Bacteroidales

Bacteroidales is an order of Gram-negative, rod-shaped, obligately anaerobic bacteria within the class Bacteroidia of the phylum Bacteroidota, characterized by their typically non-motile, non-spore-forming morphology and ability to thrive in low-oxygen environments.^[1][2] These bacteria are primarily host-associated, colonizing the gastrointestinal tracts of humans and other animals, as well as sites like the oral cavity and rumen, where they form a dominant component of the microbiota.^[1][3] The taxonomy of Bacteroidales includes at least eight families—such as Bacteroidaceae, Prevotellaceae, Rikenellaceae, and Tannerellaceae—encompassing over 50 species distributed across more than 14 genera, including prominent ones like Bacteroides, Prevotella, Phocaeicola, Alistipes, and Parabacteroides.^[3][1] Physiologically, members of this order are adept at fermenting complex dietary polysaccharides and host-derived glycans using specialized carbohydrate-active enzymes (CAZymes), thereby producing beneficial short-chain fatty acids such as acetate, propionate, and succinate that support host energy metabolism and immune function.^[3][4] They also exhibit mechanisms for genetic exchange, including integrative conjugative elements and phase-variable capsular polysaccharides, which enhance their adaptability and competitive fitness within microbial communities.^[1] In the human gut, Bacteroidales species represent one of the most abundant and stable bacterial groups, averaging approximately 13% of total bacterial abundance across healthy individuals, with roles in maintaining microbiota balance, modulating inflammation, and influencing conditions like obesity and inflammatory bowel disease.^[3] While predominantly commensal symbionts, certain species, such as Bacteroides fragilis, can become opportunistic pathogens, causing intra-abdominal infections, abscesses, and antibiotic-resistant bacteremia when they translocate outside the gut.^[5][1] Their study has advanced understanding of host-microbe interactions, with model organisms like Bacteroides thetaiotaomicron highlighting their contributions to polysaccharide utilization and gut homeostasis.^[1]

Taxonomy and Classification

Definition and Scope

Bacteroidales is an order within the class Bacteroidia of the phylum Bacteroidota, comprising primarily Gram-negative, rod-shaped bacteria that are non-spore-forming and exhibit anaerobic or microaerophilic lifestyles.^[6] These bacteria are chemoheterotrophs capable of utilizing a wide range of organic compounds, particularly complex polysaccharides, as carbon sources.^[7] The scope of Bacteroidales includes 18 families, such as Bacteroidaceae, Prevotellaceae, Porphyromonadaceae, Rikenellaceae, and Muribaculaceae, featuring dominant genera like Bacteroides and Prevotella.^[8] These taxa are phylogenetically positioned within the broader Bacteroidota phylum, which encompasses diverse environmental and host-associated bacteria.^[6] General characteristics of Bacteroidales involve fermentative metabolism, where carbohydrates are broken down to yield short-chain fatty acids (SCFAs) including acetate, propionate, and succinate, contributing significantly to host energy harvest in the gut.^[7] They are non-motile or exhibit gliding motility in some cases and possess outer membranes rich in lipopolysaccharides.^[7] In the human gut microbiota, Bacteroidales typically constitute approximately 13% of the bacterial abundance, forming a core component alongside Firmicutes and influencing microbial community stability and function.^[3]

Historical Development

The discovery of bacteria now classified within the order Bacteroidales dates back to the late 19th century, when anaerobic gram-negative rods were first isolated from human clinical samples. In 1898, Auguste Veillon and Adrien Zuber described Bacillus fragilis from cases of appendicitis and other infections, recognizing its role as a pathogen in anaerobic conditions; this organism was later reclassified as Bacteroides fragilis, the type species of the genus Bacteroides. ^[9] Early work by Theodor Escherich in 1886 further contributed by identifying anaerobic, rod-shaped bacteria in the feces of infants, laying the groundwork for understanding the gut's microbial composition, though these were not yet formally named as Bacteroides. ^[10] By the early 20th century, the significance of these bacteria in human health became clearer through studies on intestinal and oral microbiology. In the 1920s, Bacteroides species were frequently isolated from oral infections, including periodontal abscesses and necrotizing conditions like Vincent's angina, where they were noted for their association with tissue destruction alongside spirochetes and fusobacteria. ^[7] Henri Tissier, building on Escherich's observations, examined normal intestinal flora in infants and children around 1908, identifying Bacteroides as predominant anaerobes in healthy guts and advocating their potential protective role against pathogens. ^[10] The family Bacteroidaceae was formally recognized in the 1923 edition of Bergey's Manual of Determinative Bacteriology, which grouped Bacteroides and related non-spore-forming, anaerobic rods based on morphological and cultural characteristics. ^[10] Key advancements in the 1930s solidified the taxonomic foundation of these organisms. Arthur H. Eggerth and Ruth A. Gagnon isolated multiple Bacteroides species from human feces in 1933, demonstrating their high abundance (up to 10¹¹ cells per gram of feces) and describing phenotypic traits such as saccharolytic metabolism and bile sensitivity, which distinguished them from other anaerobes. ^[11] This work emphasized their dominance in the adult gut microbiota and their potential involvement in both commensal and pathogenic roles. Taxonomic refinements accelerated in the late 20th century with the integration of molecular methods. The 1984 edition of Bergey's Manual of Systematic Bacteriology elevated the family Bacteroidaceae to the order level as Bacteroidales ord. nov., based on shared gliding motility, cell wall composition, and fatty acid profiles, separating it from other anaerobic orders. ^[8] Subsequent 16S rRNA sequencing revealed deeper phylogenetic relationships, leading to reclassifications; for instance, the 2010 second edition of Bergey's Manual, edited by Noel R. Krieg and colleagues, reaffirmed Bacteroidales within the class Bacteroidia while reassigning several genera previously aligned with Fusobacteriales due to convergent morphologies, reflecting the impact of genomic data on resolving historical misplacements. ^[12] These milestones transformed Bacteroidales from a loosely defined group of pathogens into a well-delineated order central to human microbiome research.

Current Hierarchical Placement

Bacteroidales is currently classified within the domain Bacteria, phylum Bacteroidota, class Bacteroidia, and order Bacteroidales, reflecting the standardized nomenclature adopted in recent taxonomic revisions.^[13] This hierarchy aligns with the phylogenomic framework established by the International Committee on Systematics of Prokaryotes, emphasizing monophyletic groupings based on 16S rRNA gene sequences and whole-genome analyses.^[14] The type genus of Bacteroidales is Bacteroides, with Bacteroides fragilis designated as the type species, serving as the nomenclatural reference for the order.^[15] According to the List of Prokaryotic names with Standing in Nomenclature (LPSN) as of 2025, the order encompasses 18 families, including both host-associated and environmental taxa, with at least eight families dominant in the human gut.^[8] Prominent families include Bacteroidaceae, featuring genera such as Bacteroides and Phocaeicola; Prevotellaceae, which includes Prevotella and Alloprevotella; and Porphyromonadaceae, represented by genera like Porphyromonas. These families account for many of the core taxa in human and animal microbiomes, with ongoing refinements to delineate boundaries based on genomic distinctiveness.^[16] Recent taxonomic updates, particularly in the Genome Taxonomy Database (GTDB) release R07-RS207 from 2022, have incorporated genera such as Dysgonomonas (within Dysgonomonadaceae) and Odoribacter (within Odoribacteraceae), reflecting expanded genomic sampling from environmental and host sources. Additionally, the family Muribaculaceae has been formally recognized as a significant clade within Bacteroidales, dominating the mouse gut microbiota and highlighting the order's role in mammalian ecology. These additions underscore the dynamic nature of Bacteroidales classification, driven by metagenomic data integration.

Phylogeny and Evolution

Phylogenetic Relationships

Bacteroidales constitutes a monophyletic order within the class Bacteroidia of the phylum Bacteroidota, as established through phylogenetic analyses of 16S rRNA gene sequences and whole-genome data.^[17] This positioning reflects its distinct evolutionary lineage among Gram-negative bacteria, supported by genome-based taxonomic classifications that confirm the order's coherence and separation from other classes like Flavobacteriia.^[18] Within the broader Bacteroidota phylum, the class Bacteroidia, which includes Bacteroidales, shares a close sister relationship with Flavobacteriia, which includes Flavobacteriales, a pattern consistently recovered in both 16S rRNA-based trees and multi-gene phylogenomic reconstructions.^[17] This adjacency highlights shared ancestral traits, such as gliding motility in some members of the phylum, while underscoring ecological divergences, with Bacteroidales predominantly anaerobic and host-associated compared to the aerobic, free-living tendencies of Flavobacteriales.^[18] Recent genomic studies of over 400 human gut Bacteroidales isolates have further resolved internal phylogenies, supporting the monophyly of key families and highlighting genus-level diversification.^[3] The internal structure of Bacteroidales reveals distinct clades, including a core group formed by the monophyletic families Bacteroidaceae and Prevotellaceae, which dominate in anaerobic environments like the mammalian gut. In contrast, peripheral families such as Tannerellaceae occupy more divergent positions, as delineated in comprehensive alignments from the ARB-SILVA database release 138, which integrates over 10 million high-quality ribosomal sequences.^[19] These analyses emphasize the order's diversity, with core clades showing tighter clustering based on sequence similarity thresholds above 94.5%.^[18] Comparative studies across orders place the divergence of major classes within Bacteroidota, such as Bacteroidia (including Bacteroidales) and Cytophagia (including Cytophagales), at approximately 1.8 billion years ago, estimated using relaxed clock models calibrated against ancient cyanobacterial biomarkers in SSU rRNA phylogenies.^[20] This deep split aligns with the early radiation of Bacteroidota lineages during the Archean eon, reflecting adaptations to varying redox conditions in ancient microbial mats.^[21] Phylogenetic resolution within Bacteroidales is further bolstered by molecular markers, including G+C content variations—such as 40–56% in Prevotellaceae, which correlates with habitat-specific genomic adaptations—and conserved housekeeping genes like rpoB, whose sequences enable precise inference of evolutionary relationships due to their moderate evolutionary rates.^[18][22]

Evolutionary History

Bacteroidales, as part of the Bacteroidota phylum, trace their origins to the ancient bacterial diversification during the Archean and Proterozoic eons, approximately 2.5 to 1.8 billion years ago, when most bacterial lineages were ancestrally anaerobic and inhabited oxygen-poor environments such as sediments.^[23] Following the Great Oxidation Event around 2.4 billion years ago, which dramatically increased atmospheric oxygen levels, Bacteroidales adapted to persistent anaerobic niches, including sediments and later host-associated environments, by maintaining fermentative metabolisms suited to low-oxygen conditions.^[23] This adaptation allowed them to thrive in the wake of oxygenic photosynthesis's global impact, preserving their role as key degraders of organic matter in anoxic settings.^[23] A pivotal evolutionary innovation for Bacteroidales was the development of polysaccharide utilization loci (PULs), gene clusters that facilitate the detection, import, and breakdown of complex carbohydrates, enabling efficient exploitation of diverse glycans.^[24] These loci likely arose through gene duplication and horizontal transfer, providing a selective advantage for colonizing nutrient-rich environments like the vertebrate gut, which emerged around 500 million years ago during the Cambrian explosion.^[24] PULs allowed Bacteroidales to degrade host-derived and dietary polysaccharides, fostering their establishment as dominant gut commensals alongside the diversification of vertebrate digestive systems. The co-evolution of Bacteroidales with mammalian hosts accelerated during the Cenozoic era, coinciding with the radiation of placental mammals and the expansion of herbivorous and omnivorous diets that relied on microbial fermentation.^[25] Evidence from ancient microbiomes preserved in coprolites, such as a ~14,000-year-old human sample from Utah, reveals Bacteroidetes genomes with glycan-degrading capabilities similar to modern strains, indicating stable associations over millennia and minimal disruption until recent industrialization.^[26] This long-term partnership underscores how Bacteroidales diversified in response to host phylogeny and dietary shifts. Genetic plasticity in Bacteroidales is further exemplified by horizontal gene transfer (HGT) of antibiotic resistance genes from environmental Bacteroidota, particularly in settings like wastewater treatment plants where Bacteroides fragilis group bacteria serve as reservoirs for genes such as cfxA and tet(Q).^[27] These transfers, often mediated by integrons and mobile elements, enhance survival in variable environments and highlight ongoing evolutionary exchanges between gut and free-living populations.^[27]

Morphology and Physiology

Cellular Morphology

Bacteroidales bacteria are typically Gram-negative rods exhibiting pleomorphic morphology, with cells measuring 0.5–2.0 μm in width and 1–10 μm in length. These rods are often straight, curved, or filamentous, reflecting adaptability in cellular form without sporulation. The absence of endospores is a defining feature, distinguishing them from other anaerobic bacteria.^[18] The cell wall structure aligns with classic Gram-negative architecture, featuring a thin peptidoglycan layer (1–3 nm thick) sandwiched between an inner cytoplasmic membrane and an outer membrane. The outer membrane incorporates lipopolysaccharide (LPS), where lipid A exhibits penta-acylated and mono-phosphorylated variations specific to genera like Bacteroides, contributing to structural diversity and reduced endotoxic activity compared to Enterobacteriaceae. While most species lack true capsules, some produce extracellular slime layers or glycocalyx for adhesion, and others, such as Bacteroides fragilis, produce phase-variable capsular polysaccharides that contribute to virulence and host interactions.^[18][28][29] Motility in Bacteroidales is generally limited; most taxa, including the core Bacteroidaceae, are non-motile, relying on passive dispersal in anaerobic environments. Rare gliding motility occurs via type IX secretion systems in select lineages, such as certain environmental isolates, but this is uncommon in host-associated species.^[18][30] Electron microscopy reveals a multilayered ultrastructure typical of Gram-negatives, with the outer membrane displaying invaginations and blebs that facilitate nutrient uptake through porin channels and vesicle formation. The periplasmic space contains the peptidoglycan sacculus, while cytoplasmic inclusion bodies—often composed of storage polysaccharides like glycogen—appear as electron-dense granules under nutrient limitation. These features support efficient substrate scavenging in dense microbial communities.^[31][32]

Metabolic and Physiological Traits

Bacteroidales are predominantly anaerobic bacteria that rely on fermentation for energy generation, utilizing the Embden-Meyerhof-Parnas (EMP) pathway to catabolize carbohydrates such as glucose. This process yields short-chain fatty acids (SCFAs) including acetate, propionate, and succinate, which serve as key metabolic end products. For instance, in Bacteroides thetaiotaomicron, glucose fermentation proceeds via the EMP pathway, primarily producing acetate and succinate in approximately equal molar amounts, along with minor amounts of propionate and lactate. This anaerobic metabolism supports growth in oxygen-limited environments like the gut, where the produced SCFAs contribute to local pH modulation and nutrient availability.^[33][34] Nutrient utilization in Bacteroidales is facilitated by polysaccharide utilization loci (PULs), gene clusters that encode enzymes for the degradation of complex glycans, including host-derived mucin O-glycans. These systems enable the import and breakdown of polysaccharides through surface glycan-binding proteins and periplasmic hydrolases, allowing adaptation to diverse carbohydrate sources in the intestinal niche. Additionally, certain species within Bacteroidales, such as those in the genera Bacteroides and Phocaeicola, exhibit nitrate reduction capabilities, converting nitrate to nitrite as an alternative electron acceptor under anaerobic conditions, which aids in redox balance during fermentation.^[24][35][36] Physiological adaptations in Bacteroidales include tolerance to bile salts, with many strains resistant to concentrations up to 20%, achieved through mechanisms like bile salt hydrolase activity that deconjugates toxic bile acids. These bacteria also thrive at low pH levels, with optimal growth between pH 5 and 7, reflecting their adaptation to the acidic colonic environment; for example, Bacteroides species grow robustly at pH 6.7 but poorly at pH 5.5. Many are aerotolerant anaerobes, particularly in genera like Bacteroides, possessing catalase enzymes that decompose hydrogen peroxide to mitigate oxidative stress during transient oxygen exposure.^[37][38][39] Growth conditions for Bacteroidales are mesophilic, with optimal temperatures ranging from 25°C to 40°C, aligning with human body temperature for gut-associated species. Cultivation typically requires supplementation with hemin and vitamin K1 to support porphyrin synthesis and electron transport in their anaerobic metabolism, as these factors are essential or highly stimulatory for robust growth.^[40][41]

Ecology and Habitat

Environmental Distribution

Bacteroidales are prevalent in anoxic marine and freshwater sediments, where they play a key role in degrading complex organic matter through fermentative processes. In coastal marine sediments, total prokaryotic cell abundances often range from 10^7 to 10^9 cells per gram of wet sediment, with members of the Bacteroidota phylum (including Bacteroidales) comprising substantial fractions of these communities, such as up to 15.8% in eastern boundary upwelling sediments.^[42][43] These bacteria thrive in oxygen-depleted zones, facilitating carbon cycling by breaking down polymers and particulate organic material that settles from overlying waters.^[44] In aquatic environments, Bacteroidales are commonly detected in wastewater treatment systems, particularly in activated sludge, where they contribute to bioremediation efforts. These organisms aid in the degradation of recalcitrant pollutants, including azo dyes, by metabolizing complex aromatic compounds under anaerobic or low-oxygen conditions. Studies of continuous-flow systems have shown Bacteroidetes dominating the breakdown of such organics, enhancing overall treatment efficiency.^[45] Beyond aquatic settings, Bacteroidales are present in terrestrial ecosystems, including plant rhizospheres, where they contribute to the degradation of organic matter. In these root-associated zones, they utilize polysaccharide-degrading enzymes to process plant-derived polymers, promoting nutrient recycling in soil. Metagenomic analyses indicate their involvement in organic matter breakdown, aiding carbon turnover in agricultural and natural soils.^[46] Global metagenomic surveys, such as those from the Earth Microbiome Project, highlight the ecological breadth of Bacteroidales across biomes, with patterns of microbial diversity influenced by environmental factors like latitude and soil properties.^[47][43]

Interactions in Microbial Communities

Bacteroidales members play roles in microbial community dynamics through various interactions, including cross-feeding, quorum sensing, and syntrophy in anaerobic environments. Quorum sensing mechanisms facilitate Bacteroidales integration into microbial communities by coordinating interspecies behaviors. Bacteroidales produce autoinducer-2 (AI-2), a LuxS-dependent signal molecule that mediates communication across gram-negative and gram-positive bacteria, influencing biofilm formation and competitive exclusion.^[48] This system contributes to structured consortia in diverse habitats, regulating spatial organization and resource partitioning during colonization.^[49] Antagonistic interactions by Bacteroidales bolster community stability, particularly against opportunistic pathogens. Certain strains produce bacteriocin-like inhibitory substances that target pathogens by disrupting cell wall integrity.^[50] In engineered systems like anaerobic digesters, Bacteroidales engage in syntrophy, where uncultured lineages degrade amino acids into intermediates like ammonia and hydrogen, which syntrophic partners such as methanogens consume to alleviate thermodynamic barriers and sustain biogas production.^[51] These cooperative and antagonistic dynamics optimize degradation efficiency and prevent dominance by less beneficial taxa in environmental microbial communities. Bacteroidales often act as primary degraders in anaerobic consortia, employing polysaccharide utilization loci (PULs) to break down complex glycans, releasing substrates that support secondary fermenters and maintain community diversity, as observed in various metagenomic studies.^[52] This foraging strategy positions them as key players in interaction networks across habitats.

Biological and Clinical Significance

Role in Host Health

Bacteroidales, particularly members of the genus Bacteroides, play a crucial role in supporting the gut barrier through the production of short-chain fatty acids (SCFAs) such as propionate and acetate during fermentation of dietary carbohydrates.^[53] These SCFAs lower colonic pH to an acidic range (approximately 5.5), creating an environment that inhibits the growth of pathogenic bacteria while promoting the proliferation of beneficial microbes.^[54] Additionally, propionate serves as a primary energy source for colonocytes, fueling their metabolism and enhancing epithelial integrity to prevent barrier dysfunction.^[53] This metabolic activity contributes to overall gut homeostasis, with propionate further regulating appetite by activating FFAR2 receptors on enteroendocrine cells, which signal satiety to the brain and help maintain energy balance.^[53] In terms of immune modulation, polysaccharide A (PSA) from Bacteroides fragilis induces the development of Foxp3+ regulatory T cells (Tregs) in the colon, promoting IL-10 production and suppressing pro-inflammatory Th17 responses.^[55] This Treg induction, mediated via Toll-like receptor 2 signaling, enhances immune tolerance and reduces inflammation in models of inflammatory bowel disease (IBD), where PSA administration prevents and cures experimental colitis by restoring IL-10 levels and limiting IL-17-driven pathology.^[55] Such mechanisms underscore the probiotic-like functions of Bacteroidales in maintaining balanced host immunity.^[56] Bacteroidales contribute to nutrient metabolism by encoding polysaccharide utilization loci (PULs) that enable the breakdown of complex dietary fibers inaccessible to host enzymes, thereby extracting energy and preventing microbial imbalances that lead to dysbiosis.^[57] This fiber degradation supports host nutrition and has been linked to obesity prevention, as seen with Bacteroides acidifaciens, which promotes GLP-1 secretion from intestinal L-cells to suppress appetite and reduce body weight in high-fat diet models.^[58] Recent findings highlight associations between Bacteroidales and mental health via the gut-brain axis, with a 2024 review identifying decreased Prevotella levels in depression cohorts, potentially influencing neurotransmitter regulation and neuroinflammation through microbial metabolites.^[59] Emerging 2025 research also points to probiotic potential in genera like Parabacteroides for modulating host immunity and metabolism in various diseases.^[60]

Pathogenic Potential and Diseases

Members of the Bacteroidales order, such as certain Bacteroides and Porphyromonas species, primarily act as commensals in the human gut and oral microbiomes but can become opportunistic pathogens upon translocation to sterile sites, often in polymicrobial contexts following trauma, surgery, or immunosuppression.^[5][7] Bacteroides fragilis stands out as a key opportunistic pathogen, frequently isolated from intra-abdominal infections including abscesses arising from gastrointestinal perforation or surgical complications, where it contributes to abscess formation through capsule-mediated evasion of phagocytosis and synergy with facultative anaerobes like Escherichia coli.^[5][7] It is among the most common anaerobes recovered from such cases, accounting for a significant proportion of clinical isolates in polymicrobial intra-abdominal abscesses.^[5] The enterotoxigenic variant (ETBF) produces Bacteroides fragilis toxin (BFT), a zinc-dependent metalloprotease that cleaves E-cadherin on intestinal epithelial cells, leading to disrupted barrier integrity, increased permeability, and mucosal inflammation.^[5][61] ETBF strains are linked to colorectal tumorigenesis, where BFT-induced chronic inflammation promotes epithelial cell proliferation and STAT3 signaling activation, potentially accelerating adenoma-to-carcinoma progression in susceptible hosts.^[61] Studies have detected the bft gene in up to 90% of colorectal cancer tissue samples compared to 50% in healthy controls, highlighting its role in disease association.^[62] In the oral cavity, Porphyromonas gingivalis serves as a keystone pathogen in chronic periodontitis, orchestrating dysbiosis in subgingival biofilms and exacerbating periodontal tissue destruction.^[63] Its virulence relies on factors such as gingipains (cysteine proteases that degrade host proteins and modulate immune responses) and atypical lipopolysaccharide, which evade innate immunity while inducing excessive cytokine production and osteoclast activation, leading to alveolar bone loss.^[63][64] Bacteroidales pathogens exhibit intrinsic antibiotic resistance, notably to penicillin, mediated by chromosomally encoded beta-lactamases that hydrolyze beta-lactam rings.^[5] Multidrug resistance is rising in hospital settings, with carbapenem resistance in B. fragilis isolates reaching 5.2% phenotypically, often driven by the cfiA gene encoding a carbapenemase, complicating therapy for severe infections.^[65][66] Metronidazole is the first-line agent for treating Bacteroidales infections due to its efficacy against anaerobic metabolism, though resistance rates of 0.5% to 7.8% underscore the need for susceptibility testing.^[5] In polymicrobial scenarios like diabetic foot ulcers, which are present in 50-80% of cases and often involve anaerobes including Bacteroides species in approximately one-third of cultures alongside aerobes, combination therapy with beta-lactams or carbapenems plus metronidazole is often required to address mixed flora and prevent amputation.^[67][68]