Islands in the stream: from individual to communal fiber degradation in the rumen ecosystem

A Metagenomic Insight Into the Hindgut Microbiota and Their Metabolites for Dairy Goats Fed Different Rumen Degradable Starch

High starch diets have been proven to increase the risk of hindgut acidosis in high-yielding dairy animals. As an effective measurement of dietary carbohydrate for ruminants, studies on rumen degradable starch (RDS) and the effects on the gut microbiota diversity of carbohydrate-active enzymes (CAZymes), and Kyoto Encyclopedia of Genes and Genomes (KEGG) Orthology functional categories are helpful to understand the mechanisms between gut microbiota and carbohydrate metabolism in dairy goats. A total of 18 lactating goats (45.8 ± 1.54 kg) were randomly divided equally into three dietary treatments with low dietary RDS concentrations of 20.52% (LRDS), medium RDS of 22.15% (MRDS), and high RDS of 24.88% (HRDS) on a DM basis for 5 weeks. Compared with the LRDS and MRDS groups, HRDS increased acetate molar proportion in the cecum. For the HRDS group, the abundance of family Ruminococcaceae and genus Ruminococcaceae UCG-010 were significantly increased in the cecum. For the LRDS group, the butyrate molar proportion and the abundance of butyrate producer family Bacteroidale_S24-7, family Lachnospiraceae, and genus Bacteroidale_S24-7_group were significantly increased in the cecum. Based on the BugBase phenotypic prediction, the microbial oxidative stress tolerant and decreased potentially pathogenic in the LRDS group were increased in the cecum compared with the HRDS group. A metagenomic study on cecal bacteria revealed that dietary RDS level could affect carbohydrate metabolism by increasing the glycoside hydrolase 95 (GH95) family and cellulase enzyme (EC 3.2.1.4) in the HRDS group; increasing the GH13_20 family and isoamylase enzyme (EC 3.2.1.68) in the LRDS group. PROBIO probiotics database showed the relative gene abundance of cecal probiotics significantly decreased in the HRDS group. Furthermore, goats fed the HRDS diet had a lower protein expression of Muc2, and greater expression RNA of interleukin-1β and secretory immunoglobulin A in cecal mucosa than did goats fed the LRDS diet. Combined with the information from previous results from rumen, dietary RDS level altered the degradation position of carbohydrates in the gastrointestinal (GI) tract and increased the relative abundance of gene encoded enzymes degrading cellulose in the HRDS group in the cecum of dairy goats. This study revealed that the HRDS diet could bring disturbances to the microbial communities network containing taxa of the Lachnospiraceae and Ruminococcaceae and damage the mucus layer and inflammation in the cecum of dairy goats.

Changes in Digestive Microbiota, Rumen Fermentations and Oxidative Stress around Parturition Are Alleviated by Live Yeast Feed Supplementation to Gestating Ewes

Background: In ruminants, physiological and nutritional changes occur peripartum. We investigated if gastro-intestinal microbiota, rumen metabolism and antioxidant status were affected around parturition and what could be the impact of a daily supplementation of a live yeast additive in late gestating ewes. Methods: Rumen, feces and blood samples were collected from 2 groups of 14 ewes one month and a few days before parturition, and 2 weeks postpartum. Results: In the control ewes close to parturition, slight changes in the ruminal microbiota were observed, with a decrease in the concentration F. succinogenes and in the relative abundance of the Fibrobacteres phylum. Moreover, a decrease in the alpha-diversity of the bacterial community and a reduced relative abundance of the Fibrobacteres phylum were observed in their feces. Control ewes were prone to oxidative stress, as shown by an increase in malondialdehyde (MDA) concentration, a lower total antioxidant status, and higher glutathione peroxidase (GPx) activity in the blood. In the yeast supplemented ewes, most of the microbial changes observed in the control group were alleviated. An increase in GPx activity, and a significant decrease in MDA concentration were measured. Conclusions: The live yeast used in this study could stabilize gastro-intestinal microbiota and reduce oxidative stress close to parturition.

Effect of Oats and Wheat Genotype on In Vitro Gas Production Kinetics of Straw

Simple Summary

Increases in cereal grain yields cause the accumulation of large amounts of straw on the soils after grain harvest. Straw is usually burned in the field to help soil preparation for the next crop, a practice resulting in local and global pollution, erosion, loss of soil carbon, and wildfires. An alternative is feeding straw to ruminants, but straw has poor nutritive value, making this option unattractive to Chilean farmers. Oats and wheat have been bred for greater grain yield and improved agronomic traits, but it is unknown whether the straw of different varieties and breeding lines differs in nutritive quality. To investigate this possibility, we incubated the straws from 49 different varieties and breeding lines of oats and 24 of wheat with rumen microorganisms, and studied gas production as an indication of the extent of straw digestion. We found moderate differences among varieties and breeding lines of oats and wheat in gas production, which were not detrimental to agronomic characteristics of importance. If these results can be confirmed in animal experiments, gas production of straw incubated in rumen microbial cultures may be used to identify cereal genotypes whose straw has a better nutritive quality for ruminants.

Abstract

Increases in cereals grain yield in the last decades have increased the accumulation of straw on the soil after harvest. Farmers typically open burn the straw to prepare the soil for the next crop, resulting in pollution, emission of greenhouse gases, erosion, loss of soil organic matter, and wildfires. An alternative is feeding straw to ruminants, but straw nutritive value is limited by its high content of lignocellulose and low content of protein. Cereal breeding programs have focused on improving grain yield and quality and agronomic traits, but little attention has been paid to straw nutritive value. We screened straw from 49 genotypes of oats and 24 genotypes of wheat from three cereal breeding trials conducted in Chile for in vitro gas production kinetics. We found moderate effects of the genotype on gas production at 8, 24, and 40 h of incubation, and on the maximum extent and rate of gas production. Gas production was negatively associated with lignin and cellulose contents and not negatively associated with grain yield and resistance to diseases and lodging. Effects observed in vitro need to be confirmed in animal experiments before gas production kinetics can be adopted to identify cereal genotypes with more digestible straw.

Effects of three different mannans on obesity and gut microbiota in high-fat diet-fed C57BL/6J mice

To compare the effects of three mannans, Konjac glucomannan (KGM), guar gum (GG) and locust bean gum (LBG), on obesity and obesity-related metabolic disorders in mice fed with high-fat diet (HFD), and to investigate the potential modulation of gut microbiota, we performed a 14 week study on C57BL/6J mice fed a HFD with/without mannan supplementation. The results showed that supplementing 8% KGM, GG, and LBG to a HFD dramatically reduced the body weight gain and adipose accumulation, attenuated liver injury, and antagonized glycolipid metabolism and inflammation-related parameters of HFD-fed mice in different degrees. However, only LBG had such roles when the supplement dose was reduced to 2%. In addition, it was found that LBG required more time to exert its impacts on weight control and lipid metabolism. Furthermore, 16S rRNA gene sequencing of gut microbiota indicated that mannans with different structures and supplement doses affected the overall structure of the gut microbiota to a varying extent and specifically changed the abundance of some OTUs. Moreover, several OTUs belonging to the genera Muribaculum, Staphylococcus, [Eubacterium] fissicatena group, and Christensenella had a high correlation with obesity and obesity-related metabolic disorders of the host. In summary, all the three mannans had the potential to be used as alternative dietary supplements or functional foods to prevent obesity and obesity-related metabolic disorders induced by a HFD, but the effects of the dose and time varied, and the functions of the mannans were associated with their ability to regulate the gut microbiota.

The Rumen Epithelial Microbiota: Possible Gatekeepers of the Rumen Epithelium and Its Potential Contributions to Epithelial Barrier Function and Animal Health and Performance

Ruminants are characterized by their unique mode of digesting cellulose-rich plant material in their forestomach, the rumen, which is densely populated by diverse microorganisms that are crucial for the breakdown of plant material. Among ruminal microbial communities, the microorganisms in the rumen fluid or attached to feed particles have attracted considerable research interest. However, comparatively less is known about the microorganisms attached to the rumen epithelium. Generally, the tissue lining the gastrointestinal tract serves the dual role of absorbing nutrients while preventing the infiltration of unwanted compounds and molecules as well as microorganisms. The rumen epithelium fulfills critical physiological functions for the ruminant host in energy absorption, metabolism, and nutrient transport. Essential host metabolites, such as short-chain fatty acids, ammonia, urea, and minerals, are exchanged across the rumen wall, thereby exposing the rumen epithelial microbiota to these nutrients. The integrity of the gastrointestinal barrier is central to animal health and productivity. The integrity of the rumen epithelium can be compromised by high ruminal microbial fermentation activity resulting in decreased rumen pH or by stress conditions such as heat stress or feed restriction. It is important to keep in mind that feeding strategies in cattle have changed over the last decades in favor of energy- and nutrient-rich concentrates instead of fiber-rich forages. These dietary shifts support high milk yields and growth rates but raised concerns regarding a possibly compromised rumen function. This paper will provide an overview of the composition of rumen epithelial microbial communities under physiological and disease conditions and will provide insights into the knowledge about the function and in situ activity of rumen epithelial microorganisms and their relevance for animal health and production. Given that an impaired intestinal barrier will negatively affect economically significant phenotypes, a better understanding of rumen wall microbiota is urgently needed.

Exogenous enzymes and probiotics alter digestion kinetics, volatile fatty acid content and microbial interactions in the gut of Nile tilapia

Sustainable aquafeed production requires fishmeal replacement, leading to an increasing use of plant-derived ingredients. As a consequence, higher levels of antinutritional substances, such as non-starch polysaccharides and phytate, are present in aquafeeds, with negative effects on fish performance, nutrient digestibility and overall gut health. To alleviate these negative effects, providing exogenous digestive enzymes and/or probiotics can be an effective solution. In this study, we tested the effect of dietary supplementation of enzymes (phytase and xylanase) and probiotics (three strains of Bacillus amyloliquefaciens) on nutrient digestion kinetics and volatile fatty acid content along the gut, and the distal gut microbiome diversity in Nile tilapia. Chyme volatile fatty content was increased with probiotic supplementation in the proximal gut, while lactate content, measured for the first time in vivo in fish, decreased with enzymes along the gut. Enzyme supplementation enhanced crude protein, Ca and P digestibility in proximal and middle gut. Enzymes and probiotics supplementation enhanced microbial interactions as shown by network analysis, while increased the abundance of lactic acid bacteria and Bacillus species. Such results suggest that supplementation with exogenous enzymes and probiotics increases nutrient availability, while at the same time benefits gut health and contributes to a more stable microbiome environment.

Conditions stimulating neutral detergent fiber degradation by dosing branched-chain volatile fatty acids. I: Comparison with branched-chain amino acids and forage source in ruminal batch cultures

Three experiments assessed branched-chain volatile fatty acid (BCVFA) stimulation of neutral detergent fiber (NDF) disappearance after 24 h of incubation in batch cultures derived from ruminal fluid inocula that were enriched with particulate-phase bacteria. In experiment 1, a control was compared with 3 treatments with isomolar doses of all 3 BCVFA (plus valerate), all 3 branched-chain AA (BCAA), or half of each BCVFA and BCAA mix with either alfalfa or grass hays (50%) and ground corn grain (50%). A portion of the BCAA and BCVFA doses were enriched with ¹³C, and valerate (also enriched with ¹³C) was added with BCVFA. Although BCAA yielded a similar production of BCVFA compared with dosing BCVFA, equimolar substitution of BCVFA for BCAA decreased the percentage of N in bacterial pellets when alfalfa hay was fed but increased N when grass hay was fed. Substituting BCVFA for BCAA increased total fatty acid (FA) concentration with alfalfa hay. Dosing of BCAA or BCVFA did not affect total branched-chain FA, iso-FA, or anteiso-FA percentages in bacterial total FA, whereas numerous individual FA isomers and their ¹³C enrichments were affected by these treatments. Increasing recovery of the ¹³C dose from respective labeled BCVFA primers indicated facilitated BCVFA uptake and incorporation into FA compared with BCAA, whereas increased recovery of ¹³C from labeled BCAA in the bacteria pellet but not in the FA fraction suggested direct assimilation into bacterial protein. The BCVFA and valerate were dosed in varying combinations that either summed to 4 mM (experiment 2) or had only 1 mM no matter what combination (experiment 3). In general, grass hay was more responsive to stimulation in NDF digestibility by BCVFA than was alfalfa hay, which was attributed to the higher degradable protein in the latter. The net production of the BCVFA (after subtracting dose) was affected by source and combination of BCVFA. Isovalerate dosing tended to increase its own net production; in contrast, isobutyrate seemed to be used more when it was added alone, but 2-methylbutyrate seemed to be preferred over isobutyrate when 2-methylbutyrate was added. Results supported potential interactions, including potential feedback in production from feed BCAA or increased concentration-dependent competition for dosed BCVFA into cellular products. Under our conditions, the BCVFA appear to be more readily available than BCAA, probably because of regulated BCAA transport and metabolism. Valerate consistently provided no benefit. Using nonparametric ranking, all 3 BCVFA or either isovalerate or isobutyrate (both yielding iso-FA) should be combined with 2-methylbutyrate (yielding anteiso-FA) as a potential opportunity to improve NDF digestibility when rumen-degraded BCAA are limited in diets to decrease environmental impact from N in waste.

Rumen Epithelial Communities Share a Core Bacterial Microbiota: A Meta-Analysis of 16S rRNA Gene Illumina MiSeq Sequencing Datasets

In this meta-analysis, 17 rumen epithelial 16S rRNA gene Illumina MiSeq amplicon sequencing data sets were analyzed to identify a core rumen epithelial microbiota and core rumen epithelial OTUs shared between the different studies included. Sequences were quality-filtered and screened for chimeric sequences before performing closed-reference 97% OTU clustering, and de novo 97% OTU clustering. Closed-reference OTU clustering identified the core rumen epithelial OTUs, defined as any OTU present in ≥ 80% of the samples, while the de novo data was randomly subsampled to 10,000 reads per sample to generate phylum- and genus-level distributions and beta diversity metrics. 57 core rumen epithelial OTUs were identified including metabolically important taxa such as Ruminococcus, Butyrivibrio, and other Lachnospiraceae, as well as sulfate-reducing bacteria Desulfobulbus and Desulfovibrio. Two Betaproteobacteria OTUs (Neisseriaceae and Burkholderiaceae) were core rumen epithelial OTUs, in contrast to rumen content where previous literature indicates they are rarely found. Two core OTUs were identified as the methanogenic archaea Methanobrevibacter and Methanomethylophilaceae. These core OTUs are consistently present across the many variables between studies which include different host species, geographic region, diet, age, farm management practice, time of year, hypervariable region sequenced, and more. When considering only cattle samples, the number of core rumen epithelial OTUs expands to 147, highlighting the increased similarity within host species despite geographical location and other variables. De novo OTU clustering revealed highly similar rumen epithelial communities, predominated by Firmicutes, Bacteroidetes, and Proteobacteria at the phylum level which comprised 79.7% of subsampled sequences. The 15 most abundant genera represented an average of 54.5% of sequences in each individual study. These abundant taxa broadly overlap with the core rumen epithelial OTUs, with the exception of Prevotellaceae which were abundant, but not identified within the core OTUs. Our results describe the core and abundant bacteria found in the rumen epithelial environment and will serve as a basis to better understand the composition and function of rumen epithelial communities.

In Vivo Competitions between Fibrobacter succinogenes, Ruminococcus flavefaciens, and Ruminoccus albus in a Gnotobiotic Sheep Model Revealed by Multi-Omic Analyses

Fibrobacter succinogenes, Ruminococcus albus, and Ruminococcus flavefaciens are the three predominant cellulolytic bacterial species found in the rumen. In vitro studies have shown that these species compete for adherence to, and growth upon, cellulosic biomass. Yet their molecular interactions in vivo have not heretofore been examined. Gnotobiotically raised lambs harboring a 17-h-old immature microbiota devoid of culturable cellulolytic bacteria and methanogens were inoculated first with F. succinogenes S85 and Methanobrevibacter sp. strain 87.7, and 5 months later, the lambs were inoculated with R. albus 8 and R. flavefaciens FD-1. Longitudinal samples were collected and profiled for population dynamics, gene expression, fibrolytic enzyme activity, in sacco fibrolysis, and metabolite profiling. Quantitative PCR, metagenome and metatranscriptome data show that F. succinogenes establishes at high levels initially but is gradually outcompeted following the introduction of the ruminococci. This shift resulted in an increase in carboxymethyl cellulase (CMCase) and xylanase activities but not in greater fibrolysis, suggesting that F. succinogenes and ruminococci deploy different but equally effective means to degrade plant cell walls. Expression profiles showed that F. succinogenes relied upon outer membrane vesicles and a diverse repertoire of CAZymes, while R. albus and R. flavefaciens preferred type IV pili and either CBM37-harboring or cellulosomal carbohydrate-active enzymes (CAZymes), respectively. The changes in cellulolytics also affected the rumen metabolome, including an increase in acetate and butyrate at the expense of propionate. In conclusion, this study provides the first demonstration of in vivo competition between the three predominant cellulolytic bacteria and provides insight on the influence of these ecological interactions on rumen fibrolytic function and metabolomic response.IMPORTANCE Ruminant animals, including cattle and sheep, depend on their rumen microbiota to digest plant biomass and convert it into absorbable energy. Considering that the extent of meat and milk production depends on the efficiency of the microbiota to deconstruct plant cell walls, the functionality of predominant rumen cellulolytic bacteria, Fibrobacter succinogenes, Ruminococcus albus, and Ruminococcus flavefaciens, has been extensively studied in vitro to obtain a better knowledge of how they operate to hydrolyze polysaccharides and ultimately find ways to enhance animal production. This study provides the first evidence of in vivo competitions between F. succinogenes and the two Ruminococcus species. It shows that a simple disequilibrium within the cellulolytic community has repercussions on the rumen metabolome and fermentation end products. This finding will have to be considered in the future when determining strategies aiming at directing rumen fermentations for animal production.

Bioprocessing of waste biomass for sustainable product development and minimizing environmental impact

Growing concerns around the generation of biomass waste have triggered conversation around sustainable utilization of these seemingly waste materials as feedstock towards energy generation and production of chemicals and other value-added products. Thus, biotechniques such as utilization of microbes and enzymes derived thereof have become important avenues for green pretreatment and conversion of biomass wastes. Although the products of these bioconversions are greener at an overall level, their consumption and utilization still impact the environment. Hence it is important to understand the overall impact from cradle to grave through lifecycle assessment (LCA) techniques and find avenues of process optimization and better utilization of all the materials and products involved. Another factor to consider is overall cost optimization to make the process economically feasible, profitable and increase industrial adoption. This review brings forward these critical aspects to provide better understanding for the advancement of bioeconomy.

Transformation of bacterial community structure in rumen liquid anaerobic digestion of rice straw

Rumen liquid can effectively degrade lignocellulosic biomass, in which rumen microorganisms play an important role. In this study, transformation of bacterial community structure in rumen liquid anaerobic digestion of rice straw was explored. Results showed that rice straw was efficiently hydrolyzed and acidified, and the degradation efficiency of cellulose, hemicellulose and lignin reached 46.2%, 60.4%, and 12.9%, respectively. The concentration of soluble chemical oxygen demand (SCOD) and total volatile fatty acid (VFA) reached 12.9 and 8.04 g L^-1. The high-throughput sequencing results showed that structure of rumen bacterial community significantly changed in anaerobic digestion. The Shannon diversity index showed that rumen bacterial diversity decreased by 32.8% on the 5th day of anaerobic digestion. The relative abundance of Prevotella and Fibrobacter significantly increased, while Ruminococcus significantly decreased at the genus level. The Spearman correlation heatmap showed that pH and VFA were the critical factors affecting the rumen bacterial community structure. The function prediction found that rumen bacteria mainly functioned in carbohydrate transport and metabolism, which might contain a large number of lignocellulose degrading enzyme genes. These studies are conducive to the better application of rumen microorganisms in the degradation of lignocellulosic biomass.

Diversity of microbes colonizing forages of varying lignocellulose properties in the sheep rumen

Background

The rumen microbiota contributes strongly to the degradation of ingested plant materials. There is limited knowledge about the diversity of taxa involved in the breakdown of lignocellulosic biomasses with varying chemical compositions in the rumen.

Method

We aimed to assess how and to what extent the physicochemical properties of forages influence the colonization and digestion by rumen microbiota. This was achieved by placing nylon bags filled with candidate materials in the rumen of fistulated sheep for a period of up to 96 h, followed by measuring forage's chemical characteristics and community structure of biofilm-embedded microbiota.

Results

Rumen degradation for all forages appeared to have occurred mainly during the first 24 h of their incubation, which significantly slowed down after 48 h of rumen incubation, depending on their chemical properties. Random Forest analysis predicted the predominant role of Treponema and Butyrivibrio in shaping microbial diversity attached to the forages during the course of rumen incubation. Exploring community structure and composition of fiber-attached microbiota revealed significant differential colonization rates of forages depending on their contents for NDF and cellulose. The correlation analysis highlighted the significant contribution of Lachnospiraceae and Veillonellaceae to fiber degradation in the sheep rumen.

Conclusion

Our findings suggested that forage cellulose components are critical in shaping the pattern of microbial colonization and thus their final digestibility in the rumen.

Anaerobic Fungi: Past, Present, and Future

Anaerobic fungi (AF) play an essential role in feed conversion due to their potent fiber degrading enzymes and invasive growth. Much has been learned about this unusual fungal phylum since the paradigm shifting work of Colin Orpin in the 1970s, when he characterized the first AF. Molecular approaches targeting specific phylogenetic marker genes have facilitated taxonomic classification of AF, which had been previously been complicated by the complex life cycles and associated morphologies. Although we now have a much better understanding of their diversity, it is believed that there are still numerous genera of AF that remain to be described in gut ecosystems. Recent marker-gene based studies have shown that fungal diversity in the herbivore gut is much like the bacterial population, driven by host phylogeny, host genetics and diet. Since AF are major contributors to the degradation of plant material ingested by the host animal, it is understandable that there has been great interest in exploring the enzymatic repertoire of these microorganisms in order to establish a better understanding of how AF, and their enzymes, can be used to improve host health and performance, while simultaneously reducing the ecological footprint of the livestock industry. A detailed understanding of AF and their interaction with other gut microbes as well as the host animal is essential, especially when production of affordable high-quality protein and other animal-based products needs to meet the demands of an increasing human population. Such a mechanistic understanding, leading to more sustainable livestock practices, will be possible with recently developed -omics technologies that have already provided first insights into the different contributions of the fungal and bacterial population in the rumen during plant cell wall hydrolysis.

Metagenomic Analyses of Microbial and Carbohydrate-Active Enzymes in the Rumen of Dairy Goats Fed Different Rumen Degradable Starch

The objective of this study was to investigate the effects of different dietary rumen degradable starch (RDS) on the diversity of carbohydrate-active enzymes (CAZymes) and Kyoto Encyclopedia of Genes and Genomes Orthology functional categories to explore carbohydrate degradation in dairy goats. Eighteen dairy goats (second lactation, 45.8 ± 1.54 kg) were divided in three groups fed low RDS (LRDS), medium RDS (MRDS), and high RDS (HRDS) diets. The results showed that, HRDS treatment group significantly decreased the ruminal pH (P < 0.05), and increased the propionate proportion (P < 0.05), fumarate and succinate concentrations (P < 0.05), trended to increase lactate concentration (P = 0.50) compared with LRDS group. The relative abundance of acetogens, such as family Clostridiaceae and Ruminococcaceae, genera Clostridium and Blautia were higher in HRDS than LRDS feeding goats. The GH9 family (responsible for cellulose degradation) genes were lower in HRDS than MRDS diet samples, and mainly produced by Prevotellaceae, Ruminococcaceae, and Bacteroidaceae. Amylose (EC3.2.1.3) genes under HRDS treatment were more abundant than under LRDS treatment. However, the abundance of GH13_9 and CBM48 (responsible for starch degradation) were reduced in HRDS group indicating the decreased binding activity from catalytic modules to starch. This study revealed that HRDS-fed dairy goats had decreased CAZymes, which encode enzymes degrade cellulose and starch in the dairy goats.

Stochasticity constrained by deterministic effects of diet and age drive rumen microbiome assembly dynamics

How complex communities assemble through the animal's life, and how predictable the process is remains unexplored. Here, we investigate the forces that drive the assembly of rumen microbiomes throughout a cow's life, with emphasis on the balance between stochastic and deterministic processes. We analyse the development of the rumen microbiome from birth to adulthood using 16S-rRNA amplicon sequencing data and find that the animals shared a group of core successional species that invaded early on and persisted until adulthood. Along with deterministic factors, such as age and diet, early arriving species exerted strong priority effects, whereby dynamics of late successional taxa were strongly dependent on microbiome composition at early life stages. Priority effects also manifest as dramatic changes in microbiome development dynamics between animals delivered by C-section vs. natural birth, with the former undergoing much more rapid species invasion and accelerated microbiome development. Overall, our findings show that together with strong deterministic constrains imposed by diet and age, stochastic colonization in early life has long-lasting impacts on the development of animal microbiomes.

Spatially remote motifs cooperatively affect substrate preference of a ruminal GH26-type endo-β-1,4-mannanase

β-Mannanases from the glycoside hydrolase 26 (GH26) family are retaining hydrolases that are active on complex heteromannans and whose genes are abundant in rumen metagenomes and metatranscriptomes. These enzymes can exhibit distinct modes of substrate recognition and are often fused to carbohydrate-binding modules (CBMs), resulting in a molecular puzzle of mechanisms governing substrate preference and mode of action that has not yet been pieced together. In this study, we recovered a novel GH26 enzyme with a CBM35 module linked to its N terminus (CrMan26) from a cattle rumen metatranscriptome. CrMan26 exhibited a preference for galactomannan as substrate and the crystal structure of the full-length protein at 1.85 Å resolution revealed a unique orientation of the ancillary domain relative to the catalytic interface, strategically positioning a surface aromatic cluster of the ancillary domain as an extension of the substrate-binding cleft, contributing to galactomannan preference. Moreover, systematic investigation of nonconserved residues in the catalytic interface unveiled that residues Tyr195 (-3 subsite) and Trp234 (-5 subsite) from distal negative subsites have a key role in galactomannan preference. These results indicate a novel and complex mechanism for substrate recognition involving spatially remote motifs, distal negative subsites from the catalytic domain, and a surface-associated aromatic cluster from the ancillary domain. These findings expand our molecular understanding of the mechanisms of substrate binding and recognition in the GH26 family and shed light on how some CBMs and their respective orientation can contribute to substrate preference.

The microbial exometabolome: ecological resource and architect of microbial communities

All microorganisms release many metabolites, collectively known as the exometabolome. The resultant multi-way cross-feeding of metabolites among microorganisms distributes resources, thereby increasing total biomass of the microbial community, and promotes the recruitment and persistence of phylogenetically and functionally diverse taxa in microbial communities. Metabolite transfer can also select for evolutionary diversification, yielding multiple closely related but functionally distinct strains. Depending on starting conditions, the evolved strains may be auxotrophs requiring metabolic outputs from producer cells or, alternatively, display loss of complementary reactions in metabolic pathways, with increased metabolic efficiency. Metabolite cross-feeding is widespread in many microbial communities associated with animals and plants, including the animal gut microbiome, and these metabolic interactions can yield products valuable to the host. However, metabolite exchange between pairs of intracellular microbial taxa that share the same host cell or organ can be very limited compared to pairs of free-living microorganisms, perhaps as a consequence of host controls over the metabolic function of intracellular microorganisms. Priorities for future research include the development of tools for improved quantification of metabolite exchange in complex communities and greater integration of the roles of metabolic cross-feeding and other ecological processes, including priority effects and antagonistic interactions, in shaping microbial communities. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.

Effects of Urtica cannabina to Leymus chinensis Ratios on Ruminal Microorganisms and Fiber Degradation In Vitro

The study was conducted in vitro to investigate the effects of different ratios of Urtica cannabina and Leymus chinensis on fiber microstructure and digestibility in ruminal fluid. The experiment was divided into five groups based on the U. cannabina/L. chinensis ratios: A (0:100), B (30:70), C (50:50), D (70:30), and E (100:0). The culture medium was collected at 0, 1, 3, 6, 12, and 24 h. The results showed that: (1) in vitro crude protein degradability (IVCPD) was higher in group A, whereas in vitro neutral detergent fiber degradability (IVNDFD) was higher in group C (p < 0.05); (2) protozoa count was increased from 1 h to 3 h and decreased afterwards, with significant differences observed in several genera (p < 0.05); (3) microbial crude protein (MCP) contents at 1, 3, 6, and 24 h were higher in groups A and C (p < 0.05); (4) the basic tissue of U. cannabina was gradually degraded. At 24h, the secondary xylem vessel structure was observed in groups B and C, but not in groups D and E. In summary, there was higher neutral detergent fiber (NDF) digestibility, higher rumen MCP contents, and lower protozoa count, showing the significance of the 50:50 ratio for microbial growth and fiber digestibility.

Evolutionary transitions revisited: Holobiont evo-devo

John T. Bonner lists four essential transformations in the evolution of life: the emergence of the eukaryotic cell, meiosis, multicellularity, and the nervous system. This paper analyses the mechanisms for those transitions in light of three of Dr. Bonner's earlier hypotheses: (a) that the organism is its life cycle, (b) that evolution consists of alterations of the life cycle, and (c) that development extends beyond the body and into interactions with other organisms. Using the notion of the holobiont life cycle, this paper attempts to show that these evolutionary transitions can be accomplished through various means of symbiosis. Perceiving the organism both as an interspecies consortium and as a life cycle supports a twofold redefinition of the organism as a holobiont constructed by integrating together the life cycles of several species. These findings highlight the importance of symbiosis and the holobiont development in analyses of evolution.