ecosystem play an important role in dietary fiber digestion. A better understanding of the fibrolytic enzyme profiles and the fungal community along donkey caecum and colon is key for optimizing hindgut function. In the present study, the fibrolytic enzyme activities within donkey caecum and colon were firstly measured by spectrophotometry. Activities of carboxymethyl cellulase, avicelase, xylanase, and acetyl esterase were greater in donkey dorsal colon than in caecum, indicating that the colon microorganisms may be more efficient in producing fibrolytic enzymes compared to caecum microbes. The fungal community composition along donkey hindgut was determined by sequencing ITS region using Illumina MiSeq. Three fungal phyla were identified by sequence comparison: Ascomycota (66.8%–74.4%), Basidiomycota (21.6%–30.9%), and Neocallimastigomycota (0.9%–3.3%). The Aspergillus, Wallemia, Phanerochaete, Fusarium, and Penicillium were detected as the dominant genera, but their metabolic and functional significance in donkey cecum-colon ecosystem need further investigation. In terms of the anaerobic fungi Neocallimastigomycota, its abundance was greater in donkey colon than in caecum (p < 0.05), indicating that the donkey hindgut region was associated with differences in fungal community composition. Moreover, the relative abundance of enzymes related to plant cell wall degradation were predicted by PICRUSt, and they were also lower in caecum than in colon. The present study provided new information about fibrolytic enzyme profiles and fungal composition in donkey hindgut ecosystem.

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“…Great attention is paid to the study of rumen microorganisms because their composition affects productivity, the quality of meat and dairy products, and the health status of animals. The diversity and structure of the rumen microbiota is influenced by several factors, including diet [ 7 , 8 , 9 , 10 , 11 , 12 , 13 ], ruminant species [ 7 , 14 , 15 , 16 ], age [ 17 , 18 , 19 , 20 ], geographic location [ 21 ], type of production system, and host genotype [ 22 , 23 , 24 ]. The influence of each factor cannot be precisely quantified, but studies performed on large numbers of animals suggest that diet is a critical factor in shaping the rumen microbial ecosystem [ 7 , 25 ].…”

Section: Introductionmentioning

confidence: 99%

Host Species Affects Bacterial Evenness, but Not Diversity: Comparison of Fecal Bacteria of Cows and Goats Offered the Same Diet

Mahayri

Fliegerová

Mattiello

et al. 2022

Animals

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The aim of this study was to compare the diversity and composition of fecal bacteria in goats and cows offered the same diet and to evaluate the influence of animal species on the gut microbiome. A total of 17 female goats (Blond Adamellan) and 16 female cows (Brown Swiss) kept on an organic farm were fed pasture and hay. Bacterial structure in feces was examined by high-throughput sequencing using the V4–V5 region of the 16S rRNA gene. The Alpha diversity measurements of the bacterial community showed no statistical differences in species richness and diversity between the two groups of ruminants. However, the Pielou evenness index revealed a significant difference and showed higher species evenness in cows compared to goats. Beta diversity measurements showed statistical dissimilarities and significant clustering of bacterial composition between goats and cows. Firmicutes were the dominant phylum in both goats and cows, followed by Bacteroidetes, Proteobacteria, and Spirochaetes. Linear discriminant analysis with effect size (LEfSe) showed a total of 36 significantly different taxa between goats and cows. Notably, the relative abundance of Ruminococcaceae UCG-005, Christensenellaceae R-7 group, Ruminococcaceae UCG-010, Ruminococcaceae UCG-009, Ruminococcaceae UCG-013, Ruminococcaceae UCG-014, Ruminococcus 1, Ruminococcaceae UCG-002, Lachnospiraceae NK4A136 group, Treponema 2, Lachnospiraceae AC2044 group, and Bacillus was higher in goats compared to cows. In contrast, the relative abundance of Turicibacter, Solibacillus, Alloprevotella, Prevotellaceae UCG-001, Negativibacillus, Lachnospiraceae UCG-006, and Eubacterium hallii group was higher in cows compared with goats. Our results suggest that diet shapes the bacterial community in feces, but the host species has a significant impact on community structure, as reflected primarily in the relative abundance of certain taxa.

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The Effect of a High-Grain Diet on the Rumen Microbiome of Goats with a Special Focus on Anaerobic Fungi

Cited by 17 publications

References 95 publications

Effect of dietary peNDF levels on digestibility and rumen fermentation, and microbial community in growing goats

Effect of dietary peNDF levels on digestibility and rumen fermentation, and microbial community in growing goats

The Fibrolytic Enzyme Profiles and the Composition of Fungal Communities in Donkey Cecum-Colon Ecosystem

Host Species Affects Bacterial Evenness, but Not Diversity: Comparison of Fecal Bacteria of Cows and Goats Offered the Same Diet

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