Exploration of the Muribaculaceae Family in the Gut Microbiota: Diversity, Metabolism, and Function

1The second genome of the gut microbiota encodes 100 times more genes than the human genome. These microbiota can affect the digestion and absorption of dietary components, and the resulting metabolites help the host regulate the immune system, maintain intestinal mucosal barrier function, and resist pathogens. Previous studies have shown that plant-based diet intake is inversely correlated with obesity, hypertension, type 2 diabetes, and cardiovascular disease. A plant-based diet is rich in active biological ingredients such as dietary fibre and polyphenols. The gut microbiota can interact with these ingredients, which in turn affects the body’s nutritional metabolism and immunity. Therefore, elucidating the diversity, metabolism, and function of the gut microbiota is crucial for improving human health.

2The word “probiotic” comes from the Greek word “biotikos,” which means “beneficial to life”. In 2001, the Food and Agriculture Organisation of the United Nations and the World Health Organisation redefined probiotics as living microorganisms that, when consumed in sufficient quantities, can have a positive effect on the health of the host. The use of probiotics depends on their source, and different probiotics have different beneficial effects on health. For example, Lactobacillus plantarum Shinshu N-07 isolated from fermented Brassica rapa L. has anti-obesity effects via decreasing serum triglycerides, inhibiting hepatic steatosis, and alleviating inflammatory cell infiltration in diet-induced obese mice. Bacillus amyloliquefaciens TL106 isolated from Tibetan pig faeces can stabilise the gut microbiota and alleviate intestinal injury induced by enterohaemorrhagic Escherichia coli in mice. Ideally, strains used in food should be of human origin and should be able to attach to intestinal epithelial cell membranes and make active substances that benefit host metabolism without affecting the normal microbial community.

3In recent years, Muribaculaceae have attracted much attention because of their beneficial role in maintaining host health. Muribaculaceae can produce short-chain fatty acids and regulate intestinal barrier function and the immune response, and they are considered a promising “next generation probiotic”. Several studies have focused on genomics to reveal the gene sequence and function of the Muribaculaceae family. To date, few isolates have been obtained from Muribaculaceae, and the results obtained via 16S rRNA high-throughput sequencing technology represent norank_f_Muribaculaceae. Although few studies have investigated Muribaculaceae, the potential effects on host physiology have yet to be clarified. Thus, the present study systematically summarises the current research achievements related to Muribaculaceae. By exploring the putative functional and probiotic mechanisms, we hope to understand Muribaculaceae comprehensively.

4We conducted a comprehensive search of research and reviews on the Muribaculaceae family in three databases: Google Scholar (https://scholar.google.com/), Web of Science (http://apps.webofknowledge.com), and PubMed (https://pubmed.ncbi.nlm.nih.gov/). The keywords searched included Muribaculaceae family, functional foods, inflammatory bowel disease, obesity, and type 2 diabetes between 2014 and 2024. To identify more relevant studies, we examined the reference lists of the studies included in the current review. On the basis of the title and abstract, we excluded some irrelevant citations and searched 105 articles for further evaluation.

5The Gram-negative Bacteroidetes genus, including Muribaculaceae, Bacteroidaceae, Rikenellaceae, and Prevotellaceae, is one of the most abundant in the gut microbiota of mammals. Muribaculaceae belong to Bacteroidia and Bacteroidales, which are predominantly present in the intestinal tracts of endotherms. Muribaculaceae are highly abundant in the intestinal tract of mice, accounting for 54.99–83.44% of the total Bacteroides content. Faeces from C57BL/6J mice constitute the primary source of Muribaculaceae, which were previously known as Candidatus homeothermaceae or family S24-7. In 2019, Ilias et al. reviewed the relevant data, reannotated and renamed this family Muribaculaceae, and used metagenomics to cluster 685 species. To date, the isolates and gene sequences of this family have been identified. As shown in Table 1, 10 genera have been described in the family Muribaculaceae: Muribaculum, Duncaniella, Paramuribaculum, Sodaliphilus, Heminiphilus, Lepagella, Candidatus amulumruptor, Candidatus merdivivens, Candidatus homeothermus and Sangeribacter. Among these, Muribaculum and Duncaniella comprise the highest content.

6Muribaculaceae can metabolise endogenous and exogenous polysaccharides, including α-glucan, plant glycan, and host glycan. As the dominant family of Bacteroidetes, Muribaculaceae encode a large number of enzymes that hydrolyse carbohydrates. These enzymes account for approximately 6% of the gene sequence and use starch as the basic source of energy. Youn et al. used metagenomic and metatranscriptomic analyses and reported that the Muribaculum and Duncaniella genera have a high proportion of carbohydrate-metabolising genes. At the species level, Muribaculaceae contain various enzymes that hydrolyse carbohydrates. For example, Muribaculum gordoncarteri, Duncaniella dubosii, and Duncaniella freteri present high activities of β-glucosidase, α-arabinase, and α-fucosidase, whereas Heminiphilus faecis presents α-arabinase activity and positive reactions in fermentation experiments involving mannan and L-arabinose. The results of animal assays revealed that dietary fibres such as resistant starch and inulin significantly increase the abundance of Muribaculaceae in the gut microbiota (Table 2). Mammals do not have the enzymes to hydrolyse dietary fibre. Muribaculaceae can use dietary fibre as an energy source, which promote their colonisation in the gut.

7The scarcity of dietary fibre in the host diet prompts Muribaculaceae to metabolise host glycan for usage. Mucin, a highly glycosylated protein, is the primary major source of nutrients for the gut microbiota. Lee et al. used Raman spectroscopy and metagenomics to analyse mucin-degrading bacteria in the mouse colon and reported that Muribaculaceae encode O-glycanases and sialidases. O-glycanase is a critical enzyme for mucin degradation, whereas sialidase cleaves the terminal sialic acid and sulphate residues from mucin O-glycans. Similarly, Pereira et al. used Raman-activated cell sorting, mini-metagenomics, and single-cell stable isotope probing and identified Muribaculaceae as major mucin monosaccharide foragers in the intestinal tract. In recent years, Akkermansia muciniphila has been deemed a new generation of probiotics because of its ability to degrade mucin and regulate intestinal permeability and barrier integrity. Muribaculaceae are also a mucin-degrading bacterium; however, their potential probiotic effects need to be explored further.

8Short-chain fatty acids are produced through the glycolysis pathway of dietary fibre in intestinal microorganisms, and the core metabolic ability of the Muribaculaceae family is the degradation of various complex polysaccharides. Byron et al. reported that the Muribaculaceae family produces propionic acid, whereas Kate et al. reported that it produces acetic acid, propionic acid, and succinate. Table 2 shows that some dietary fibre interventions, such as inulin, resistant starch, and soluble fibre, increased the abundance of the Muribaculaceae family in the intestinal tract of mice. Moreover, the abundances of Muribaculum, Paramuribaculum, and Duncaniella and the contents of acetic, propionic, and butyric acids increased markedly. In addition, potato and lotus seeds have high contents of resistant starch, and black cherry powder is rich in pectin. A similar phenomenon was observed in animal intervention assays on these plant-based foods rich in dietary fibre. These results suggest that Muribaculaceae can produce short-chain fatty acids by metabolising dietary fibre (Figure 1). Lactobacilli intake increased the abundance of the intestinal microbiota of the Muribaculaceae family and short-chain fatty acids simultaneously. For example, Lactobacillus delbrueckii and Streptococcus thermophilus 1131 increased the content of propionic and butyric acids, whereas Lactobacillus plantarum Y44 increased the levels of acetic, propionic, butyric, and valeric acids. Some studies have shown that Lactobacillus only encodes genes that produce lactic acid, which can be used by microorganisms that decompose polysaccharides to produce butyric acid. Therefore, it can be inferred that the Muribaculaceae family can produce short-chain fatty acids and cross-feed with other bacteria to produce short-chain fatty acids.

9Positive and negative interspecific relationships have been established between various populations of intestinal microbes, among which positive relationships include co-operation, symbiosis and cross-feeding. Bacteroidetes are among the most abundant intestinal microbiota that interact strongly with other species. For example, Bacteroidetes has many outer membrane vesicles that share glycan metabolites with other microbiota. The Muribaculaceae family is a vital member of Bacteroidetes that can tolerate and reduce low intestinal oxygen levels. It can adapt to and improve the intestinal environment and can coexist with other species. Table 3 shows that the ingestion of Bifidobacterium bifidum NK175, Bifidobacterium lactis XLTG11, and Bifidobacterium longum BR-108 increased the abundance of the Muribaculaceae family in the intestinal tract of mice. However, the relationship between Muribaculaceae and Bifidobacterium has rarely been reported. Previous studies have shown that Bacteroides and Bifidobacterium metabolise endogenous and exogenous glycans as symbionts. Specifically, Bifidobacterium uses oligosaccharides, whereas Bacteroides breaks down polysaccharides into oligosaccharides that can be fed to Bifidobacterium. Since Muribaculaceae are active users of polysaccharides in the gut, we speculated that there is an interspecific cross-feeding relationship between Muribaculaceae and Bifidobacterium. In addition, Lactobacillus plantarum Shinshu N-07, Lactobacillus paracasei NL41, Saccharomyces boulardii BR14, Streptococcus thermophilus 1131, and Faecalibacterium prausnitzii significantly increased the Muribaculaceae content in the gut of mice (Table 3). Overall, Muribaculaceae are strongly correlated with probiotics, such as Bifidobacterium and Lactobacillus, and exhibit a cross-feeding or co-operative symbiotic association.

10The Muribaculaceae family produces vitamins for the host, including B1 (thiamine), B2 (riboflavin), B3 (niacin), B5 (pantothenic acid), B7 (biotin), and B9 (folate). This phenomenon could be attributed to the ability of the Muribaculaceae family to encode genes encoding vitamin transporters. In terms of amino acid metabolism, metagenomics predicted that 75–100% of the species in the Muribaculaceae family synthesise aspartate, glutamine, glutamic acid, glycine, methionine, valine, leucine, and isoleucine. In addition, Muribaculaceae also produce some rare enzymes in Bacteroidetes, such as genes encoding ureases, IgA-degrading peptidases, and oxalate-degrading enzymes. Importantly, the Muribaculaceae family produces oxaloyl CoA decarboxylase and formyl CoA transferase for the degradation of oxalic acid. Most plant-based foods contain oxalic acid, which might underscore the plant-based diet-promoted growth of Muribaculaceae in the gut.

11A complete mucus barrier is the first line of defence that protects intestinal health, and impaired mucus barrier function is one of the major signs of IBD. The structure and function of mucus depend mainly on mucin, which moistens and lubricates the intestinal wall. These properties protect intestinal epithelial cells from mechanical stress and exert immune effects, enhancing intestinal homeostasis. The Muribaculaceae family is attached to the mucous layer and is a symbiotic user of myxoglycan in the intestine, showing a strong correlation with IBD. Strikingly, IBD decreases the abundance of the Muribaculaceae family in the intestinal microbiota. Volk et al. reported that the abundance of the Muribaculaceae family was significantly lower in the mucous layer of Nlrp6−/− and IL18−/− deficient mice than in an intact mucous layer. A similar phenomenon has been observed in animal models of IBD, such as following the administration of dextran sulphate sodium (DSS), lipopolysaccharide (LPS), and excessive antibiotics, because IBD destroys the structural integrity of the mucous layer, which is the attachment site and a major nutrient source of the Muribaculaceae family. Some plant foods (ginger and cranberry bean) and plant-derived active substances, such as dietary fibre (garlic and fucoidan polysaccharides), polyphenols (Sophora flavescens extract, oryzanol), oligosaccharides (galactose oligosaccharide and 2′-fucosyllactose), saponins (Pulsatilla saponin), and terpenoids (total diterpenoids), alleviate the symptoms of IBD (Table 4). Concurrently, these interventions increase the abundance of Muribaculaceae and improve intestinal barrier function. The role of Muribaculaceae in IBD remission may be affected via the following three mechanisms: (1) Increased gene expression levels and regeneration of mucin alleviate colon tissue injury and reduce intestinal permeability. (2) The metabolism of polysaccharides produces short-chain fatty acids that stimulate the release of mucus and activate the signalling pathway to exert anti-inflammatory effects. (3) The species competes with pathogens for the ecological niche and nutrients in the intestinal mucus layer and resists the colonisation of intestinal pathogens. In summary, IBD destroys the mucous layer of the intestinal tract of mice, decreasing the number of ecological sites of intestinal symbiotic bacteria and the abundance of Muribaculaceae. Consequently, the expression of mucin decreases, which damages the mucous layer, resulting in a vicious cycle. Effective intervention substances for alleviating IBD are beneficial for the colonisation of Muribaculaceae and the recovery of the mucus layer.

12T2D is a metabolic disorder characterised by hyperglycaemia and insulin resistance. The gut microbiota are involved in the progression of T2D via host energy homeostasis, glucose and lipid metabolism, insulin sensitivity, and the inflammatory response. The intake of plant-derived dietary fibres, such as Sargassum, Konjac glucomannan, wakame polysaccharide, moutan cortex polysaccharide, and black seed polysaccharide, alleviates insulin resistance, glucose tolerance, dyslipidaemia, and liver and kidney damage in diabetic animal models; together, these features are related to an increased presence of the Muribaculaceae family in the intestinal microbiota (Table 5). Notably, polysaccharides from Sargassum, wakame polysaccharides, and black seed polysaccharides increase the abundance of Muribaculaceae and activated the insulin receptor/phosphatidylinositol-3-kinase/protein kinase B (IRS/PI3K/Akt) signalling pathway. These phenomena regulate the insulin signal transduction and glucose metabolism pathways, in turn increasing glucose uptake and glycogen synthesis. Mannan plays a synergistic role with metformin in the treatment of C57BL/6J diabetic mice; this therapeutic effect is related to the increased abundance of Akkermansia muciniphila in the Muribaculaceae family. Additionally, acarbose treats diabetes by preventing the breakdown of starch in the small intestine and altering the composition of the gut microbiota. Byron et al. used metagenomics and reported that the nine most responsive bacteria under the intervention of acarbose are classified in the Muribaculaceae family. Although further investigation is needed on other bacterial genera/species that improve blood glucose metabolism and insulin resistance, these findings suggest that an increase in Muribaculaceae could help exert the anti-diabetic properties of hypoglycaemic drugs.

13Obesity underlies the disruption of the intestinal microbiota, and an increase in the Firmicutes/Bacteroides ratio is considered one of the indicators of obesity. The Muribaculaceae family is a major member of Bacteroides, and a significant negative correlation has been established between Muribaculaceae and the risk of obesity (Table 6). A population investigation revealed a high content of the Muribaculaceae family in the gut of the Yanomami people, who consumed a plant-based diet dominated by fruits and grains. Osborne et al. analysed the intestinal microbiota of 248 subjects in Bangladesh and reported that the Muribaculaceae family was negatively correlated with body weight, hip circumference, waist circumference, and other physical indicators. In a dietary survey of 29 Chinese people, Qian et al. reported a lower content of Muribaculaceae in the intestines of people with a high-fat diet and a higher content in those with a diet dominated by plant foods. Similarly, Muribaculaceae abundance significantly decreased in a high-fat-diet-fed mouse model. Some functional components of plant sources, such as dietary fibre (resistant starch and asparagus soluble fibre), polyphenols (naringin), and pomegranate acid, improve the symptoms of obesity and reverse the intestinal microbiota disturbance caused by a high-fat diet, increasing the abundance of Muribaculaceae (Table 6). Moreover, the Muribaculaceae family is also involved in anti-inflammatory reactions in the gut. For example, high-amylose resistant starch increases serum adiponectin and decreases the level of the inflammatory factor IL-17; these phenomena are related to increased Muribaculaceae family content. Muhomah et al. reported that the decreased level of secretory immunoglobulin A in mice fed a high-fat diet is related to reduced Muribaculaceae, acetic acid, and butyric acid contents. Together, these studies reveal the relevant role of the gut microbiota in regulating metabolic disorders and immune inflammation, suggesting that probiotics, especially Muribaculaceae, could be used as a therapeutic tool for obesity.

14In summary, we conducted a comprehensive review of studies related to the Muribaculaceae family to find evidence of associations between Muribaculaceae and plant foods, functional components, and various diseases. The results showed that Muribaculaceae had a strong capacity to metabolise endogenous (mucin glycans) and exogenous (dietary fibre) polysaccharides, could produce short-chain fatty acids, and had cross-feeding relationships with Bifidobacterium and Lactobacillus. Additionally, IBD, obesity, and T2D cause intestinal microbiota imbalance and decrease the abundance of the Muribaculaceae family. The intake of plant-derived foods (cereals, fruits, and tea), plant-derived active functional components (polysaccharides, polyphenols, and saponins), and probiotics (Lactobacillus, Bifidobacterium, and yeast) is conducive to the intestinal colonisation of the Muribaculaceae family. However, several issues related to the Muribaculaceae family need to be investigated: (1) The functional identification of Muribaculaceae isolates has been based mainly on mouse faeces, whereas that in the human gut has rarely been studied. (2) The reasons for the decline in Muribaculaceae in disease models of IBD, obesity, and T2D, as well as the molecular mechanisms of disease alleviation, remain to be explored. (3) The cross-feeding relationship between Muribaculaceae and probiotics such as Bifidobacterium and Lactobacillus needs to be substantiated by in vitro fermentation culture.