Bacteroides caecimuris 盲肠鼠拟杆菌

一 产品基本信息与遗传学背景

• 细菌名称：Bacteroides caecimuris

• 分类学地位：拟杆菌门 (Bacteroidota)、拟杆菌目 (Bacteroidales)、拟杆菌科 (Bacteroidaceae)、拟杆菌属 (Bacteroides)。

• 主要生物学特征：革兰氏阴性、专性厌氧。该菌最初自健康小鼠的盲肠（Caecum）内容物中分离获得，是构建小鼠标准化定殖模型（如 gnotobiotic mices 实验）的核心菌株之一。

• 生物安全级别：1级 (BSL-1)。

二 核心科研与代谢功能

1. 多糖降解与复杂碳水化合物利用：具备拟杆菌属典型的多糖利用位点 (Polysaccharide Utilization Loci, PUL)。能高效分解宿主日常摄入的膳食纤维（非淀粉多糖），并将其转化为宿主可吸收的短链脂肪酸 (SCFAs)。

2. 实验室标准化肠道菌群构建：由于其在小鼠肠道内的极高定殖率和生态稳定性，常被纳入经典的合成菌群（如 Oligo-MM12 或其它多菌株组合），用于研究肠道菌群屏障抵抗外来病原菌入侵的竞争机制。

三 培养环境与技术参数

• 推荐培养基：BioVector® 拟杆菌专用 GAM 培养基（含血红素和维生素K1）、Wilkins-Chalgren 厌氧菌培养基。

• 气体环境：严格厌氧。

• 生长温度：37 摄氏度。

3. Phocaeicola vulgatus 普通霍夫曼氏菌（原名：普通拟杆菌）

一 产品基本信息与遗传学背景

• 细菌名称：Phocaeicola vulgatus（旧分类名为 Bacteroides vulgatus，近年依据多基因组进化分析重新分类归入 Phocaeicola 属）。

• 分类学地位：拟杆菌门、拟杆菌目、拟杆菌科、霍夫曼氏菌属 (Phocaeicola)。

• 主要生物学特征：革兰氏阴性、专性厌氧、多形性杆菌。它是人类肠道中丰度最高的拟杆菌目细菌之一，在维持肠道内稳态和免疫平衡中扮演着“基石菌株”的角色。

• 生物安全级别：1级 (BSL-1)。

二 核心科研与代谢功能

1. 抗宿主免疫调节与减轻炎症：虽然早期在特定敏感动物模型中曾被怀疑与炎症性肠病 (IBD) 相关，但最新研究表明，在健康宿主中它能诱导抗炎细胞因子（如 IL-10）的分泌，并抑制致病性大肠杆菌引起的肠道过度免疫反应。

2. 抗宿主耐糖量与二甲双胍靶向交互：临床研究发现其在部分糖尿病患者肠道中丰度发生改变。它参与了宿主肠道碳水化合物流向的再分配，并且其丰度受二甲双胍（Metformin）等降糖药物的直接调控。

三 培养环境与技术参数

• 推荐培养基：BioVector® 营养肉汤添加 0.5% 酵母提取物、血红素（5 $\mu$g/mL）及 维生素 K1（1 $\mu$g/mL），或标准 BBE 琼脂平板。

• 气体环境：严格厌氧。

• 生长温度：37 摄氏度。

4. Phocaeicola dorei 多氏霍夫曼氏菌（原名：多氏拟杆菌）

一 产品基本信息与遗传学背景

• 细菌名称：Phocaeicola dorei（旧分类名为 Bacteroides dorei）。

• 分类学地位：拟杆菌门、拟杆菌目、拟杆菌科、霍夫曼氏菌属 (Phocaeicola)。

• 主要生物学特征：革兰氏阴性、专性厌氧。与 P. vulgatus 亲缘关系极近，但在临床免疫学和表型上具有独特的标志性意义。

• 生物安全级别：1级 (BSL-1)。

二 核心科研与代谢功能

1. 自身免疫性疾病与1型糖尿病（T1D）早期预警：这是一株在儿科自身免疫领域备受关注的菌株。纵向临床队列研究显示，在儿童体内，Phocaeicola dorei 的早期过度增殖与随后发生的自身抗体转阳及 1型糖尿病 的发病具有显著的正相关性。

2. 内毒素（LPS）结构与免疫耐受阻断：其细胞壁产生的脂多糖 (LPS) 分子结构与大肠杆菌截然不同。它所含有的四酰基/五酰基单磷酰脂质A不仅不具备免疫激活毒性，反而能够竞争性地阻断 TLR4 受体，从而改变婴幼儿早期的免疫耐受建立。

三 培养环境与技术参数

• 推荐培养基：BioVector® 厌氧 GAM 液体培养基、Modified Trypticase Soy Broth (TSB) 补充血红素。

• 气体环境：严格厌氧。

• 生长温度：37 摄氏度。

5. Flavonifractor plautii 普氏黄酮降解菌

一 产品基本信息与遗传学背景

• 细菌名称：Flavonifractor plautii（旧分类名曾为 Fusobacterium plautii 或 Clostridium plautii）。

• 分类学地位：厚壁菌门 (Attributes to Bacillota/Firmicutes)、梭菌纲 (Clostridia)、欧克留菌目 (Eubacteriales)、颤螺菌科 (Oscillospiraceae)、黄酮降解菌属 (Flavonifractor)。

• 主要生物学特征：革兰氏阴性至可变、专性厌氧、不运动、能产弱芽孢的杆菌。

• 生物安全级别：1级 (BSL-1)。

二 核心科研与代谢功能

1. 天然黄酮类化合物代谢中枢：该菌是肠道中降解黄酮类物质（Flavonoids，如儿茶素 Catechin、槲皮素 Quercetin）的核心功能菌。它能够打破黄酮类分子的 C 环，将其转化为具有强抗氧化和抗炎活性的酚酸类代谢产物。

2. 生物抗癌与免疫免疫检查点调控：最新研究揭示，该菌在特定的结直肠癌 (CRC) 生物标志物和癌症免疫治疗中扮演双重角色。在部分队列中它被视为结直肠癌的富集标志物，而在另一些免疫研究中，其代谢产物被发现能参与调节宿主的 T 细胞极化。

三 培养环境与技术参数

• 推荐培养基：BioVector® 修改版 PYG 培养基、哥伦比亚血琼脂（Columbia Blood Agar）添加厌氧抑菌剂。

• 气体环境：严格厌氧。

• 生长温度：37 摄氏度。

6. Bacteroides intestinalis 肠拟杆菌

一 产品基本信息与遗传学背景

• 细菌名称：Bacteroides intestinalis

• 分类学地位：拟杆菌门 (Bacteroidota)、拟杆菌目 (Bacteroidales)、拟杆菌科 (Bacteroidaceae)、拟杆菌属 (Bacteroides)。

• 主要生物学特征：革兰氏阴性、专性厌氧。分离自健康成年人的肠道粪便标本，是一株高效的营养降解代谢株。

• 生物安全级别：1级 (BSL-1)。

二 核心科研与代谢功能

1. 多糖高效降解与碳水化合物交叉喂养（Cross-feeding）：拥有庞大且特异的糖苷水解酶（Glycoside Hydrolases）基因库。能够水解极其复杂的植物细胞壁多糖（如阿拉伯半乳聚糖、木聚糖），并释放出单糖或短链低聚糖，为肠道内其它无法直接利用复杂纤维的益生菌（如双歧杆菌）提供基础碳源。

2. 肠道纤维屏障与上皮保护：通过高效率地将膳食纤维转化为乙酸（Acetate）和丙酸（Propionate），直接为宿主结肠上皮细胞供能，并帮助维持肠道粘液层的厚度和完整性。

三 培养环境与技术参数

• 推荐培养基：BioVector® 基础 GAM 肉汤、Medium 78（厌氧菌标准培养基）。

• 气体环境：严格厌氧。

• 生长温度：37 摄氏度。

7. Bacteroides thetaiotaomicron 多形拟杆菌

一 产品基本信息与遗传学背景

• 细菌名称：Bacteroides thetaiotaomicron (常用代号如 VPI-5482)

• 分类学地位：拟杆菌门 (Bacteroidota)、拟杆菌目 (Bacteroidales)、拟杆菌科 (Bacteroidaceae)、拟杆菌属 (Bacteroides)。

• 主要生物学特征：革兰氏阴性、专性厌氧、无芽孢、杆状。它是宿主-微生物共生学、肠道多糖代谢和基因组学研究中应用最广泛的国际标准模式菌株。

• 生物安全级别：1级 (BSL-1)。

二 核心科研与代谢功能

1. 肠道多糖利用的“百科全书”：其基因组编码了数百种糖苷水解酶和多糖裂解酶。它是多糖利用位点 (PUL) 机制的经典发现株。无论是膳食植物多糖（淀粉、果胶、纤维素），还是宿主内源性的粘蛋白糖链（Mucin glycans），它都能精准识别并高效降解。当宿主节食或缺乏膳食纤维时，它会转换为消耗粘蛋白，维持肠道生态平衡。

2. 肠道血管发育与免疫成熟引导：作为发育生物学中的经典模型，研究证实 B. thetaiotaomicron 能刺激无菌小鼠生后肠道微血管系统的精密网状发育，并参与诱导肠道粘膜分泌型 IgA (sIgA) 的正常产生。

3. 合成生物学通用厌氧宿主：由于其遗传背景清晰、基因敲除和敲入技术成熟，它是目前用于设计“活体生物药 (LBP)”、体内定向递送抗炎因子或肿瘤靶向分子的最常用工程化宿主菌之一。

三 培养环境与技术参数

• 推荐培养基：BioVector® 经典 TYG 培养基、标准 BHI 厌氧培养基添加 0.5% 葡萄糖及血红素。

• 气体环境：严格厌氧。

• 生长温度：37 摄氏度。

8. Bacteroides cellulosilyticus 降纤维素拟杆菌

一 产品基本信息与遗传学背景

• 细菌名称：Bacteroides cellulosilyticus

• 分类学地位：拟杆菌门 (Bacteroidota)、拟杆菌目 (Bacteroidales)、拟杆菌科 (Bacteroidaceae)、拟杆菌属 (Bacteroides)。

• 主要生物学特征：革兰氏阴性、专性厌氧。该菌株在降解植物不可溶性核心骨架——纤维素（Cellulose）方面表现出极强的特异性进化。

• 生物安全级别：1级 (BSL-1)。

二 核心科研与代谢功能

1. 顽固纤维素与半纤维素的强力降解者：拥有高度富集的内切麦芽糖酶、纤维素酶和木聚糖酶系统。能直接锚定并降解常规肠道菌群难以破坏的致密结晶纤维素，是肠道能量捕获（Energy Harvesting）链条中极其关键的起点菌株。

2. 提升宿主 SCFA 丰度与抗炎潜能：通过对纤维素的高效发酵，大量产生丁酸（Butyrate）和丙酸等短链脂肪酸。这些产物能通过结合 G 蛋白偶联受体（如 GPR41/43），在体内发挥强大的全身性抗炎、控制食欲以及维持血糖稳态的功能。

三 培养环境与技术参数

• 推荐培养基：BioVector® 纤维素/羧甲基纤维素 (CMC) 限制性选择厌氧培养基、GAM 肉汤。

• 气体环境：严格厌氧。

• 生长温度：37 摄氏度。

PART 2 ENGLISH SECTION

1. Parabacteroides goldsteinii

I General Information & Genetics

• Name: Parabacteroides goldsteinii

• Taxonomy: Phylum Bacteroidota, Class Bacteroidia, Order Bacteroidales, Family Tannerellaceae, Genus Parabacteroides.

• Key Traits: Gram-negative, obligately anaerobic, non-spore-forming straight rod. It represents a vital commensal core within mammalian intestinal niches.

• Biosafety Level: BSL-1.

II Core Scientific & Metabolic Functions

1. Anti-Obesity and Metabolic Syndrome Alleviation: Prominently studied as a Next-Generation Probiotic (NGP). Evidence underscores its capacity to mitigate high-fat diet-induced obesity by reinforcing gut barrier integrity, curbing metabolic endotoxemia, and ameliorating systemic low-grade chronic inflammation.

2. Bile Acid Biotransformation: Secretes specialized hydrolases that convert primary bile acids into secondary bile acids. This modulates host FXR and TGR5 signaling networks, enhancing adipose tissue thermogenesis and expanding insulin sensitivity.

III Cultivation Parameters

• Recommended Media: BioVector® Enhanced Modified PYG Broth, or Brain Heart Infusion (BHI) broth supplemented with 5% sheep blood and 0.05% L-cysteine.

• Atmosphere: Strict anaerobic parameters ($10\%\ H_2,\ 10\%\ CO_2,\ 80\%\ N_2$).

• Incubation Temperature: 37°C.

2. Bacteroides caecimuris

I General Information & Genetics

• Name: Bacteroides caecimuris

• Taxonomy: Phylum Bacteroidota, Order Bacteroidales, Family Bacteroidaceae, Genus Bacteroides.

• Key Traits: Gram-negative, strictly anaerobic rod. Originally isolated from the cecal contents of healthy laboratory mice, serving as a signature organism for murine gut microbiome modeling.

• Biosafety Level: BSL-1.

II Core Scientific & Metabolic Functions

1. Polysaccharide Digestion Profiling: Features evolutionary Polysaccharide Utilization Loci (PULs) optimized to dismantle complex dietary plant fibers (non-starch polysaccharides), turning complex carbohydrates into Short-Chain Fatty Acids (SCFAs).

2. Synthetic Consortium Assemblies: Due to its reliable colonization dynamics and stable metabolic output in mice, it is a staple component within synthetic reference communities (such as the Oligo-MM12 consortium) to investigate colonization resistance against enteric pathobionts.

III Cultivation Parameters

• Recommended Media: BioVector® Specialized GAM Anaerobic Broth (enriched with hemin and vitamin K1), or Wilkins-Chalgren Anaerobic Medium.

• Atmosphere: Strict anaerobic setup.

• Incubation Temperature: 37°C.

3. Phocaeicola vulgatus

I General Information & Genetics

• Name: Phocaeicola vulgatus (Formerly recognized as Bacteroides vulgatus; reclassified into the genus Phocaeicola following multi-locus phylogenomic corrections).

• Taxonomy: Phylum Bacteroidota, Order Bacteroidales, Family Bacteroidaceae, Genus Phocaeicola.

• Key Traits: Gram-negative, obligately anaerobic, pleomorphic rod. It stands as one of the most numerically dominant commensal species within the human distal gut ecosystem.

• Biosafety Level: BSL-1.

II Core Scientific & Metabolic Functions

1. Immunomodulation and Anti-inflammatory Homeostasis: While historic models linked it with specific colitis settings under strict hyper-sensitive backgrounds, modern research validates its protective status in healthy hosts, where it prompts anti-inflammatory cytokine (such as IL-10) secretion and subverts pathogenic Enterobacteriaceae expansion.

2. Glucose Tolerance Interaction: Clinically highlighted for its shifts in abundance across metabolic patient cohorts. It alters carbohydrate flux variations in the intestinal lumen and exhibits high sensitivity to pharmacological interventions like Metformin treatment.

III Cultivation Parameters

• Recommended Media: BioVector® Nutrient Broth supplemented with 0.5% yeast extract, hemin ($5\ \mu$g/mL), and vitamin K1 ($1\ \mu$g/mL), or BBE (Bacteroides Bile Esculin) agar configurations.

• Atmosphere: Strict anaerobic parameters.

• Incubation Temperature: 37°C.

4. Phocaeicola dorei

I General Information & Genetics

• Name: Phocaeicola dorei (Formerly recognized as Bacteroides dorei).

• Taxonomy: Phylum Bacteroidota, Order Bacteroidales, Family Bacteroidaceae, Genus Phocaeicola.

• Key Traits: Gram-negative, obligately anaerobic rod. Phylogenetically close to P. vulgatus but displays distinct immunophenotypic features.

• Biosafety Level: BSL-1.

II Core Scientific & Metabolic Functions

1. Autoimmune Pathogenesis & Type 1 Diabetes (T1D) Tracing: Heavily tracked in pediatric autoantibody longitudinal cohorts. Accelerated early abundance blooms of P. dorei in infant microbiomes serve as a strong predictive biomarker preceding the development of islet autoantibodies and clinical Type 1 Diabetes onset.

2. Atypical Endotoxin (LPS) Subversion: Synthesizes a distinct tetra-/penta-acylated lipid A structure within its lipopolysaccharide (LPS) cell envelope. This variant lacks the classical inflammatory toxicity seen in E. coli LPS, acting instead as a competitive TLR4 antagonist that delays immune maturation during early development.

III Cultivation Parameters

• Recommended Media: BioVector® Anaerobic GAM Broth, or Trypticase Soy Broth (TSB) supplemented with standard yeast fractions and hemin.

• Atmosphere: Strict anaerobic setups.

• Incubation Temperature: 37°C.

5. Flavonifractor plautii

I General Information & Genetics

• Name: Flavonifractor plautii (Historically cataloged as Fusobacterium plautii or Clostridium plautii).

• Taxonomy: Phylum Bacillota/Firmicutes, Class Clostridia, Order Eubacteriales, Family Oscillospiraceae, Genus Flavonifractor.

• Key Traits: Gram-negative to Gram-variable, obligately anaerobic, non-motile, weakly spore-forming bacillus.

• Biosafety Level: BSL-1.

II Core Scientific & Metabolic Functions

1. Dietary Flavonoid Biodegradation Hub: Acts as a key functional metabolic strain in the gut capable of parsing dietary flavonoids (such as catechins and quercetin). It cleaves the characteristic heterocyclic C-ring structure of flavonoids, translating them into bioactive phenolic acid residues with strong antioxidant qualities.

2. Oncology Diagnostics and Immune Checkpoint Regulation: Exhibits a dual role in modern colorectal cancer (CRC) metagenomic screens. It is often detected as an enriched biomarker in CRC fecal diagnostics, yet concurrently researched for its metabolites' capacity to regulate host T-cell polarization during checkpoint immunotherapies.

III Cultivation Parameters

• Recommended Media: BioVector® Modified PYG Broth, or Columbia Blood Agar bases equipped with anaerobic optimization mixtures.

• Atmosphere: Strict anaerobic parameters.

• Incubation Temperature: 37°C.

6. Bacteroides intestinalis

I General Information & Genetics

• Name: Bacteroides intestinalis

• Taxonomy: Phylum Bacteroidota, Order Bacteroidales, Family Bacteroidaceae, Genus Bacteroides.

• Key Traits: Gram-negative, obligately anaerobic, non-spore-forming rod isolated from healthy adult human fecal specimens.

• Biosafety Level: BSL-1.

II Core Scientific & Metabolic Functions

1. Glycan Disassembly and Cross-Feeding Dynamics: Holds a versatile genome heavily enriched with Glycoside Hydrolases (GHs) tailored to cleave tough plant cell wall matrix polysaccharides like arabinogalactans and xylans. It liberates oligosaccharide fragments into the lumen, driving cross-feeding networks that nourish neighboring beneficial species (e.g., Bifidobacterium).

2. Epithelial Protection and Energetics: Maximizes the transformation of non-digestible plant polysaccharides into valuable short-chain fatty acids, notably acetate and propionate, which directly fuel colonocyte energetics and preserve mucosal structural thickness.

III Cultivation Parameters

• Recommended Media: BioVector® Base GAM Broth, or Standard DSMZ Medium 78 formulas.

• Atmosphere: Strict anaerobic setup.

• Incubation Temperature: 37°C.

7. Bacteroides thetaiotaomicron

I General Information & Genetics

• Name: Bacteroides thetaiotaomicron (Reference Standard Strain: VPI-5482)

• Taxonomy: Phylum Bacteroidota, Order Bacteroidales, Family Bacteroidaceae, Genus Bacteroides.

• Key Traits: Gram-negative, obligately anaerobic, non-spore-forming rod. It stands as the premier global standard model organism for investigating host-microbe symbiosis and complex carbohydrate metabolism.

• Biosafety Level: BSL-1.

II Core Scientific & Metabolic Functions

1. The Encyclopedic Glycan Consumer: Encodes an exceptional array of glycoside hydrolases and polysaccharide lyases. It serves as the definitive reference model for mapping Polysaccharide Utilization Loci (PUL) systems. It switches seamlessly between processing dietary fiber arrays (pectins, amylose) and host endogenous mucin O-glycans, maintaining luminal ecosystem equilibrium during host fasting phases.

2. Angiogenesis Instruction and Mucosal Maturation: Proven to orchestrate post-natal microvascular cellular networks in germ-free mouse models, and heavily guides the homeostatic synthesis of secretory Immunoglobulin A (sIgA) across intestinal linings.

3. Synthetic Biology Host Platform: Due to its fully mapped genomic architecture and refined CRISPR-based genetic engineering protocols, it serves as a leading living biotherapeutic (LBP) chassis designed for the target delivery of anti-inflammatory molecules or tumor-directed payloads.

III Cultivation Parameters

• Recommended Media: BioVector® Traditional TYG Broth, or Anaerobic BHI Broth bases fortified with 0.5% glucose, vitamin complexes, and hemin.

• Atmosphere: Strict anaerobic setups.

• Incubation Temperature: 37°C.

8. Bacteroides cellulosilyticus

I General Information & Genetics

• Name: Bacteroides cellulosilyticus

• Taxonomy: Phylum Bacteroidota, Order Bacteroidales, Family Bacteroidaceae, Genus Bacteroides.

• Key Traits: Gram-negative, obligately anaerobic rod exhibiting high specialization in parsing insoluble plant cellulose infrastructures.

• Biosafety Level: BSL-1.

II Core Scientific & Metabolic Functions

1. Crystalline Cellulose Degradation: Encodes a hyper-concentrated array of endoglucanases, cellobiohydrolases, and xylanases. It targets and metabolizes crystalline cellulose frameworks that typically resist digestion by other gut bacteria, positioning it at the apex of the intestinal energy-harvesting cascade.

2. SCFA Enrichment and Metabolic Homeostasis: Fermentative breakdown of complex fibers by this strain yields robust concentrations of butyrate and propionate. These short-chain fatty acids bind host G-protein coupled receptors (GPR41/GPR43), promoting systemic anti-inflammatory cascades, appetite regulation, and glucose homeostasis.

III Cultivation Parameters

• Recommended Media: BioVector® Cellulose/Carboxymethylcellulose (CMC) Defined Selective Anaerobic Broth, or baseline GAM media matrices.

• Atmosphere: Strict anaerobic parameters.

• Incubation Temperature: 37°C.

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