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MBio Jul 2024Copious amounts of methane, a major constituent of greenhouse gases currently driving climate change, are emitted by livestock, and efficient methods that curb such...
UNLABELLED
Copious amounts of methane, a major constituent of greenhouse gases currently driving climate change, are emitted by livestock, and efficient methods that curb such emissions are urgently needed to reduce global warming. When fed to cows, the red seaweed (AT) can reduce enteric methane emissions by up to 80%, but the achieved results can vary widely. Livestock produce methane as a byproduct of methanogenesis, which occurs during the breakdown of feed by microbes in the rumen. The ruminant microbiome is a diverse ecosystem comprising bacteria, protozoa, fungi, and archaea, and methanogenic archaea work synergistically with bacteria to produce methane. Here, we find that an effective reduction in methane emission by high-dose AT (0.5% dry matter intake) was associated with a reduction in methanol-utilizing within the rumen, suggesting that they may play a greater role in methane formation than previously thought. However, a later spike in suggested an acquired resistance, possibly via the reductive dehalogenation of bromoform. While we found that AT inhibition of methanogenesis indirectly impacted ruminal bacteria and fermentation pathways due to an increase in spared H, we also found that an increase in butyrate synthesis was due to a direct effect of AT on butyrate-producing bacteria such as , and . Together, our findings provide several novel insights into the impact of AT on both methane emissions and the microbiome, thereby elucidating additional pathways that may need to be targeted to maintain its inhibitory effects while preserving microbiome health and animal productivity.
IMPORTANCE
Livestock emits copious quantities of methane, a major constituent of the greenhouse gases currently driving climate change. Methanogens within the bovine rumen produce methane during the breakdown of feed. While the red seaweed (AT) can significantly reduce methane emissions when fed to cows, its effects appear short-lived. This study revealed that the effective reduction of methane emissions by AT was accompanied by the near-total elimination of methane-generating . However, populations subsequently rebounded due to their ability to inactivate bromoform, a major inhibitor of methane formation found in AT. This study presents novel findings on the contribution of to ruminal methanogenesis, the mode of action of AT, and the possibility for complementing different strategies to effectively curb methane emissions.
PubMed: 38953639
DOI: 10.1128/mbio.00782-24 -
Frontiers in Microbiology 2024[This corrects the article DOI: 10.3389/fmicb.2024.1334045.].
[This corrects the article DOI: 10.3389/fmicb.2024.1334045.].
PubMed: 38952449
DOI: 10.3389/fmicb.2024.1433047 -
Journal of Dairy Science Jun 2024Microbes play an important role in human and animal health as well as animal productivity. The host microbial interactions within ruminants play a critical role in...
Microbes play an important role in human and animal health as well as animal productivity. The host microbial interactions within ruminants play a critical role in animal health and productivity and provide up to 70% of the animal's energy need in the form of fermentation products. As such, many studies have investigated microbial community composition to understand microbial community changes and factors that affect microbial colonization and persistence. The advances in next generation sequencing (NGS) technologies and low cost of sequencing have gravitated many studies to utilize 16S rDNA-based analysis tools for interrogation of microbiomes at a much finer scale than traditional culturing. However, such methods that rely on single base pair differences for bacterial taxa clustering may inflate or underestimate diversity leading to inaccurate identification of bacterial diversity. Therefore, in this study, we sequenced mock communities of known membership and abundance to establish filtration parameters to reduce inflation of microbial diversity due to PCR and sequencing errors. Additionally, we evaluated the effect of the resulting filtering parameters proposed using established bioinformatic pipelines on a study consisting of Holstein and Jersey cattle to identify bread and treatment effects on the bacterial community composition and the impact of the filtering on global microbial community structure analysis and results. Filtration resulted in a sharp reduction in bacterial taxa identified, yet retain most sequencing data (retaining > 79% of sequencing reads) when analyzed using 3 different microbial analysis pipelines (DADA2, Mothur, USEARCH). After filtration, conclusions from α and β-diversity tests show very similar results across all analysis methods. The mock community-based filtering parameters proposed in this study help provide a more realistic estimation of bacterial diversity. Additionally, the filtration reduced the variation between microbiome analysis methods and help identify microbial community differences that could have been missed due to large animal to animal variation observed in the unfiltered data. As such, we believe, the new filtering parameters described in this study will help obtain diversity estimates closer to realistic values and will improve the ability of detecting microbial community differences and help better understand microbial community changes in 16S rDNA-based studies.
PubMed: 38945268
DOI: 10.3168/jds.2023-24479 -
Journal of Dairy Science Jun 2024The aims of this research were to evaluate how prolonged feeding of a high-concentrate diet affects the ruminal degradation kinetics of fiber and starch, and to evaluate...
The aims of this research were to evaluate how prolonged feeding of a high-concentrate diet affects the ruminal degradation kinetics of fiber and starch, and to evaluate the effects of the high-concentrate diet on apparent total-tract nutrient digestibility in dairy cows. We also investigated the dysbiotic effects and the remodeling of the hindgut microbiome with prolonged high-concentrate feeding. Nine Holstein cows were used in 2 experimental periods; in each period, cows were first fed a 100% forage diet (Forage) for 1 week, followed by stepwise adaptation during one week to a high-concentrate diet (HC; 65% concentrate), which was then fed for 4 consecutive weeks. The kinetics of in situ ruminal degradability of grass silage (DM and NDF), corn grain and wheat grain (DM and starch) as well as the apparent total-tract nutrient digestibility were evaluated in the Forage feeding and in wk 4 on HC. Whereas the hindgut microbiome and fermentation profile were evaluated on a weekly basis. Regarding the in situ ruminal degradability due to grain type, the rate of degradation of the potentially degradable fraction of the grain and the effective rumen degradability of wheat grain were greater compared with corn grain. The in situ ruminal degradability of NDF decreased with the HC diet. However, the apparent total-tract digestibility of crude protein, fat, starch, NDF, ADF and NFC increased with HC compared with Forage feeding. In addition, the HC diet increased the concentration of short-chain fatty acids in the hindgut, lowering fecal pH by 0.6 units, which correlated positively with microbial α diversity. This resulted in lower α diversity with HC; however, α diversity (number of ASVs) showed recovery in wk 3 and 4 on HC; in addition, microbial β diversity did not change from wk 2 on HC onwards. Two microbial enterotypes were identified: one for the Forage diet with abundance of Akkermansia and Anaerosporobacter, and another enterotype for the HC diet with enrichment in Bifidobacterium and Butyrivibrio. Overall, results show that major microbial shifts and hindgut dysbiosis occurred in wk 1 on HC. However, the hindgut microbial diversity of cows adapted after 3 weeks of consuming the starch-rich ration. Thus, feeding HC diet impaired fiber degradation in the rumen, but increased apparent total-tract nutrient digestibility. Likely, the forage diet contained less digestible NDF than the HC diet due to greater inclusion of forages with lower NDF digestibility and lower inclusion of more digestible non-forage NDF. Results also suggest that the adaptation of the hindgut microbial diversity of cows observed 3 weeks after the diet transition likely contributed to enhance total-tract nutrient digestibility.
PubMed: 38945264
DOI: 10.3168/jds.2024-24919 -
Animal Microbiome Jun 2024Pinus koraiensis cone essential oil (PEO) contains functional compounds such as monoterpene hydrocarbons, and the administration of PEO reduced methane (CH) emissions...
Metataxonomic and metabolomic profiling revealed Pinus koraiensis cone essential oil reduced methane emission through affecting ruminal microbial interactions and host-microbial metabolism.
BACKGROUND
Pinus koraiensis cone essential oil (PEO) contains functional compounds such as monoterpene hydrocarbons, and the administration of PEO reduced methane (CH) emissions during growing phase of goats. However, the mode of action of PEO driven CH reduction is not known, especially how the administration of PEO can affect rumen microbiota and host metabolism in goats during the fattening phase. This study aimed to elucidate the potential microbial and host responses PEO supplementation in goats using metataxonomics (prokaryotes and protozoa) and metabolomics (rumen fluid and serum).
RESULTS
Ten fattening Korean native goats were divided into two dietary groups: control (CON; basal diet without additives) and PEO (basal diet + 1.5 g/d of PEO) with a 2 × 2 crossover design and the treatment lasted for 11 weeks. Administration of PEO reduced CH concentrations in the exhaled gas from eructation by 12.0-13.6% (P < 0.05). Although the microbial composition of prokaryotes (bacteria and archaea) and protozoa in the rumen was not altered after PEO administration. MaAsLin2 analysis revealed that the abundance of Selenomonas, Christensenellaceae R-7 group, and Anaerovibrio were enriched in the rumen of PEO supplemented goats (Q < 0.1). Co-occurrence network analysis revealed that Lachnospiraceae AC2044 group and Anaerovibrio were the keystone taxa in the CON and PEO groups, respectively. Methane metabolism (P < 0.05) was enriched in the CON group, whereas metabolism of sulfur (P < 0.001) and propionate (P < 0.1) were enriched in the PEO group based on microbial predicted functions. After PEO administration, the abundance of 11 rumen and 4 serum metabolites increased, whereas that of 25 rumen and 14 serum metabolites decreased (P < 0.1). Random forest analysis identified eight ruminal metabolites that were altered after PEO administration, among which four were associated with propionate production, with predictive accuracy ranging from 0.75 to 0.88. Additionally, we found that serum sarcosine (serum metabolite) was positively correlated with CH emission parameters and abundance of Methanobrevibacter in the rumen (|r|≥ 0.5, P < 0.05).
CONCLUSIONS
This study revealed that PEO administration reduced CH emission from of fattening goats with altered microbial interactions and metabolites in the rumen and host. Importantly, PEO administration affected utilizes various mechanisms such as formate, sulfur, methylated amines metabolism, and propionate production, collectively leading to CH reduction. The knowledge is important for future management strategies to maintain animal production and health while mitigate CH emission.
PubMed: 38943213
DOI: 10.1186/s42523-024-00325-4 -
Journal of Dairy Science Jul 2024The objective was to evaluate the effects of separate offering of feed ingredients (SF) and frequency of concentrate feeding versus offering a TMR, on lactational...
Separate offering of forages and concentrates to lactating dairy cows: Effects on lactational performance, enteric methane emission, and efficiency of nutrient utilization.
The objective was to evaluate the effects of separate offering of feed ingredients (SF) and frequency of concentrate feeding versus offering a TMR, on lactational performance, ruminal fermentation, enteric CH emissions, nutrient digestibility, N use efficiency, milk fatty acid profile, and blood variables in mid-lactation dairy cows. Twenty-four Holstein cows (12 primi- and 12 multiparous) averaging (±SD) 141 ± 35 DIM and 43 ± 6 kg/d of milk yield (MY) at the beginning of the study were used in a replicated 3 × 3 Latin square design experiment with 3 periods of 28 d each, composed of 7 d for adaptation to the diets, 11 d for estimation of net energy and metabolizable protein requirements, and 10 d for data and samples collection. Cows were grouped based on parity, DIM, and MY into 4 Latin squares. Treatment allocation was balanced for carryover effects, and cows within square were assigned to (1) basal diet fed ad libitum as TMR; (2) basal diet fed as SF with forages fed ad libitum and concentrates fed 3×/d (SF×3); or (3) basal diet fed as SF with forages fed ad libitum and concentrates fed 6×/d (SF×6). Compared with TMR, SF decreased total DMI by 1.2 kg/d. Treatments did not affect MY, milk components, or ECM yield, except for a decrease in milk fat concentration and an increase in milk urea N by SF×3, compared with TMR. Feed efficiency (kg of MY/kg of DMI) was increased by 7% in SF, compared with TMR. Ruminal molar proportion of acetate and acetate-to-propionate ratio were decreased, whereas molar proportion of propionate was increased by SF×3, compared with TMR and SF×6. There was a 9% decrease in daily CH production by SF, compared with TMR. Enteric CH yield (per kg of DMI) was not affected by treatments in the current study. Methane intensity per kilogram of MY tended to be decreased by 10% in SF, compared with TMR. The sums of odd- and branched-chain, odd-chain, and anteiso milk fatty acids tended to be or were increased by SF, compared with TMR. Intake of nutrients tended to be or were decreased by SF, compared with TMR. The digestibility of amylase-treated NDF tended to be decreased and ADF digestibility was decreased by 3% in SF, compared with TMR. Urinary and fecal N excretions were not affected by treatments. As a percentage of total N intake, separate offering of feed ingredients increased milk N secretion, indicating an increased N use efficiency by SF, compared with TMR. Blood total fatty acid concentration was decreased by SF relative to TMR. Compared with both TMR and SF×6, SF×3 increased blood urea N concentration. Overall, feed and N use efficiencies were increased by separate offering of feed ingredients, and increasing the frequency of concentrate feeding promoted ruminal fermentation effects similar to those obtained by feeding a TMR.
Topics: Animals; Cattle; Lactation; Female; Milk; Diet; Methane; Animal Feed; Digestion; Nutrients; Rumen; Fermentation
PubMed: 38942562
DOI: 10.3168/jds.2023-24261 -
Journal of Dairy Science Jul 2024This study investigated the effects of feeding an amylase-enabled corn silage (ACS) on the performance and enteric gas emissions in lactating dairy cows. Following a...
This study investigated the effects of feeding an amylase-enabled corn silage (ACS) on the performance and enteric gas emissions in lactating dairy cows. Following a 2-wk covariate period, 48 mid-lactation Holstein cows were assigned to 1 of 3 treatments in a 10-wk randomized complete block design experiment. Treatments were diets containing the same proportion of corn silage (40% of dietary DM) as follows: (1) a conventional hybrid corn silage control (CON), (2) ACS replacing the control silage (ADR), and (3) the ADR diet replacing soybean hulls with ground corn grain to achieve the same dietary starch concentration as CON (ASR). Control corn silage and ACS were harvested on the same day and contained 40.3% and 37.1% DM and (% of DM): 37.2% and 41.0% NDF and 37.1% and 30.0% starch, respectively. Enteric gas emissions were measured using the GreenFeed system. Two cows were culled due to health-related issues during the covariate period. Ruminal fluid was collected from 24 cows (8 per treatment) using the orogastric ruminal sampling technique. When compared with CON, cows fed ADR had increased DMI during experimental wk 3, 4, and 9, but treatment did not affect milk or ECM milk yields (39.0 kg/d on average; SEM = 0.89). Compared with CON, feed efficiency (per unit of milk, but not ECM) tended to be lower for ADR, whereas milk true protein concentration (a tendency) and yield were lower for ASR. Milk urea N was decreased by both ADR and ASR diets relative to CON. Compared with CON, daily CH emission and emission intensity were increased by ADR but not ASR. Total protozoal count tended to be increased by both diets formulated with ACS when compared with control corn silage. Total-tract digestibility of dietary NDF was greater for ASR, and that of ADF was greater for both ADR and ASR versus CON. The molar proportion of acetate (a tendency) and acetate-to-propionate ratio were increased by ADR, but not ASR, when compared with CON. Replacement of CON with ACS (having lower starch concentration) in the diet of dairy cows increased DMI during the initial weeks of the experiment, maintained ECM, tended to decrease feed efficiency, and increased enteric CH emissions, likely due to increased intake of digestible fiber, compared with CON.
Topics: Animals; Cattle; Female; Starch; Lactation; Zea mays; Silage; Rumen; Diet; Milk; Fermentation; Amylases; Animal Feed; Gases
PubMed: 38942561
DOI: 10.3168/jds.2023-23957 -
Journal of Dairy Science Jul 2024Methane, both enteric and from manure management, is the most important greenhouse gas from ruminant livestock, and its mitigation can deliver substantial decreases in... (Review)
Review
Methane, both enteric and from manure management, is the most important greenhouse gas from ruminant livestock, and its mitigation can deliver substantial decreases in the carbon footprint of animal products and potentially contribute to climate change mitigation. Although choices may be limited, certain feeding-related practices can substantially decrease livestock enteric CH emission. These practices can be generally classified into 2 categories: diet manipulation and feed additives. Within the first category, selection of forages and increasing forage digestibility are likely to decrease enteric CH emission, but the size of the effect, relative to current forage practices in the United States dairy industry, is likely to be minimal to moderate. An opportunity also exists to decrease enteric CH emissions by increasing dietary starch concentration, but interventions have to be weighed against potential decreases in milk fat yield and farm profitability. A similar conclusion can be made about dietary lipids and oilseeds, which are proven to decrease CH emission but can also have a negative effect on rumen fermentation, feed intake, and milk production and composition. Sufficient and robust scientific evidence indicates that some feed additives, specifically the CH inhibitor 3-nitrooxypropanol, can substantially reduce CH emissions from dairy and beef cattle. However, the long-term effects and external factors affecting the efficacy of the inhibitor need to be further studied. The practicality of mass-application of other mitigation practices with proven short-term efficacy (i.e., macroalgae) is currently unknown. One area that needs more research is how nutritional mitigation practices (both diet manipulation and feed additives) interact with each other and whether there is synergism among feed additives with different mode of action. Further, effects of diet on manure composition and greenhouse gas emissions during storage (e.g., emission trade-offs) have not been adequately studied. Overall, if currently available mitigation practices prove to deliver consistent results and novel, potent, and safe strategies are discovered and are practical, nutrition alone can deliver up to 60% reduction in enteric CH emissions from dairy farms in the United States.
Topics: Methane; Animals; Animal Feed; Diet; Cattle; Milk; Dairying
PubMed: 38942560
DOI: 10.3168/jds.2023-24440 -
Methods in Molecular Biology (Clifton,... 2024The development of high throughput methods has enabled the study of hundreds of samples and metaproteomics is not the exception. However, the study of thousands of...
The development of high throughput methods has enabled the study of hundreds of samples and metaproteomics is not the exception. However, the study of thousands of proteins of different organisms represents different challenges from the protein extraction to the bioinformatic analysis. Here, the sample preparation, protein extraction and protein purification for livestock microbiome research throughout metaproteomics are described. These methods are essential because the quality of the final protein pool depends on them. For that reason, the following workflow is a combination of different chemical and physical methods that intend an initial separation of the microbial organisms from the host cells and other organic materials, as well as the extraction of high concentrate pure samples.
Topics: Animals; Livestock; Proteomics; Microbiota; Proteins
PubMed: 38941014
DOI: 10.1007/978-1-0716-3910-8_6 -
Animal Bioscience Jun 2024The objective of this study was to reveal the influence of acute and chronic heat stress (HS) on the abundance and function of rumen microbiome and host metabolism.
OBJECTIVE
The objective of this study was to reveal the influence of acute and chronic heat stress (HS) on the abundance and function of rumen microbiome and host metabolism.
METHODS
The forty mid-lactation goats were randomly divided into two artificial environments a control group and a heat-stressed group. This study was collected from two periods, 1 day and 28 days. The first day was defined as control 1 (CT1) and HS 1 (acute HS), and the last day was defined as CT28 and HS28 (chronic HS). On the first and last day, 6 dairy goats in each group were randomly selected to collect rumen liquid after the morning feeding through oral stomach tubes. The barn temperature and humidity were recorded every day.
RESULTS
Disruption of the rumen microbiome was observed under chronic HS, represented by an increase in the abundance of Prevotella and Bacteroidales (p<0.05), and upregulation of carbohydrate transport and metabolism functions (p<0.05). Additionally, the abundance of Succinimonas and Ruminobacter in chronic HS is lower than in acute HS (p<0.05), and the functions of intracellular trafficking, secretion and vesicular transport, and the cytoskeleton were downregulated (p<0.05).
CONCLUSION
HS affected the interaction between the microbiota and host, thereby regulating milk production in dairy goats. These findings increased understanding of the crosstalk between hosts and microorganisms.
PubMed: 38938027
DOI: 10.5713/ab.24.0120