Can rumen bacteria communicate to each other?

Rumen fluid pretreatment promotes anaerobic methane production: revealing microbial dynamics driving increased acid yield from different concentrations of corn straw

In this work, the corn straw (CS) with concentrations of 3%, 6%, and 9% (w/v) were pretreated by rumen fluid (RF) and then used for batched mesophilic biogas production. The results showed that after a 6-day pretreatment, volatile fatty acid (VFAs) production of 3.78, 8.27, and 10.4 g/L could be found in 3%, 6%, and 9%, respectively. When concerning with biogas production, the highest accumulative methane production of 149.1 mL CH4/g volatile solid was achieved by 6% pretreated CS, which was 22% and 45% higher than 3% and 9%, respectively. Also, it was 3.6 times higher than the same concentration of unpretreated CS. The results of the microbial community structure analysis revealed that the 6% CS pretreatment not only maintained a microbial community with the highest richness and diversity, but also exhibited the highest relative abundance of Firmicutes (45%) and Euryarchaeota (3.9%). This high abundance was conducive to its elevated production of VFAs and methane. These findings provide scientific reference for the utilization of CS and support the development of agricultural waste resource utilization and environmental protection.

Rumen microbes, enzymes, metabolisms, and application in lignocellulosic waste conversion - A comprehensive review

The rumen of ruminants is a natural anaerobic fermentation system that efficiently degrades lignocellulosic biomass and mainly depends on synergistic interactions between multiple microbes and their secreted enzymes. Ruminal microbes have been employed as biomass waste converters and are receiving increasing attention because of their degradation performance. To explore the application of ruminal microbes and their secreted enzymes in biomass waste, a comprehensive understanding of these processes is required. Based on the degradation capacity and mechanism of ruminal microbes and their secreted lignocellulose enzymes, this review concentrates on elucidating the main enzymatic strategies that ruminal microbes use for lignocellulose degradation, focusing mainly on polysaccharide metabolism-related gene loci and cellulosomes. Hydrolysis, acidification, methanogenesis, interspecific H2 transfer, and urea cycling in ruminal metabolism are also discussed. Finally, we review the research progress on the conversion of biomass waste into biofuels (bioethanol, biohydrogen, and biomethane) and value-added chemicals (organic acids) by ruminal microbes. This review aims to provide new ideas and methods for ruminal microbe and enzyme applications, biomass waste conversion, and global energy shortage alleviation.

Life at the borderlands: microbiomes of interfaces critical to One Health

Microbiomes are foundational components of the environment that provide essential services relating to food security, carbon sequestration, human health, and the overall well-being of ecosystems. Microbiota exert their effects primarily through complex interactions at interfaces with their plant, animal, and human hosts, as well as within the soil environment. This review aims to explore the ecological, evolutionary, and molecular processes governing the establishment and function of microbiome-host relationships, specifically at interfaces critical to One Health-a transdisciplinary framework that recognizes that the health outcomes of people, animals, plants, and the environment are tightly interconnected. Within the context of One Health, the core principles underpinning microbiome assembly will be discussed in detail, including biofilm formation, microbial recruitment strategies, mechanisms of microbial attachment, community succession, and the effect these processes have on host function and health. Finally, this review will catalogue recent advances in microbiology and microbial ecology methods that can be used to profile microbial interfaces, with particular attention to multi-omic, advanced imaging, and modelling approaches. These technologies are essential for delineating the general and specific principles governing microbiome assembly and functions, mapping microbial interconnectivity across varying spatial and temporal scales, and for the establishment of predictive frameworks that will guide the development of targeted microbiome-interventions to deliver One Health outcomes.

Effect of high corn straw loads on short-chain fatty acid production in semi-continuous rumen reactor

Ruminal microorganisms can efficiently hydrolyze biomass waste for short-chain fatty acid (SCFA) production. However, the continuous SCFA production by ruminal microorganisms at high loads is unclear. In this study, the effectiveness of a rumen semi-continuous reactor at high load for SCFA production was explored. Results showed that SCFA concentration reached 13.3 g/L at 8 % (w/v) corn straw load. The higher the corn straw load, the lower the volatile solid removal. Rumen microbial community composition changed significantly with increasing corn straw load. A significant decrease in bacterial diversity and abundance was observed at 8 % corn straw load. Some core genera such as Prevotella, Saccharofermentans, and Ruminococcus significantly increased. As corn straw loads increased, the expression of functional genes related to hydrolysis and acidogenesis gradually increased. Thus, the 8.0 % load is suitable for SCFA production. These findings provide new insights into high load fermentation of ruminal microorganisms.

Response of rumen microorganisms to pH during anaerobic hydrolysis and acidogenesis of lignocellulose biomass

Rumen microorganisms can efficiently degrade lignocellulosic wastes to produce volatile fatty acids (VFAs). pH is a key factor in controlling the type and yield of VFAs by affecting the microorganisms involved in rumen fermentation. However, the effects of different pH on rumen microbial diversity, communities, and mechanisms are unclear. In this study, the hydrolysis and acidogenesis of corn straw and diversity, communities, and mechanisms of rumen microorganisms were explored at different initial pHs. Results showed that the highest hemicellulose, cellulose, and lignin degradation efficiency of corn straw was 55.2 %, 38.3 %, and 7.01 %, respectively, and VFA concentration was 10.2 g/L at pH 7.0. Low pH decreased the bacterial diversity and increased the fungal diversity. Rumen bacteria and fungi had different responses to initial pHs, and the community structure of bacteria and fungi had obviously differences at the genus level. The core genera Succiniclasticum, Treponema, and Neocallimastix relative abundance at initial pH 7.0 samples were significantly higher than that at lower initial pHs, reaching 6.01 %, 1.61 %, and 5.35 %, respectively. The bacterial network was more complex than that of fungi. pH, acetic acid, and propionic acid were the main factors influencing the bacterial and fungal community structure. Low pH inhibited the expression of functional genes related to hydrolysis and acidogenesis, explaining the lower hydrolysis and acidogenesis efficiency. These findings will provide a better understanding for rumen fermentation to produce VFAs.

- Invited Review - Chemical signalling within the rumen microbiome

Ruminants possess a specialized four-compartment forestomach, consisting of the reticulum, rumen, omasum, and abomasum. The rumen, the primary fermentative chamber, harbours a dynamic ecosystem comprising bacteria, protozoa, fungi, archaea, and bacteriophages. These microorganisms engage in diverse ecological interactions within the rumen microbiome, primarily benefiting the host animal by deriving energy from plant material breakdown. These interactions encompass symbiosis, such as mutualism and commensalism, as well as parasitism, predation, and competition. These ecological interactions are dependent on many factors, including the production of diverse molecules, such as those involved in quorum sensing (QS). QS is a density-dependent signalling mechanism involving the release of autoinducer (AIs) compounds, when cell density increases AIs bind to receptors causing the altered expression of certain genes. These AIs are classified as mainly being N-acyl-homoserine lactones (AHL; commonly used by Gram-negative bacteria) or autoinducer-2 based systems (AI-2; used by Gram-positive and Gram-negative bacteria); although other less common AI systems exist. Most of our understanding of QS at a gene-level comes from pure culture in vitro studies using bacterial pathogens, with much being unknown on a commensal bacterial and ecosystem level, especially in the context of the rumen microbiome. A small number of studies have explored QS in the rumen using 'omic' technologies, revealing a prevalence of AI-2 QS systems among rumen bacteria. Nevertheless, the implications of these signalling systems on gene regulation, rumen ecology, and ruminant characteristics are largely uncharted territory. Metatranscriptome data tracking the colonization of perennial ryegrass by rumen microbes suggest that these chemicals may influence transitions in bacterial diversity during colonization. The likelihood of undiscovered chemicals within the rumen microbial arsenal is high, with the identified chemicals representing only the tip of the iceberg. A comprehensive grasp of rumen microbial chemical signalling is crucial for addressing the challenges of food security and climate targets.

Megasphaera elsdenii: Its Role in Ruminant Nutrition and Its Potential Industrial Application for Organic Acid Biosynthesis

The Gram-negative, strictly anaerobic bacterium Megasphaera elsdenii was first isolated from the rumen in 1953 and is common in the mammalian gastrointestinal tract. Its ability to use either lactate or glucose as its major energy sources for growth has been well documented, although it can also ferment amino acids into ammonia and branched-chain fatty acids, which are growth factors for other bacteria. The ruminal abundance of M. elsdenii usually increases in animals fed grain-based diets due to its ability to use lactate (the product of rapid ruminal sugar fermentation), especially at a low ruminal pH (<5.5). M. elsdenii has been proposed as a potential dietary probiotic to prevent ruminal acidosis in feedlot cattle and high-producing dairy cows. However, this bacterium has also been associated with milk fat depression (MFD) in dairy cows, although proving a causative role has remained elusive. This review summarizes the unique physiology of this intriguing bacterium and its functional role in the ruminal community as well as its role in the health and productivity of the host animal. In addition to its effects in the rumen, the ability of M. elsdenii to produce C2-C7 carboxylic acids-potential precursors for industrial fuel and chemical production-is examined.

Analysis of Rumen Degradation Characteristics, Attached Microbial Community, and Cellulase Activity Changes of Garlic Skin and Artemisia argyi Stalk

The purpose of this study was to study the chemical composition, rumen degradation characteristics, surface attached microbial community and cellulase activity of garlic skin (GS) and Artemisia argyi stalk (AS), in order to explain their feeding value. Four 14-month-old healthy Min Dong male goats with permanent rumen fistula were selected as experimental animals. The rumen degradation characteristics of GS and AS were determined by using the nylon bag method, and the bacterial composition, cellulase activity and their relationship on the surface of the two groups were analyzed with high-throughput sequencing of 16S rRNA gene. The results showed that in GS and AS, the effective degradation rate (ED) values of dry matter (DM) were 42.53% and 37.12%, the ED values of crude protein (CP) were 37.19% and 43.38%, the ED values of neutral detergent fiber (NDF) were 36.83% and 36.23%, and the ED values of acid detergent fiber (ADF) were 33.81% and 34.77%. During rumen degradation, the richness and evenness of bacteria attached to the AS surface were higher. At the phylum level, Bacteroidetes and Firmicutes were always the main rumen bacteria in the two groups. At the genus level, fiber-degrading bacteria such as Prevotella, Treponema, and Ruminococcus showed higher levels in GS (p < 0.05). Compared with GS, the activity of β-glucosidase (BG enzyme), endo-β-1,4-glucanase (C1 enzyme), exo-β-1,4-glucanase (Cx enzyme) and neutral xylanase (NEX enzyme) attached to AS surface showed a higher trend. Correlation analysis showed that the relative abundance of Succinivibrio and Rikenellaceae_RC9_gut_group was positively correlated with the rumen degradability of nutrients in GS, and the relative abundance of Christensenellaceae R-7_group, Succinivibrio and Ruminococcus was positively correlated with the rumen degradability of nutrients in AS. The conclusion of this study shows that AS has more potential to become ruminant roughage than GS. In addition, this study also revealed the relationship between cellulase activity and bacteria, which provided new information for us to better analyze the effects of GS and AS on the rumen of ruminants and provided an important theoretical basis for the development and utilization of agricultural by-products.

Metagenomic analysis reveals the efficient digestion mechanism of corn stover in Angus bull rumen: Microbial community succession, CAZyme composition and functional gene expression

Ruminant rumen is a biological fermentation system that can efficiently degrade lignocellulosic biomass. The knowledge about mechanisms of efficient lignocellulose degradation with rumen microorganisms is still limited. In this study, composition and succession of bacteria and fungi, carbohydrate-active enzymes (CAZymes), and functional genes involved in hydrolysis and acidogenesis were revealed during fermentation in Angus bull rumen via metagenomic sequencing. Results showed that degradation efficiency of hemicellulose and cellulose reached 61.2% and 50.4% at 72 h fermentation, respectively. Main bacterial genera were composed of Prevotella, Butyrivibrio, Ruminococcus, Eubacterium, and Fibrobacter, and main fungal genera were composed of Piromyces, Neocallimastix, Anaeromyces, Aspergillus, and Orpinomyces. Principal coordinates analysis indicated that community structure of bacteria and fungi dynamically changed during 72 h fermentation. Bacterial networks with higher complexity had stronger stability than fungal networks. Most CAZyme families showed a significant decrease trend after 48 h fermentation. Functional genes related to hydrolysis decreased at 72 h, while functional genes involved in acidogenesis did not change significantly. These findings provide a in-depth understanding of mechanisms of lignocellulose degradation in Angus bull rumen, and may guide the construction and enrichment of rumen microorganisms in anaerobic fermentation of waste biomass.

Quorum sensing-mediated microbial interactions: Mechanisms, applications, challenges and perspectives

Microbial community in natural or artificial environments playes critical roles in substance cycles, products synthesis and species evolution. Although microbial community structures have been revealed via culture-dependent and culture-independent approaches, the hidden forces driving the microbial community are rarely systematically discussed. As a mode of cell-to-cell communication that modifies microbial interactions, quorum sensing can regulate biofilm formation, public goods secretion, and antimicrobial substances synthesis, directly or indirectly influencing microbial community to adapt to the changing environment. Therefore, the current review focuses on microbial community in the different habitats from the quorum sensing perspective. Firstly, the definition and classification of quorum sensing were simply introduced. Subsequently, the relationships between quorum sensing and microbial interactions were deeply explored. The latest progressives regarding the applications of quorum sensing in wastewater treatment, human health, food fermentation, and synthetic biology were summarized in detail. Finally, the bottlenecks and outlooks of quorum sensing driving microbial community were adequately discussed. To our knowledge, this current review is the first to reveal the driving force of microbial community from the quorum sensing perspective. Hopefully, this review provides a theoretical basis for developing effective and convenient approaches to control the microbial community with quorum sensing approaches.

Taxonomic and enzymatic basis of the cellulolytic microbial consortium KKU-MC1 and its application in enhancing biomethane production

Lignocellulosic biomass is a promising substrate for biogas production. However, its recalcitrant structure limits conversion efficiency. This study aims to design a microbial consortium (MC) capable of producing the cellulolytic enzyme and exploring the taxonomic and genetic aspects of lignocellulose degradation. A diverse range of lignocellulolytic bacteria and degrading enzymes from various habitats were enriched for a known KKU-MC1. The KKU-MC1 was found to be abundant in Bacteroidetes (51%), Proteobacteria (29%), Firmicutes (10%), and other phyla (8% unknown, 0.4% unclassified, 0.6% archaea, and the remaining 1% other bacteria with low predominance). Carbohydrate-active enzyme (CAZyme) annotation revealed that the genera Bacteroides, Ruminiclostridium, Enterococcus, and Parabacteroides encoded a diverse set of cellulose and hemicellulose degradation enzymes. Furthermore, the gene families associated with lignin deconstruction were more abundant in the Pseudomonas genera. Subsequently, the effects of MC on methane production from various biomasses were studied in two ways: bioaugmentation and pre-hydrolysis. Methane yield (MY) of pre-hydrolysis cassava bagasse (CB), Napier grass (NG), and sugarcane bagasse (SB) with KKU-MC1 for 5 days improved by 38-56% compared to non-prehydrolysis substrates, while MY of prehydrolysed filter cake (FC) for 15 days improved by 56% compared to raw FC. The MY of CB, NG, and SB (at 4% initial volatile solid concentration (IVC)) with KKU-MC1 augmentation improved by 29-42% compared to the non-augmentation treatment. FC (1% IVC) had 17% higher MY than the non-augmentation treatment. These findings demonstrated that KKU-MC1 released the cellulolytic enzyme capable of decomposing various lignocellulosic biomasses, resulting in increased biogas production.

Microbiome and the inflammatory pathway in peri-implant health and disease with an updated review on treatment strategies

Crestal bone preservation around the dental implant for aesthetic and functional success is widely researched and documented over a decade. Several etiological factors were put forth for crestal bone loss; of which biofilm plays a major role. Biofilm is formed by the colonization of wide spectra of bacteria inhabited around dental implants. Bacterial adherence affects the regulators of bone growth and an early intervention preserves the peri-implant bone. Primary modes of therapy stated in early literature were either prevention or treatment of infection caused by biofilm. This narrative review overviews the microbiome during different stages of peri-implant health, the mechanism of bone destruction, and the expression of the biomarkers at each stage. Microbial contamination and the associated biomarkers varied depending on the stage of peri-implant infection. The comprehensive review helps in formulating a research plan, both in diagnostics and treatment aspects in improving peri-implant health.

Combinations of bacterial cultures, exogenous enzymes, and yeast-based feed additives and their impact on ruminal microbiome

Our objective was to evaluate the effects of bacteria (Lactobacillus animalis, Propionibacterium freudenreichii, Bacillus lichenformis, Bacillus subtilis, and Enterococcus faecium), enzymes (amylase, hemicellulose, and xylanase), and yeast as additives on the ruminal microbiome. We hypothesized that inclusion of bacteria, enzymes, and yeast would impact butyric bacterial populations. Eight fermenters were arranged in a duplicated 4 × 4 Latin square with the following treatments: 1) control without additives (CTRL); 2) bacterial culture and enzyme blend (EB); 3) bacterial culture and enzyme blend with a live yeast and yeast culture blend (EBY); and 4) double dose of bacterial culture and enzyme blend and the yeast products blend (2X). We conducted four fermentation periods of 10 d each, with the last 3 d for collection of samples. Overall, 64 solid and liquid samples were analyzed by amplification of the V4 region of bacterial 16S rRNA. Data were analyzed with R and SAS. The following orthogonal contrasts were used: 1) ADD-the control compared to all treatments with additives (CTRL vs. EB, EBY, and 2X); 2) YEAST-treatment without yeast compared to those with yeast (EB vs. EBY and 2X); and 3) DOSE-the single dose of enzymes, bacteria, and yeast compared to the doubled dose (EBY vs. 2X). Family Prevotellaceae was more abundant when additives were added (ADD). Additives (ADD) also increased relative abundance of Prevotellaceae Ga6A1 and YAB2003 in solid fraction, and of Prevotellaceae Ga6A1 and two members of Lachnospiracea family in liquid fraction. Yeast (YEAST) decreased relative abundance of Succinivibrionaceae UCG-001 and increased abundance of Ruminococcus and Prevotellaceae UCG-003 in solid fraction. Doubling the dose of enzymes and microbial additives (DOSE) decreased the abundance of Succiniclasticum in solid fraction and Selenomonadaceae in the liquid. Molar proportion of butyrate was highly correlated with abundance of Prevotellaceae Ga6A1 in solid (r = 0.68) and liquid fraction (r = 0.79), and with Unclassified Lachnospiraceae in liquid (r = 0.70). Our results demonstrate that YEAST decreases abundance of succinate synthesizing bacteria, while DOSE decreases abundance of bacteria that metabolize succinate into propionate. Combined bacteria, enzymes, and yeast increase the relative abundance of specific genera primarily within the Prevotellaceae family, which may explain the increase in butyrate molar proportion observed with ADD.

Exploring AI-2-mediated interspecies communications within rumen microbial communities

BACKGROUND

The rumen is an ecosystem with a complex microbial microflora in which microbes initiate biofilm formation by attaching to plant surfaces for plant degradation and are capable of converting feed to nutrients and energy via microbial processes. Quorum sensing (QS) is a cell-to-cell communication mechanism that allows microbes to synchronize the expression of multiple genes in the group to perform social behaviors such as chemotaxis and biofilm formation using self-synthesized QS signaling molecules. Whereas QS has been extensively studied in model microorganisms under pure culture conditions, QS mechanisms are poorly understood in complex bacterial communities, such as the rumen microflora, in which cell-to-cell communication may be common.

RESULTS

Here, we analyzed 981 rumens bacterial and archaeal genomes from the Joint Genome Institute (JGI) and GenBank databases and identified 15 types of known QS signaling molecule-related genes. The analysis of the prevalence and abundance of genes involved in QS showed that 767 microbial genomes appeared to possess QS-related genes, including 680 bacterial genomes containing autoinducer-2 (AI-2) synthase- or receptor-encoding genes. Prevotella, Butyivibrio, Ruminococcus, Oribacterium, Selenomonas, and Treponema, known abundant bacterial genera in the rumen, possessed the greatest numbers of AI-2-related genes; these genes were highly expressed within the metatranscriptome dataset, suggesting that intra- and interspecies communication mediated by AI-2 among rumen microbes was universal in the rumen. The QS processes mediated by the dCache_1-containing AI-2 receptors (CahRs) with various functional modules may be essential for degrading plants, digesting food, and providing energy and nutrients to the host. Additionally, a universal natural network based on QS revealed how rumen microbes coordinate social behaviors via the AI-2-mediated QS system, most of which may potentially function via AI-2 binding to the extracellular sensor dCache_1 domain to activate corresponding receptors involved in different signal transduction pathways, such as methyl-accepting chemotaxis proteins, histidine kinases, serine phosphatases, c-di-GMP synthases and phosphodiesterases, and serine/threonine kinases in the rumen.

CONCLUSIONS

The exploration of AI-2-related genes, especially CahR-type AI-2 receptors, greatly increased our insight into AI-2 as a potentially "universal" signal mediating social behaviors and will help us better understand microbial communication networks and the function of QS in plant-microbe interactions in complex microecosystems. Video Abstract.

Microbiome-driven breeding strategy potentially improves beef fatty acid profile benefiting human health and reduces methane emissions

BACKGROUND

Healthier ruminant products can be achieved by adequate manipulation of the rumen microbiota to increase the flux of beneficial fatty acids reaching host tissues. Genomic selection to modify the microbiome function provides a permanent and accumulative solution, which may have also favourable consequences in other traits of interest (e.g. methane emissions). Possibly due to a lack of data, this strategy has never been explored.

RESULTS

This study provides a comprehensive identification of ruminal microbial mechanisms under host genomic influence that directly or indirectly affect the content of unsaturated fatty acids in beef associated with human dietary health benefits C18:3n-3, C20:5n-3, C22:5n-3, C22:6n-3 or cis-9, trans-11 C18:2 and trans-11 C18:1 in relation to hypercholesterolemic saturated fatty acids C12:0, C14:0 and C16:0, referred to as N3 and CLA indices. We first identified that ~27.6% (1002/3633) of the functional core additive log-ratio transformed microbial gene abundances (alr-MG) in the rumen were at least moderately host-genomically influenced (HGFC). Of these, 372 alr-MG were host-genomically correlated with the N3 index (n=290), CLA index (n=66) or with both (n=16), indicating that the HGFC influence on beef fatty acid composition is much more complex than the direct regulation of microbial lipolysis and biohydrogenation of dietary lipids and that N3 index variation is more strongly subjected to variations in the HGFC than CLA. Of these 372 alr-MG, 110 were correlated with the N3 and/or CLA index in the same direction, suggesting the opportunity for enhancement of both indices simultaneously through a microbiome-driven breeding strategy. These microbial genes were involved in microbial protein synthesis (aroF and serA), carbohydrate metabolism and transport (galT, msmX), lipopolysaccharide biosynthesis (kdsA, lpxD, lpxB), or flagellar synthesis (flgB, fliN) in certain genera within the Proteobacteria phyla (e.g. Serratia, Aeromonas). A microbiome-driven breeding strategy based on these microbial mechanisms as sole information criteria resulted in a positive selection response for both indices (1.36±0.24 and 0.79±0.21 sd of N3 and CLA indices, at 2.06 selection intensity). When evaluating the impact of our microbiome-driven breeding strategy to increase N3 and CLA indices on the environmental trait methane emissions (g/kg of dry matter intake), we obtained a correlated mitigation response of -0.41±0.12 sd.

CONCLUSION

This research provides insight on the possibility of using the ruminal functional microbiome as information for host genomic selection, which could simultaneously improve several microbiome-driven traits of interest, in this study exemplified with meat quality traits and methane emissions. Video Abstract.

Diet Shift May Trigger LuxS/AI-2 Quorum Sensing in Rumen Bacteria

Recent studies have revealed that LuxS/AI-2 quorum sensing (QS) is the most universal cell-to-cell communication in rumen bacteria; however, it remains unknown how they respond to nutritional stress from a diet shift. This study aimed to explore whether a diet shift could trigger rumen bacterial LuxS/AI-2 QS and its influences on rumen fermentation characteristics and bacterial community diversity and composition. A total of fifteen Hu sheep were selected to undergo a pre-shift diet (Pre, concentrate to forage ratio 75:25) for one month and then abruptly switch to a post-shift diet (Post, concentrate to forage ratio 49:51). Results showed that the serum cortisol and immunoglobulin G concentrations were higher in Post than in Pre (p < 0.05). The microbial density, AI-2 concentration, biofilm formation, and the gene expression of ftsH were higher in Post when compared with Pre (p < 0.05), whilst the gene expression of luxS tended to be lower in Post (p = 0.054). The molar concentration of valerate and fermentation efficiency decreased after the diet shift, while the acetate to propionate ratio and the molar proportion of butyrate were higher in Post compared to Pre (p < 0.05). Moreover, the diet shift increased the richness of ruminal bacteria and the relative abundances of Roseburia, Prevotellaceae UCG-001, and Lachnospira, and decreased the relative abundances of Prevotella, Megasphaera, and Dialister (p < 0.05). A difference in trends was also observed in an analysis of similarity (R = 0.1208 and p = 0.064). This study suggests that a diet shift could trigger rumen bacterial LuxS/AI-2 QS by altering microbial density, AI-2 concentration, biofilm formation, and related gene expression, as well as affect the rumen fermentation pattern and bacterial community diversity and composition. This study may provide insight into a potential strategy for relieving nutritional stress via regulating bacterial communication.

Long-term rumen microorganism fermentation of corn stover in vitro for volatile fatty acid production

Rumen microorganisms have the ability to efficiently hydrolyze and acidify lignocellulosic biomass. The effectiveness of long-term rumen microorganism fermentation of lignocellulose in vitro for producing volatile fatty acids (VFAs) is unclear. The feasibility of long-term rumen microorganism fermentation of lignocelluose was evaluated in this study, and a stable VFA production was successfully realized for 120 d. Results showed that VFA concentration reached to 5.32-8.48 g/L during long-term fermentation. Hydrolysis efficiency of hemicellulose and cellulose reached 36.5%-52.2% and 29.4%-38.4%, respectively. A stable bacterial community was mainly composed of Prevotella, Rikenellaceae_RC9_gut_group, Ruminococcus, and Succiniclasticum. VFA accumulation led to a pH decrease, which caused the change of bacterial community structure. Functional prediction showed that the functional genes related to hydrolysis and acidogenesis of corn stover were highly expressed during long-term fermentation. The successful long-term rumen fermentation to produce VFAs is of great significance for the practical application of rumen microorganisms.

3-oxo-C12:2-HSL, quorum sensing molecule from human intestinal microbiota, inhibits pro-inflammatory pathways in immune cells via bitter taste receptors

In the gut ecosystem, microorganisms regulate group behaviour and interplay with the host via a molecular system called quorum sensing (QS). The QS molecule 3-oxo-C12:2-HSL, first identified in human gut microbiota, exerts anti-inflammatory effects and could play a role in inflammatory bowel diseases where dysbiosis has been described. Our aim was to identify which signalling pathways are involved in this effect. We observed that 3-oxo-C12:2-HSL decreases expression of pro-inflammatory cytokines such as Interleukine-1β (− 35%) and Tumor Necrosis Factor-α (TNFα) (− 40%) by stimulated immune RAW264.7 cells and decreased TNF secretion by stimulated PBMC in a dose-dependent manner, between 25 to 100 µM. Transcriptomic analysis of RAW264.7 cells exposed to 3-oxo-C12:2-HSL, in a pro-inflammatory context, highlighted JAK-STAT, NF-κB and TFN signalling pathways and we confirmed that 3-oxo-C12:2-HSL inhibited JAK1 and STAT1 phosphorylation. We also showed through a screening assay that 3-oxo-C12:2-HSL interacted with several human bitter taste receptors. Its anti-inflammatory effect involved TAS2R38 as shown by pharmacologic inhibition and led to an increase in intracellular calcium levels. We thus unravelled the involvement of several cellular pathways in the anti-inflammatory effects exerted by the QS molecule 3-oxo-C12:2-HSL.

Effects of Dietary Supplementation with Glycerol Monolaurate (GML) or the Combination of GML and Tributyrin on Growth Performance and Rumen Microbiome of Weaned Lambs

Our objective was to evaluate the effects of dietary supplementation with glycerol monolaurate (GML) or the combination (Solider, SOL) of GML and tributyrin (TB) on the growth performance and rumen microbiome of weaned lambs. Thirty-six male Hu lambs (11.46 ± 0.88 kg BW and 40 ± 5 days of age) were divided into three treatment groups: (1) CON: basal diet, (2) GML: basal diet supplemented with GML at 1.84 g/kg DM, and (3) SOL: basal diet supplemented with SOL at 3 g/kg DM. GML increased the final BW (p = 0.04) and ADG (p = 0.02) compared with CON. There were no significant differences in the DMI (p > 0.10) among the three treatment groups. GML and SOL tended to decrease the dry matter intake/average daily gain (p = 0.07) compared with CON. GML tended to increase the apparent digestibility of CP (p = 0.08) compared with CON. SOL increased the apparent digestibility of NDF (p = 0.04) compared with CON. The Chao1 and Shannon indexes of SOL were both significantly higher than those of the other groups (p = 0.01). LefSE analysis showed that Bifidobacteriaceae of the Bifidobacteriales was enriched in the GML group. In addition, compared with GML, SOL reduced the relative abundance of Actinobacteria (p < 0.01) and increased the relative abundance of Verrucomicrobia (p = 0.05), and GML reduced the relative abundance of Ruminococcus (p = 0.03). Our results indicated that dietary supplementation with GML or SOL improved growth performance and feed conversion, and changed the rumen microbiome of weaned lambs.

Metagenomic and Transcriptomic Analyses Reveal the Differences and Associations Between the Gut Microbiome and Muscular Genes in Angus and Chinese Simmental Cattle

Gut microbiome and heredity are two important factors affecting the intramuscular fat (IMF) of cattle, excluding age, sex, and nutrition. This study aimed at deciphering these two differences by analyzing the gut microbiome and intramuscular differentially expressed genes (DEGs) in the Angus and Chinese Simmental cattle. Feces and longissimus dorsi were collected from the two groups of animals (n = 20/group) for multiomics analysis. Angus holds a significantly higher diversity than Chinese Simmental, and the relative abundance of Roseburia, Prevotella, Coprococcus, etc., was obviously higher in Angus. Chinese Simmental had higher levels of isobutyrate, isovalerate, and valerate, although similar levels of acetate, propionate, and butyrate were observed for the two groups. The DEGs upregulated in Chinese Simmental were mainly involved in immune and inflammatory responses, while those in Angus were associated with the regulation of muscle system and myofibril. We finally identified 17 species, including Eubacterium rectale, etc., which were positively correlated to muscle and fat metabolism genes (MSTN, MYLPF, TNNT3, and FABP3/4) and illustrate the associations between them. Our study unveils the gut microbial differences and significant DEGs as well as their associations between the two breeds, providing valuable guidance for future mechanism research and development of intervention strategies to improve meat quality.

Metagenomics reveals differences in microbial composition and metabolic functions in the rumen of dairy cows with different residual feed intake

Background

Rumen microbial composition and functions have vital roles in feed digestion and fermentation and are linked to feed efficiency in cattle. This study selected Holstein cows, which are high in both milk protein content and milk yield, to analyse the relationship between the rumen microbiota and residual feed intake (RFI). Eighteen multiparous lactating cows were divided into low RFI (LRFI, high efficiency, n = 9) and high RFI (HRFI, low efficiency, n = 9) groups to investigate the differences in microbial composition and functions.

Results

The relative abundances of butyrate producers, including the Clostridium, Butyrivibrio, Eubacterium and Blautia genera, were higher in HRFI cows than in LRFI cows (P < 0.05). Four carbohydrate metabolic pathways (glycolysis/gluconeogenesis, pentose phosphate pathway, fructose and mannose metabolism, and butanoate metabolism) and one energy metabolism pathway (methane metabolism), were more abundant in HRFI animals (P < 0.05). Quorum sensing and DNA replication pathways were more abundant in HRFI cows. For CAZyme profiles, 14 out of 19 genes encoding carbohydrates-deconstructing enzymes were more abundant in HRFI cows (P < 0.05). Seven Lachnospiraceae species associated with carbohydrate metabolism and quorum sensing may contribute to the difference in feed efficiency. Moreover, the LRFI cows had lower abundances of Methanosphaera (P < 0.01), Methanobrevibacter ruminantium (P = 0.09) and methanogenesis functions (P = 0.04).

Conclusions

The rumen microbiota of low-efficiency cows has stronger abilities to degrade carbohydrates and produce methane, and quorum sensing pathways could also be associated with differences in feed efficiency. This study provides a deeper understanding of the microbial ecology of dairy cows with different feed efficiencies and highlights the possibility of modulating the rumen microbiome or microbial functions to improve the feed efficiency of dairy cows.

Supplementary Information

The online version contains supplementary material available at 10.1186/s42523-022-00170-3.

Differences in the Gut Microbiota Composition and Metabolites Associated With Feeding Intolerance in VLBW Infants With a Gestational Age of ≤ 30 Weeks: A Pilot Study

Objective

To explore the main variations in gut microbiota compositions, short-chain fatty acids (SCFAs) concentrations and autoinducer-2 (AI-2) levels in very-low-birth-weight (VLBW) infants with feeding intolerance (FI).

Methods

Twenty-seven VLBW infants with gestational ages of ≤30 weeks were divided into the FI group (n=14) and feeding tolerance (FT) group (n=13). The gut microbiota composition and SCFAs concentrations and AI-2 levels in feces were detected at 2 and 4 weeks after birth.

Results

There was no difference in alpha diversity between the two groups at 2 and 4 weeks after birth (P>0.05). Although the Chao index decreased (P<0.05), there was no difference in the Shannon index from 2 weeks to 4 weeks in either the FI or FT group (P>0.05). Additionally, there was no difference in beta diversity between the FI and FT groups at 2 weeks (P>0.05), but there was a significant difference in beta diversity between the two groups at 4 weeks (P<0.05) and a large difference from 2 weeks to 4 weeks in both the FI and FT groups (P<0.05). Furthermore, the composition of the microbiota at 4 weeks was significantly different from that at 2 weeks in the FI group (P<0.05). The Veillonella abundance was lower at 4 weeks in the FI group (P<0.05), but there were no differences in the compositions of the other main microbes between the two groups (P>0.05). Proteobacteria and Firmicutes were dominant in both the FI and FT groups. The concentrations of propanoic, valeric and hexanoic acids were lower in the FI group at 2 weeks, and the levels of isobutyric and valeric acids were lower at 4 weeks after birth (P<0.05). The areas under the curves (AUCs) of propanoic, butanoic and valeric acids in predicting FI were 0.878, 0.816 and 0.744, respectively. Compared with that in the FT group, the relative bioluminescence of AI-2 was lower in the FI group at 2 weeks (P<0.05), and the AUC was 0.736.

Conclusions

The main composition of the microbiota was not obviously different in infants with FI. Some SCFAs and AI-2 have moderate value in predicting FI.

Metagenomic analysis of community, enzymes and metabolic pathways during corn straw fermentation with rumen microorganisms for volatile fatty acid production

Anaerobic fermentation of corn straw with rumen microorganisms as inoculum to produce volatile fatty acids (VFAs) is important for biomass valorization. In this study, dynamic variation in bacterial and fungal community composition, carbohydrate-active enzymes (CAZymes) and key functional genes related with VFA production was explored via metagenomic sequencing. Rumen microorganisms efficiently hydrolyzed and acidified corn straw, and VFA concentration reached 8.99 g/L in 72 h. Bacterial and fungal community significantly changed, but the core genera kept stable. Low pH and VFA accumulation were the main factors affecting bacterial and fungal communities. The positive correlations between bacteria were more complex than those between fungi. Most CAZyme abundance significantly decreased after 72 h fermentation, and functional gene abundance participating in VFA generation also decreased. This study provided new insights into dynamic variation of bacteria and fungi during anaerobic ruminal fermentation in vitro, promoting the application of rumen microorganisms in practice.

Rumen Fermentation, Digestive Enzyme Activity, and Bacteria Composition between Pre-Weaning and Post-Weaning Dairy Calves

Simple Summary

Weaning is very important for young ruminants. At this stage, calves’ main source of nutrients is transferred from milk into solid feed, such as starter and roughage. At the same time, the rumen function of calves undergoes tremendous changes, such as bacteria, which are the main players in rumen function. Our research found that the rumen bacteria network of post-weaning calves was more complex. The fermentation end products, such as acetate, propionate, and butyrate, were higher in the post-weaning calves than the pre-weaning group. However, digestive enzymes such as protease, carboxymethyl cellulase, cellobiohydrolase, and glucosidase were lower in the post-weaning calves than the pre-weaning calves. These findings provided useful information for reference regarding the feeding management of calves.

Abstract

To better understand the transition of rumen function during the weaning period in dairy calves, sixteen Holstein dairy calves were selected and divided into two groups: pre-weaning (age = 56 ± 7 day, n = 8) and post-weaning (age = 80 ± 6 day, n = 8). The rumen fluid was obtained by an oral gastric tube. The rumen fermentation profile, enzyme activity, bacteria composition, and their inter-relationship were investigated. The results indicated that the post-weaning calves had a higher rumen acetate, propionate, butyrate, and microbial crude protein (MCP) than the pre-weaning calves (p < 0.05). The rumen pH in the post-weaning calves was lower than the pre-weaning calves (p < 0.05). The protease, carboxymethyl cellulase, cellobiohydrolase, and glucosidase in the post-weaning calves had a lower trend than the pre-weaning calves (0.05 < p < 0.1). There was no difference in α and β diversity between the two groups. Linear discriminant analysis showed that the phylum of Fibrobacteres in the post-weaning group was higher than the pre-weaning group. At the genus level, Shuttleworthia, Rikenellaceae, Fibrobacter, and Syntrophococcus could be worked as the unique bacteria in the post-weaning group. The rumen bacteria network node degree in the post-weaning group was higher than the pre-weaning group (16.54 vs. 9.5). The Shuttleworthia genus was highly positively correlated with MCP, propionate, total volatile fatty acid, glucosidase, acetate, and butyrate (r > 0.65, and p < 0.01). Our study provided new information about the rumen enzyme activity and its relationship with bacteria, which help us to better understand the effects of weaning on the rumen function.

Antioxidant and antibacterial study of 10 flavonoids revealed rutin as a potential antibiofilm agent in Klebsiella pneumoniae strains isolated from hospitalized patients

The emergence of multidrug resistance (MDR) and extensive drug resistance (XDR) in Klebsiella pneumoniae strains has posed great threats to conventional antibiotics. Previous studies have shown that plant-derived flavonoids have inhibitory functions against pathogens. However, in K. pneumoniae, the antibacterial activity of different flavonoids against growth and biofilm formation remains a mystery. The aim of the present study was to evaluate the antioxidant abilities of different flavonoids, to screen active ingredients and to identify their inhibitory effects on K. pneumoniae growth and biofilm formation. In total, 10 flavonoids representing 4 major categories were screened and used in this study. The antioxidant capacity of each flavonoid was evaluated through a DPPH (2,2-diphenyl-1-picrylhydrazyl) assay. Rutin showed the highest level of free radical scavenging capacity, followed by kaempferol, luteolin, quercetin, apigenin, hesperidin, sinensetin, naringenin, naringin and 3,5,6,7,8,3',4'-heptamethoxyflavone. The inhibitory effects of rutin and naringin on bacterial growth were also compared. The lowest MICs of rutin were found against K. pneumoniae ATCC700603 (1024 μg/mL) and E. coli ATCC25922 (512 μg/mL). However, the MBICs were not found. Rutin showed strong inhibitory ability against both the growth curve and biofilm production. The expression profiles of 15 biofilm-related genes were analyzed in biofilm cells both with and without rutin treatment. The luxS gene and wabG gene were downregulated significantly by rutin treatment. Correlation analysis showed that mrkA gene expression was positively correlated with biofilm biomass accumulation. Our study indicated that biofilm production is correlated with the expression of several genes rather than one. MrkA gene expression was positively correlated with biofilm biomass accumulation. Our study screened rutin as a potential agent to inhibit K. pneumoniae biofilm formation.

Fecal Bacteria Implicated in Biofilm Production Are Enriched and Associate to Gastrointestinal Symptoms in Patients With APECED - A Pilot Study

Backgrounds and Aims

APECED is a rare autoimmune disease caused by mutations in the Autoimmune Regulator gene. A significant proportion of patients also have gastrointestinal symptoms, including malabsorption, chronic diarrhea, and obstipation. The pathological background of the gastrointestinal symptoms remains incompletely understood and involves multiple factors, with autoimmunity being the most common underlying cause. Patients with APECED have increased immune responses against gut commensals. Our objective was to evaluate whether the intestinal microbiota composition, predicted functions or fungal abundance differ between Finnish patients with APECED and healthy controls, and whether these associate to the patients' clinical phenotype and gastrointestinal symptoms.

Methods

DNA was isolated from fecal samples from 15 patients with APECED (median age 46.4 years) together with 15 samples from body mass index matched healthy controls. DNA samples were subjected to analysis of the gut microbiota using 16S rRNA gene amplicon sequencing, imputed metagenomics using the PICRUSt2 algorithm, and quantitative PCR for fungi. Extensive correlations of the microbiota with patient characteristics were determined.

Results

Analysis of gut microbiota indicated that both alpha- and beta-diversity were altered in patients with APECED compared to healthy controls. The fraction of Faecalibacterium was reduced in patients with APECED while that of Atopobium spp. and several gram-negative genera previously implicated in biofilm formation, e.g. Veillonella, Prevotella, Megasphaera and Heamophilus, were increased in parallel to lipopolysaccharide (LPS) synthesis in imputed metagenomics. The differences in gut microbiota were linked to patient characteristics, especially the presence of anti-Saccharomyces cerevisiae antibodies (ASCA) and severity of gastrointestinal symptoms.

Conclusions

Gut microbiota of patients with APECED is altered and enriched with predominantly gram-negative bacterial taxa that may promote biofilm formation and lead to increased exposure to LPS in the patients. The most pronounced alterations in the microbiota were associated with more severe gastrointestinal symptoms.

Effects of peripartal yeast culture supplementation on lactation performance, blood biomarkers, rumen fermentation, and rumen bacteria species in dairy cows

Feeding yeast culture fermentation products has been associated with improved feed intake and milk yield in transition dairy cows. These improvements in performance have been further described in terms of rumen characteristics, metabolic profile, and immune response. The objective of this study was to evaluate the effects of a commercial yeast culture product (YC; Culture Classic HD, Phibro Animal Health) on performance, blood biomarkers, rumen fermentation, and rumen bacterial population in dairy cows from -30 to 50 d in milk (DIM). Forty Holstein dairy cows were enrolled in a randomized complete block design from -30 to 50 DIM and blocked according to expected calving day, parity, previous milk yield, and genetic merit. At -30 DIM, cows were assigned to either a basal diet plus 114 g/d of ground corn (control; n = 20) or a basal diet plus 100 g/d of ground corn and 14 g/d of YC (n = 20), fed as a top-dress. Cows received the same close-up diet from 30 d prepartum until calving [1.39 Mcal/kg of dry matter (DM) and 12.3% crude protein (CP)] and lactation diet from calving to 50 DIM (1.60 Mcal/kg of DM and 15.6% CP). Blood samples and rumen fluid were collected at various time points from -30 to 50 d relative to calving. Cows fed YC compared with control showed a trend for increased energy-corrected milk (+3.2 kg/d). Lower somatic cell counts were observed in YC cows than in control. We detected a treatment × time interaction in nonesterified fatty acids (NEFA) that could be attributed to a trend for greater NEFA in YC cows than control at 7 DIM, followed by lower NEFA in YC cows than control at 14 and 30 DIM. In the rumen, YC contributed to mild changes in rumen fermentation, mainly increasing postpartal valerate while decreasing prepartal isovalerate. This was accompanied by alterations in rumen microbiota, including a greater abundance of cellulolytic (Fibrobacter succinogenes) and lactate-utilizing bacteria (Megasphaera elsdenii). These results describe the potential benefits of supplementing yeast culture during the late pregnancy through early lactation, at least in terms of rumen environment and performance.

Microbiomes attached to fresh perennial ryegrass are temporally resilient and adapt to changing ecological niches

BACKGROUND

Gut microbiomes, such as the rumen, greatly influence host nutrition due to their feed energy-harvesting capacity. We investigated temporal ecological interactions facilitating energy harvesting at the fresh perennial ryegrass (PRG)-biofilm interface in the rumen using an in sacco approach and prokaryotic metatranscriptomic profiling.

RESULTS

Network analysis identified two distinct sub-microbiomes primarily representing primary (≤ 4 h) and secondary (≥ 4 h) colonisation phases and the most transcriptionally active bacterial families (i.e Fibrobacteriaceae, Selemondaceae and Methanobacteriaceae) did not interact with either sub-microbiome, indicating non-cooperative behaviour. Conversely, Prevotellaceae had most transcriptional activity within the primary sub-microbiome (focussed on protein metabolism) and Lachnospiraceae within the secondary sub-microbiome (focussed on carbohydrate degradation). Putative keystone taxa, with low transcriptional activity, were identified within both sub-microbiomes, highlighting the important synergistic role of minor bacterial families; however, we hypothesise that they may be 'cheating' in order to capitalise on the energy-harvesting capacity of other microbes. In terms of chemical cues underlying transition from primary to secondary colonisation phases, we suggest that AI-2-based quorum sensing plays a role, based on LuxS gene expression data, coupled with changes in PRG chemistry.

CONCLUSIONS

In summary, we show that fresh PRG-attached prokaryotes are resilient and adapt quickly to changing niches. This study provides the first major insight into the complex temporal ecological interactions occurring at the plant-biofilm interface within the rumen. The study also provides valuable insights into potential plant breeding strategies for development of the utopian plant, allowing optimal sustainable production of ruminants. Video Abstract.

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.

Phytogenic Additives Can Modulate Rumen Microbiome to Mediate Fermentation Kinetics and Methanogenesis Through Exploiting Diet-Microbe Interaction

Ruminants inhabit the consortia of gut microbes that play a critical functional role in their maintenance and nourishment by enabling them to use cellulosic and non-cellulosic feed material. These gut microbes perform major physiological activities, including digestion and metabolism of dietary components, to derive energy to meet major protein (65-85%) and energy (ca 80%) requirements of the host. Owing to their contribution to digestive physiology, rumen microbes are considered one of the crucial factors affecting feed conversion efficiency in ruminants. Any change in the rumen microbiome has an imperative effect on animal physiology. Ruminal microbes are fundamentally anaerobic and produce various compounds during rumen fermentation, which are directly used by the host or other microbes. Methane (CH4) is produced by methanogens through utilizing metabolic hydrogen during rumen fermentation. Maximizing the flow of metabolic hydrogen in the rumen away from CH4 and toward volatile fatty acids (VFA) would increase the efficiency of ruminant production and decrease its environmental impact. Understanding of microbial diversity and rumen dynamics is not only crucial for the optimization of host efficiency but also required to mediate emission of greenhouse gases (GHGs) from ruminants. There are various strategies to modulate the rumen microbiome, mainly including dietary interventions and the use of different feed additives. Phytogenic feed additives, mainly plant secondary compounds, have been shown to modulate rumen microflora and change rumen fermentation dynamics leading to enhanced animal performance. Many in vitro and in vivo studies aimed to evaluate the use of plant secondary metabolites in ruminants have been conducted using different plants or their extract or essential oils. This review specifically aims to provide insights into dietary interactions of rumen microbes and their subsequent consequences on rumen fermentation. Moreover, a comprehensive overview of the modulation of rumen microbiome by using phytogenic compounds (essential oils, saponins, and tannins) for manipulating rumen dynamics to mediate CH4 emanation from livestock is presented. We have also discussed the pros and cons of each strategy along with future prospective of dietary modulation of rumen microbiome to improve the performance of ruminants while decreasing GHG emissions.

The Rhodamine Isothiocyanate Analogue as a Quorum Sensing Inhibitor Has the Potential to Control Microbially-Induced Biofouling

Quorum sensing inhibitors (QSIs) have been proven to be an innovative approach to interfering with biofilm formation, since this process is regulated by QS signals. However, most studies have focused on single-species biofilm formation, whereas studies of the effects of signal interference on the development of multispecies biofilm, especially in the natural environment, are still lacking. Here we develop and evaluate the anti-biofilm capability of a new QSI (rhodamine isothiocyanate analogue, RIA) in natural seawater. During the experiment, biofilm characteristics, microbial communities/functions and network interactions were monitored at 36, 80, and 180 h, respectively. The results showed that the biomass and 3D structure of the biofilm were significantly different in the presence of the QSI. The expression of genes involved in extracellular polysaccharide synthesis was also downregulated in the QSI-treated group. Dramatic differences in microbial composition, β-diversity and functions between the RIA-treated group and the control group were also observed, especially in the early stage of biofilm development. Furthermore, co-occurrence model analysis showed that RIA reduced the complexity of the microbial network. This study demonstrates that rhodamine isothiocyanate analogue is an efficient QS inhibitor and has potential applications in controlling biofouling caused by multispecies biofilm, especially in the early stage of biofouling formation.

Impact of N-Acyl-Homoserine Lactones, Quorum Sensing Molecules, on Gut Immunity

Among numerous molecules found in the gut ecosystem, quorum sensing (QS) molecules represent an overlooked part that warrants highlighting. QS relies on the release of small molecules (auto-inducers) by bacteria that accumulate in the environment depending on bacterial cell density. These molecules not only are sensed by the microbial community but also interact with host cells and contribute to gut homeostasis. It therefore appears entirely appropriate to highlight the role of these molecules on the immune system in dysbiosis-associated inflammatory conditions where the bacterial populations are imbalanced. Here, we intent to focus on one of the most studied QS molecule family, namely, the type I auto-inducers represented by N-acyl-homoserine lactones (AHL). First described in pathogens such as Pseudomonas aeruginosa, these molecules have also been found in commensals and have been recently described within the complex microbial communities of the mammalian intestinal tract. In this mini-review, we will expound on this emergent field of research. We will first recall evidence on AHL structure, synthesis, receptors, and functions regarding interbacterial communication. Then, we will discuss their interactions with the host and particularly with agents of the innate and adaptive gut mucosa immunity. This will reveal how this new set of molecules, driven by microbial imbalance, can interact with inflammation pathways and could be a potential target in inflammatory bowel disease (IBD). The discovery of the general impact of these compounds on the detection of the bacterial quorum and on the dynamic and immune responses of eukaryotic cells opens up a new field of pathophysiology.

Droplet-based high-throughput cultivation for accurate screening of antibiotic resistant gut microbes

Traditional cultivation approaches in microbiology are labor-intensive, low-throughput, and yield biased sampling of environmental microbes due to ecological and evolutionary factors. New strategies are needed for ample representation of rare taxa and slow-growers that are often outcompeted by fast-growers in cultivation experiments. Here we describe a microfluidic platform that anaerobically isolates and cultivates microbial cells in millions of picoliter droplets and automatically sorts them based on colony density to enhance slow-growing organisms. We applied our strategy to a fecal microbiota transplant (FMT) donor stool using multiple growth media, and found significant increase in taxonomic richness and larger representation of rare and clinically relevant taxa among droplet-grown cells compared to conventional plates. Furthermore, screening the FMT donor stool for antibiotic resistance revealed 21 populations that evaded detection in plate-based assessment of antibiotic resistance. Our method improves cultivation-based surveys of diverse microbiomes to gain deeper insights into microbial functioning and lifestyles.