The ruminant gut microbiome vs enteric methane emission: The essential microbes may help to mitigate the global methane crisis

Ruminants release enteric methane into the atmosphere, significantly increasing greenhouse gas emissions and degrading the environment. A common focus of traditional mitigation efforts is on dietary management and manipulation, which may have limits in sustainability and efficacy, exploring the potential of essential microorganisms as a novel way to reduce intestinal methane emissions in ruminants; a topic that has garnered increased attention in recent years. Fermentation and feed digestion are significantly aided by essential microbes found in the rumen, such as bacteria, fungi, and archaea. The practical implications of the findings reported in various studies conducted on rumen gut concerning methane emissions may pave the way to understanding the mechanisms of CH4 production in the rumen to enhance cattle feed efficiency and mitigate CH4 emissions from livestock. This review discussed using essential bacteria to reduce intestinal methane emissions in ruminants. It investigates how particular microbial strains or consortia can alter rumen fermentation pathways to lower methane output while preserving the health and productivity of animals. We also describe the role of probiotics and prebiotics in managing methane emissions using microbial feed additives. Further, recent studies involving microbial interventions have been discussed. The use of new methods involving functional metagenomics and meta-transcriptomics for exploring the rumen microbiome structure has been highlighted. This review also emphasizes the challenges faced in altering the gut microbiome and future directions in this area.

Potential to reduce methane production of using cultivated seaweeds supplementation to reshape the community structure of rumen microorganisms

Methane is a short-lived greenhouse gas but has a far greater warming effect than carbon dioxide. At the same time, the livestock sector serves as a large contributor to global emissions of anthropogenic methane. Herein, this work aimed to use cultivated seaweed supplementation to reduce methane emissions and investigate the potential influencing mechanism. To evaluate the feasibility, two cultivated seaweeds, Laminaria japonica Aresch, and Porphyra tenera, along with the enzymatic hydrolysates derived from L. japonica, underwent in vitro trials, and they were both added into corn silage feed (CSF) with different concentrations (1%, 5%, and 10% of CSF) for methane reduction evaluation. The results indicated that >75% and 50% reductions in methane production were observed for the seaweeds and seaweed enzymatic hydrolysates in 9- and 30-day, respectively. Combined high-throughput sequencing and multivariate analysis revealed that supplementation with seaweed and seaweed enzymatic hydrolysates had a notable impact on the prokaryotic community structure. Mantel tests further revealed that significant correlations between the prokaryotic community and methane accumulation (P < 0.05), implying the prokaryotic community plays a role in reducing methane emissions within the rumen. Correspondingly, the networks within the prokaryotic community unveiled the crucial role of propionate/butyrate-producing bacteria in regulating methane emissions through microbial interactions. The predicted function of the prokaryotic community exhibited a significant reduction in the presence of the narB gene in seaweed-supplemented treatments. This reduction may facilitate an increased rate of electron flow toward the nitrate reduction pathway while decreasing the conversion of H2 to methane. These results indicated the supplementation of cultivated seaweeds and the enzymatic hydrolysates has the potential to reshape the community structure of rumen microbial communities, and this alteration appears to be a key factor contributing to their methane production-reduction capability.

Examining homoacetogens in feces from adult and juvenile kangaroos with the aim of finding competitive strains to hydrogenotrophic methanogens

We examined the microbial populations present in fecal samples of macropods capable of utilizing a mixture of hydrogen and carbon dioxide (70:30) percent. The feces samples were cultured under anaerobic conditions, and production of methane or acetic acids characteristic for methanogenesis and homoacetogenesis was measured. While the feces of adult macropods mainly produced methane from the substrate, the sample from a 2-month-old juvenile kangaroo only produced acetic acid and no methane. The stable highly enriched culture of the joey kangaroo was sequenced to examine the V3 and V4 regions of the 16S rRNA gene. The results showed that over 70% of gene copies belonged to the Clostridia class, with Paraclostridium and Blautia as the most predominant genera. The culture further showed the presence of Actinomyces spp., a genus which has only been identified in the GI tract of macropods in a few studies, and where none, to our knowledge, have been classified as homoacetogenic. The joey kangaroo mixed culture showed a doubling time of 3.54 h and a specific growth rate of 0.199/h, faster than what has been observed for homoacetogenic bacteria in general.

IMPORTANCE

Enteric methane emissions from cattle are a significant contributor to greenhouse gas emissions worldwide. Methane emissions not only contribute to climate change but also represent a loss of energy from the animal's diet. However, methanogens play an important role as hydrogen sink to rumen systems; without it, the performance of hydrolytic organisms diminishes. Therefore, effective strategies of methanogen inhibition would be enhanced in conjunction with the addition of alternative hydrogen sinks to the rumen. The significance of our research is to identify homoacetogens present in the GI tract of kangaroos and to present their performance in vitro, demonstrating their capability to serve as alternatives to rumen methanogens.

Quantitative TMT-based proteomics revealing host, dietary and microbial proteins in bovine faeces including barley serpin Z4, a prominent component in the head of beer

There has been little information about the proteome of bovine faeces or about the contribution to the faecal proteome of proteins from the host, the feed or the intestinal microbiome. Here, the bovine faecal proteome and the origin of its component proteins was assessed, while also determining the effect of treating barley, the major carbohydrate in the feed, with either ammonia (ATB) or sodium propionate (PTB) preservative. Healthy continental crossbreed steers were allocated to two groups and fed on either of the barley-based diets. Five faecal samples from each group were collected on Day 81 of the trial and analysed by quantitative proteomics using nLC-ESI-MS/MS after tandem mass tag labelling. In total, 281 bovine proteins, 199 barley proteins, 176 bacterial proteins and 190 archaeal proteins were identified in the faeces. Mucosal pentraxin, albumin and digestive enzymes were among bovine proteins identified. Serpin Z4 a protease inhibitor was the most abundant barley protein identified which is also found in barley-based beer, while numerous microbial proteins were identified, many originating bacteria from Clostridium, while Methanobrevibacter was the dominant archaeal genus. Thirty-nine proteins were differentially abundant between groups, the majority being more abundant in the PTB group compared to the ATB group. SIGNIFICANCE: Proteomic examination of faeces is becoming a valuable means to assess the health of the gastro-intestinal tract in several species, but knowledge on the proteins present in bovine faeces is limited. This investigation aimed to characterise the proteome of bovine faecal extracts in order to evaluate the potential for investigations of the proteome as a means to assess the health, disease and welfare of cattle in the future. The investigation was able to identify proteins in bovine faeces that had been (i) produced by the individual cattle, (ii) present in the barley-based feed eaten by the cattle or (iii) produced by bacteria and other microbes in the rumen or intestines. Bovine proteins identified included mucosal pentraxin, serum albumin and a variety of digestive enzymes. Barley proteins found in the faeces included serpin Z4, a protease inhibitor that is also found in beer having survived the brewing process. Bacterial and archaeal proteins in the faecal extracts were related to several pathways related to the metabolism of carbohydrates. The recognition of the range of proteins that can be identified in bovine faeces raises the possibility that non-invasive sample collection of this material could provide a novel diagnostic approach to cattle health and welfare.

Role of Polysaccharides from Marine Seaweed as Feed Additives for Methane Mitigation in Ruminants: A Critical Review

Given the increasing concerns regarding greenhouse gas emissions associated with livestock production, the need to discover effective strategies to mitigate methane production in ruminants is clear. Marine algal polysaccharides have emerged as a promising research avenue because of their abundance and sustainability. Polysaccharides, such as alginate, laminaran, and fucoidan, which are extracted from marine seaweeds, have demonstrated the potential to reduce methane emissions by influencing the microbial populations in the rumen. This comprehensive review extensively examines the available literature and considers the effectiveness, challenges, and prospects of using marine seaweed polysaccharides as feed additives. The findings emphasise that marine algal polysaccharides can modulate rumen fermentation, promote the growth of beneficial microorganisms, and inhibit methanogenic archaea, ultimately leading to decreases in methane emissions. However, we must understand the long-term effects and address the obstacles to practical implementation. Further research is warranted to optimise dosage levels, evaluate potential effects on animal health, and assess economic feasibility. This critical review provides insights for researchers, policymakers, and industry stakeholders dedicated to advancing sustainable livestock production and methane mitigation.

Measurement of Methane and Ammonia Emissions from Compost-Bedded Pack Systems in Dairy Barns: Tilling Effect and Seasonal Variations

Dairy cattle contribute to environmental harm as a source of polluting gas emissions, mainly of enteric origin, but also from manure management, which varies among housing systems. Compost-bedded pack systems use manure as bedding material, which is composted in situ daily. As current literature referring to their impact on NH3 and CH4 emissions is scarce, this study aims to characterize the emissions of these two gases originating from three barns of this system, differentiating between two emission phases: static emission and dynamic emission. In addition, the experiment differentiated emissions between winter and summer. Dynamic emission, corresponding to the time of the day when the bed is being composted, increased over 3 and 60 times the static emission of NH3 and CH4, respectively. In terms of absolute emissions, both gases presented higher emissions during summer (1.86 to 4.08 g NH3 m-2 day-1 and 1.0 to 4.75 g CH4 m-2 day-1 for winter and summer, respectively). In this way, contaminant gases produced during the tilling process of the manure, especially during the warmer periods of the year, need to be taken into account as they work as a significant factor in emissions derived from compost-bedded pack systems.

First Steps into Ruminal Microbiota Robustness

Despite its central role in ruminant nutrition, little is known about ruminal microbiota robustness, which is understood as the ability of the microbiota to cope with disturbances. The aim of the present review is to offer a comprehensive description of microbial robustness, as well as its potential drivers, with special focus on ruminal microbiota. First, we provide a briefing on the current knowledge about ruminal microbiota. Second, we define the concept of disturbance (any discrete event that disrupts the structure of a community and changes either the resource availability or the physical environment). Third, we discuss community resistance (the ability to remain unchanged in the face of a disturbance), resilience (the ability to return to the initial structure following a disturbance) and functional redundancy (the ability to maintain or recover initial function despite compositional changes), all of which are considered to be key properties of robust microbial communities. Then, we provide an overview of the currently available methodologies to assess community robustness, as well as its drivers (microbial diversity and network complexity) and its potential modulation through diet. Finally, we propose future lines of research on ruminal microbiota robustness.

Microbial short-chain fatty acids: a bridge between dietary fibers and poultry gut health

The maintenance of poultry gut health is complex depending on the intricate balance among diet, the commensal microbiota, and the mucosa, including the gut epithelium and the superimposing mucus layer. Changes in microflora composition and abundance can confer beneficial or detrimental effects on fowl. Antibiotics have devastating impacts on altering the landscape of gut microbiota, which further leads to antibiotic resistance or spread the pathogenic populations. By eliciting the landscape of gut microbiota, strategies should be made to break down the regulatory signals of pathogenic bacteria. The optional strategy of conferring dietary fibers (DFs) can be used to counterbalance the gut microbiota. DFs are the non-starch carbohydrates indigestible by host endogenous enzymes but can be fermented by symbiotic microbiota to produce short-chain fatty acids (SCFAs). This is one of the primary modes through which the gut microbiota interacts and communicate with the host. The majority of SCFAs are produced in the large intestine (particularly in the caecum), where they are taken up by the enterocytes or transported through portal vein circulation into the bloodstream. Recent shreds of evidence have elucidated that SCFAs affect the gut and modulate the tissues and organs either by activating G-protein-coupled receptors or affecting epigenetic modifications in the genome through inducing histone acetylase activities and inhibiting histone deacetylases. Thus, in this way, SCFAs vastly influence poultry health by promoting energy regulation, mucosal integrity, immune homeostasis, and immune maturation. In this review article, we will focus on DFs, which directly interact with gut microbes and lead to the production of SCFAs. Further, we will discuss the current molecular mechanisms of how SCFAs are generated, transported, and modulated the pro-and anti-inflammatory immune responses against pathogens and host physiology and gut health.

Emission factors for Vietnamese beef cattle manure sun-drying and the effects of drying on manure microbial community

Livestock manure and its management are significant sources of greenhouse gas (GHG). In most Southeast Asian countries, the current GHG emissions are estimated by the Intergovernmental Panel on Climate Change (IPCC) Tier 1 approach using default emission factors. Sun-drying is the dominant manure treatment in Vietnam, and in this study, we measured GHG emissions during manure drying using a chamber-based approach. Results show the emission factors for CH4 and N2O were 0.295 ± 0.078 g kg-1 volatile solids (VS) and 0.132 ± 0.136 g N2O-N kg-1 Ninitial, respectively. We monitored the total bacterial/archaeal community using 16S rRNA gene amplicon sequencing and measured the abundance of functional genes required for methanogenesis (mcrA), nitrification (amoA) and denitrification (nirK, nirS and nosZ) processes. Methane emission occurred only at the beginning of the drying process (days 1 to 3). The results of amplicon sequencing indicated that the relative abundance of methanogens also decreased during this period. Although some nitrification activity was detected, there was no significant N2O emission. These findings well describe the manure management system in south Vietnam and the GHG emission from this manure category, paving the way for higher Tier estimations using country-specific values.

Strategies to Mitigate Enteric Methane Emissions from Ruminant Animals

Human activities account for approximately two-thirds of global methane emissions, wherein the livestock sector is the single massive methane emitter. Methane is a potent greenhouse gas of over 21 times the warming effect of carbon dioxide. In the rumen, methanogens produce methane as a by-product of anaerobic fermentation. Methane released from ruminants is considered as a loss of feed energy that could otherwise be used for productivity. Economic progress and growing population will inflate meat and milk product demands, causing elevated methane emissions from this sector. In this review, diverse approaches from feed manipulation to the supplementation of organic and inorganic feed additives and direct-fed microbial in mitigating enteric methane emissions from ruminant livestock are summarized. These approaches directly or indirectly alter the rumen microbial structure thereby reducing rumen methanogenesis. Though many inorganic feed additives have remarkably reduced methane emissions from ruminants, their usage as feed additives remains unappealing because of health and safety concerns. Hence, feed additives sourced from biological materials such as direct-fed microbials have emerged as a promising technique in mitigating enteric methane emissions.

Sustainability of the Dairy Industry: Emissions and Mitigation Opportunities

Dairy cattle provide a major benefit to the world through upcycling human inedible feedstuffs into milk and associated dairy products. However, as beneficial as this process has become, it is not without potential negatives. Dairy cattle are a source of greenhouse gases through enteric and waste fermentation as well as excreting nitrogen emissions through their feces and urine. However, these negative impacts vary widely due to how and what these animals are fed. In addition, there are many promising opportunities for further reducing emissions through feed and waste additives. The present review aims to further expand on where the industry is today and the potential avenues for improvement. This area of research is still not complete and additional information is required to further improve our dairy systems impact on sustainable animal products.

Microbial community structure of the bovine rumen as affected by feeding cashew nut shell liquid, a methane-inhibiting and propionate-enhancing agent

The effect of cashew nut shell liquid (CNSL) feeding on bacterial and archaeal community of the bovine rumen was investigated by analyzing clone libraries targeting 16S rRNA genes, methyl-coenzyme reductase A-encoding genes (mcrA), and their respective transcripts. Rumen samples were collected from three non-lactating cows fed on a hay and concentrate diet with or without CNSL supplementation. DNA and complementary DNA (cDNA) libraries were generated for investigating rumen microbial communities. MiSeq analysis also was performed to understand more comprehensively the changes in the microbial community structures. Following CNSL supplementation, the number of operational taxonomical unit (OTU) and diversity indices of bacterial and archaeal community were decreased. Bacterial OTUs belonging to Proteobacteria, including Succinivibrio, occurred at a higher frequency with CNSL feeding, especially in cDNA libraries. The methanogenic archaeal community became dominated by Methanomicrobium. A bacterial community shift also was observed in the MiSeq data, indicating that CNSL increased the proportion of Succinivibrio and other genera known to be involved in propionate production. Methanogenic archaeal community shifts to increase Methanoplanus and to decrease Methanobrevibacter also were observed. Together, these results imply the occurrence of significant changes in rumen communities, not only for bacteria but also for methanogens, following CNSL feeding.

The Impact of Producing Type and Dietary Crude Protein on Animal Performances and Microbiota Together with Greenhouse Gases Emissions in Growing Pigs

Simple Summary

To study the effect of dietary crude protein (CP) restriction in two different pig producing types and the role of gut microbiota, 32 pure castrated male Duroc and 32 entire male hybrid (F2) piglets were raised in a three-phase feeding regime with a restriction in CP content of the diets. The average body weight of hybrid animals were higher compared to Duroc pigs. No changes were found in average daily feed intake (ADFI) of hybrid animals in comparison to Duroc pigs. Hybrid animals apparently digested more CP than Duroc and Duroc pigs emitted more CH₄ and ammonia with respect to the hybrids. Dietary protein restriction did not alter emissions of contaminant gases nor microbial community structure in terms of diversity, although some genera were affected by the dietary challenge.

Abstract

In order to reduce dietary nitrogen and achieve an efficient protein deposition as well as decrease N wastage, we challenged the nutrient utilization efficiency of two different producing types in front of a dietary crude protein (CP) restriction and studied the role of the microbiota in such an adaptation process. Therefore, 32 pure castrated male Duroc (DU) and 32 entire male hybrid (F2) piglets were raised in a three-phase feeding regime. At each phase, two iso caloric diets differing in CP content, also known as normal protein (NP) and low protein (LP), were fed to the animals. LP diets had a fixed restriction (2%) in CP content in regards to NP ones throughout the phases of the experiment. At the end of third phase, fecal samples were collected for microbiota analysis purposes and greenhouse gases emissions, together with ammonia, were tested. No changes were found in average daily feed intake (ADFI) of animals of two producing types (Duroc vs. F2) or those consumed different experimental diets (NP vs. LP) throughout the course of study. However, at the end of each experimental phase the average body weight (BW) of hybrid animals were higher compared to Duroc pigs, whereas a reverse trend was observed for average daily gain (ADG), where Duroc pigs showed greater values with respect to hybrid ones. Despite, greater CH₄ and ammonia emissions in Duroc pigs with respect to F2, no significant differences were found in contaminant gases emissions between diets. Moreover, LP diets did not alter the microbial community structure, in terms of diversity, although some genera were affected by the dietary challenge. Results suggest that the impact of reducing 2% of CP content was limited for reduction in contaminant gases emissions and highlight the hypothesis that moderate change in the dietary protein levels can be overcome by long-term adaptation of the gut microbiota. Overall, the influence of the producing type on performance and digestive microbiota composition was more pronounced than the dietary effect. However, both producing types responded differently to CP restriction. The use of fecal microbiota as biomarker for predicting feed efficiency has a great potential that should be completed with robust predictive models to achieve consistent and valid results.