本發明係基於與對照BT菌株相比BT菌株BT2013具有更有效抗炎作用之發現。
BT菌株BT2013已於2014年12月3日以登錄號42341保藏於National Collections of Industrial, Food and Marine Bacteria (NCIMB)，其位於NCIMB Ltd, Ferguson Building, Craibstone Estate, Bucksburn, Aberdeen, UK, AB21 9YA。該保藏係根據布達佩斯條約(Budapest Treaty)之條款進行。該保藏係由GT Biologics Ltd. (Life Sciences Innovation Building, Aberdeen, AB25 2ZS, Scotland)進行。GT Biologics Ltd.後來更名為4D Pharma Research Limited。衍生物
本發明涵蓋所保藏菌株之衍生物。術語「衍生物」包括子代菌株(子代)或由原始菌株培養(次選殖)但以某方式(包括在基因層面)經修飾而未負向改變生物活性之菌株，即衍生菌株將至少具有與原始BT2013菌株相同之免疫調節活性。生物型
菌株BT2013之基因組序列提供於SEQ ID NO:1中。
作為以登錄號NCIMB 42341保藏之細菌的生物型的細菌菌株亦預期有效治療或預防炎性病症及/或自體免疫病症及/或過敏性病症。生物型為具有相同或非常類似之生理及生物化學特徵之密切相關之菌株。
在某些實施例中，用於本發明中之細菌菌株具有與以登錄號NCIMB 42341保藏之細菌之16s rRNA序列至少95%、96%、97%、98%、99%、99.5%或99.9%一致的16s rRNA序列。
或者，作為以登錄號NCIMB 42341保藏之細菌的生物型且適合用於本發明中之菌株可藉由對以登錄號NCIMB 42341保藏之細菌的其他核苷酸序列進行定序來鑑別。舉例來說，實質上可對整個基因組進行定序，且用於本發明中之生物型菌株可在其整個基因組之至少80%中(例如在至少85%、90%、95%或99%中，或在其整個基因組中)具有至少95%、96%、97%、98%、99%、99.5%或99.9%序列一致性。其他適合用於鑑別生物型菌株之序列可包括hsp60或重複序列，諸如BOX、ERIC、(GTG)5
或REP (Masco等人(2003)Systematic and Applied Microbiology,
26:557-563)。生物型菌株可具有與以登錄號NCIMB 42341保藏之細菌之對應序列具有至少95%、96%、97%、98%、99%、99.5%或99.9%序列一致性的序列。
在某些實施例中，用於本發明中之細菌菌株具有與SEQ ID NO:1具有序列一致性之基因組。在較佳實施例中，用於本發明中之細菌菌株具有在SEQ ID NO:1之至少60% (例如至少65%、70%、75%、80%、85%、95%、96%、97%、98%、99%或100%)中與SEQ ID NO:1具有至少90%序列一致性(例如至少92%、94%、95%、96%、97%、98%、99%或100%序列一致性)的基因組。舉例來說，用於本發明中之細菌菌株的基因組可在SEQ ID NO:1之70%中與SEQ ID NO:1具有至少90%之序列一致性，或在SEQ ID NO:1之80%中與SEQ ID NO:1具有至少90%之序列一致性，或在SEQ ID NO:1之90%中與SEQ ID NO:1具有至少90%之序列一致性，或在SEQ ID NO:1之100%中與SEQ ID NO:1具有至少90%之序列一致性，或在SEQ ID NO:1之70%中與SEQ ID NO:1具有至少95%之序列一致性，或在SEQ ID NO:1之80%中與SEQ ID NO:1具有至少95%之序列一致性，或在SEQ ID NO:1之90%中與SEQ ID NO:1具有至少95%之序列一致性，或在SEQ ID NO:1之100%中與SEQ ID NO:1具有至少95%之序列一致性，或在SEQ ID NO:1之70%中與SEQ ID NO:1具有至少98%之序列一致性，或在SEQ ID NO:1之80%中與SEQ ID NO:1具有至少98%之序列一致性，或在SEQ ID NO:1之90%中與SEQ ID NO:1具有至少98%之序列一致性，或在SEQ ID NO:1之100%中與SEQ ID NO:1具有至少98%之序列一致性。
或者，作為以登錄號NCIMB 42341保藏之細菌的生物型且適合用於本發明中之菌株可藉由使用登錄號NCIMB 42341保藏及限制片段分析及/或PCR分析進行鑑別，例如藉由使用螢光擴增片段長度多態性(FAFLP)及重複DNA元件(rep)-PCR指紋分析或蛋白質表現譜分析或部分16S或23s rDNA定序來進行。
在某些實施例中，作為以登錄號NCIMB 42341保藏之細菌的生物型且適合用於本發明中之菌株為當藉由擴增核糖體DNA限制分析(ARDRA)分析時，例如當使用Sau3AI限制酶時(關於示例性方法及指導參見例如Srůtková等人(2011)J. Microbiol. Methods,
87(1):10-6)提供與以登錄號NCIMB 42341保藏之細菌相同之模式的菌株。或者，生物型菌株經鑑別為具有與以登錄號NCIMB 42341保藏之細菌相同之碳水化合物發酵模式的菌株。
作為以登錄號NCIMB 42341保藏之細菌的生物型且適合用於本發明之組合物及方法中之細菌菌株可使用任何適當之方法或策略來鑑別。舉例來說，與以登錄號NCIMB 42341保藏之細菌具有類似生長模式、代謝類型及/或表面抗原之細菌菌株可適合用於本發明。生物型菌株將具有與NCIMB 42341菌株可比之免疫調節活性。舉例來說，與功能分析中所示之影響相比，生物型菌株將引發對DSS誘導型結腸炎模型之可比擬之影響及對Treg水準、MPO酶活性、炎症相關基因表現及結腸組織病理學之可比擬之影響，此可藉由使用功能分析中所描述之方案來鑑別。病症
多形擬桿菌菌株BT2013可用於治療及/或預防個體之病症，其中該病症為炎性病症及/或自體免疫病症。
在一個實施例中，病症影響消化道、消化道之一部分、肝臟、肝細胞、免疫細胞、上皮細胞、表皮細胞、神經元細胞、內皮細胞、纖維母細胞、胰腺及/或胰腺細胞(諸如胰島)。
消化道之部分(即部件)之實例包括食管、胃及腸道(諸如小腸(例如十二指腸、空腸及迴腸)及/或大腸(例如盲腸、升結腸、橫結腸、降結腸及乙狀結腸))。
上皮細胞之實例包括腸道上皮細胞。免疫細胞之實例包括樹突細胞、單核細胞/巨噬細胞、T細胞及嗜中性粒細胞。
在一個實施例中，病症選自由以下組成之群：
器官相關病症，諸如腸易激症候群(IBS)、炎性腸道疾病(包括克羅恩氏病(Crohn’s disease)及潰瘍性結腸炎)、壞死性小腸結腸炎、囊炎、腹腔疾病、多發性硬化(腦部)、I型糖尿病、古德帕斯特氏症候群(Goodpasture’s syndrome)、橋本氏甲狀腺炎(Hashimoto thyroiditis)、慢性活動性肝炎、心肌病、葡萄膜炎及鼻炎。
全身性病症，諸如類風濕性關節炎、全身性紅斑狼瘡、硬皮病、銀屑病、特應性皮炎、白斑病、多發性硬化、斑禿、結節病、多肌炎及其組合。
在一個態樣中，病症影響腸道。
在一個態樣中，病症為炎性病症。舉例來說，病症為炎性腸病症(IBD)，諸如克羅恩氏病。
在一個態樣中，病症為自體免疫病症。舉例來說，自體免疫病症選自由以下組成之群：潰瘍性結腸炎、囊炎、類風濕性關節炎、銀屑病、多發性硬化、I型糖尿病、過敏症(包括腹腔疾病)、特應性皮炎及鼻炎。個體
在一個實施例中，個體為單胃動物。
單胃動物之實例包括禽、人類、大鼠、豬、犬、貓、馬及兔。
在另一個實施例中，個體為哺乳動物，諸如單胃哺乳動物。
單胃哺乳動物之實例包括雜食動物(諸如人類、大鼠及豬)、食肉動物(諸如犬及貓)及草食動物(諸如馬及兔)。
較佳地，個體為人類。
在一個態樣中，個體具有選自由以下組成之群的病症：炎性腸病症(IBD)、結腸炎、類風濕性關節炎、銀屑病、多發性硬化、I型糖尿病、腹腔疾病、特應性皮炎、鼻炎、腸易激症候群(IBS)、潰瘍性結腸炎、囊炎、克羅恩氏病、機能性消化不良、特應性疾病、壞死性小腸結腸炎、非酒精性脂肪肝疾病、胃腸道感染及其組合。舉例來說，個體具有IBD。 調節 / 調控
術語「調節」及「調控」在本文中可為可互換使用的。
在一個實施例中，多形擬桿菌菌株BT2013用於調節個體之細胞、組織或器官之炎症。
在一個實施例中，術語「調節」係指增加及/或誘導及/或促進及/或啟動。在一替代實施例中，術語「調節」係指降低及/或減少及/或抑制。
在一個實施例中，術語「調控」係指上調。在一替代實施例中，術語「調控」係指下調。
在一個實施例中，如本文所描述之多形擬桿菌菌株BT2013減輕細胞、組織或器官之炎症。舉例來說，減輕消化道、消化道之一部分(即部件)(諸如腸道)、肝臟、肝細胞、上皮細胞、表皮細胞、神經元細胞、內皮細胞、纖維母細胞、胰腺及/或胰腺細胞(諸如胰島)之炎症。
在一個實例中，減輕消化道或其部件(諸如腸道)之炎症。
在另一實例中，減輕由組織或器官之免疫細胞引起之炎症。
在另一實例中，減輕由組織或器官之上皮細胞引起之炎症。
如本文所用之術語「炎症」係指以下中之一或多者：發紅、腫脹、疼痛、觸痛、發熱及歸因於由免疫系統之過反應觸發之炎性過程之細胞、組織或器官功能擾亂。
在一個實施例中，當與在向個體投與如本文所描述之菌株BT2013之前個體中發炎之細胞的數目相比時，在投與如本文所描述之多肽或多核苷酸或宿主細胞之後，個體中發炎之細胞的數目低至少10%、20%、30%、40%或50%。
在一個實施例中，當與在向個體投與菌株BT2013之前個體中發炎之組織或器官的量相比時，在投與菌株BT2013之後，個體中發炎之組織或器官的量低至少10%、20%、30%、40%或50%。
在一個實施例中，菌株BT2013減輕由組織或器官之上皮細胞引起之炎症。
舉例來說，上皮細胞為消化道或其部件(諸如腸道)之上皮細胞。
在不希望受理論限制之情況下，菌株BT2013增加個體中T細胞(諸如調控T細胞，其亦可稱為Treg)之產量。此Treg數目增加可對抗驅動炎症、自體免疫及過敏性/特應性病狀之其他效應T細胞(亦稱為Teff，諸如Th1、Th17及Th2)之作用。在克羅恩氏病及潰瘍性結腸炎中，Teff/Treg細胞平衡喪失。
在一個實施例中，個體中T細胞之產量增加，使得當與在向個體投與菌株BT2013之前個體中之T細胞數目相比時，在投與如本文所描述之多肽或多核苷酸或宿主細胞之後存在至少多10%、20%、30%、40%或50%之T細胞，或多大於100%之T細胞。腸道障壁完整性
在一個實施例中，菌株BT2013用於改良個體之腸道障壁完整性。
如本文所用之術語「改良腸道障壁完整性」係指當與在投與如本文所描述之菌株BT2013之前個體中自腸道擴散至其他細胞中之微生物的數目及/或類型相比時，在投與菌株BT2013之後，個體中自腸道擴散至其他細胞中之微生物的數目及/或類型減少。
在一個實施例中，當與在投與之前個體中自腸道擴散至其他細胞中之微生物的數目相比時，在投與菌株BT2013之後，個體中自腸道擴散至其他細胞中之微生物的數目低至少10%、20%、30%、40%或50%。
在一個實施例中，當與在投與之前個體中自腸道擴散至其他細胞中之微生物類型相比時，在投與菌株BT2013之後，個體中自腸道擴散至其他細胞中之微生物類型少至少5%、10%、15%或20%。腸道破壞
在一個實施例中，菌株BT2013用於降低對個體(諸如具有IBD之個體)之腸道(例如大腸)的破壞。
如本文所用之術語「對個體之腸道的破壞」係指對黏膜上皮之完整性的影響及/或對上皮中杯狀細胞之數目的影響及/或對浸潤固有層之免疫細胞的數目的影響。
在一個實施例中，菌株BT2013降低或預防對黏膜上皮之完整性的破壞及/或降低或預防上皮中杯狀細胞之數目的減少及/或降低或預防免疫細胞浸潤至固有層中。
在一個實施例中，對黏膜上皮之完整性的破壞降低為當與在投與之前個體中自腸腔穿入腸道細胞中之細菌數目相比時，在投與菌株BT2013之後，自腸腔穿入腸道細胞中之細菌數目減少至少5%、10%、15%或20%。
在一個實施例中，上皮中杯狀細胞之數目減少為當與在投與之前個體之上皮中杯狀細胞之數目相比時，在投與菌株BT2013之後，個體之上皮中杯狀細胞之數目減少至少2%、5%、10%、15%或20%。
在一個實施例中，免疫細胞浸潤至固有層中減少為使得當與在投與之前個體中穿入固有層細胞中之免疫細胞(例如T細胞)的數目相比時，在投與菌株BT2013之後，在固定時間段(諸如24小時)內，穿入固有層細胞中之免疫細胞(例如T細胞)之數目減少至少5%、10%、15%、20%或30%。促炎基因及障壁完整性基因
在一個實施例中，菌株BT2013用於調控一或多種促炎基因及/或一或多種障壁完整性基因於個體之細胞中的表現。
在一個實施例中，術語「調控」係指一或多種促炎基因之表現的上調。在一替代實施例中，術語「調控」係指一或多種促炎基因之表現的下調。
在一個實施例中，菌株BT2013下調一或多種促炎基因於個體之細胞中的表現。
如本文所用之術語「促炎基因」係指當表現時促進炎症之基因。促炎基因之實例包括(但不限於)編碼以下各項之基因：IL1-β、IL4、IL5、IL6、IL8、IL12、IL13、IL17、IL21、IL22、IL23、IL27、IFN、CCL2、CCL3、CCL5、CCL20、CXCL5、CXCL10、CXCL12、CXCL13及TNF-α。
在一個實施例中，促炎基因選自由以下組成之群：IL1-β、IL6及IL8。
在一個實施例中，一或多種促炎基因之表現水準(例如mRNA水準)降低(即下調)，使得當與在投與之前個體中之水準相比時，在投與菌株BT2013之後，水準低至少10%、20%、30%、40%或50%。
如本文所用之術語「障壁完整性基因」係指當表現時在腸道之障壁功能(諸如修復障壁及防止微生物穿過障壁)中起作用之基因。障壁完整性基因之實例包括編碼以下各項之基因：Retnlg|Retnlb、Si、Defa24、Hsd11b2、Hsd17b2及Nr1d1|Thra。
在一個實施例中，術語「調控」係指一或多種障壁完整性基因之表現的上調。在一替代實施例中，術語「調控」係指一或多種障壁完整性基因之表現的下調。
在一個實施例中，菌株BT2013上調障壁完整性基因於個體之細胞中的表現
在一個實施例中，障壁完整性基因選自由以下組成之群：Retnlg|Retnlb、Si、Defa24、Hsd11b2、Hsd17b2及Nr1d1|Thra。
在一個實施例中，一或多種障壁完整性基因之表現水準(例如mRNA水準)增加(即上調)，使得當與在投與之前個體中之水準相比時，在投與菌株BT2013之後，水準高至少10%、20%、30%、40%或50%。 消化道
消化道之部件包括食管、胃及腸道(諸如小腸(例如十二指腸、空腸及迴腸)及/或大腸(例如盲腸、升結腸、橫結腸、降結腸及乙狀結腸))。
在本文中，術語「大腸」可為與術語「結腸」可互換使用的。
在一個實施例中，菌株BT2013用於改良個體之消化道健康。
如本文所用之術語「改良消化道健康」係指降低消化道或其部件中之炎症程度及/或改良腸道微生物群。
在一個實施例中，當與在投與之前個體之消化道中之炎症程度相比時，在投與菌株BT2013之後，消化道中之炎症程度低至少10%、20%、30%、40%或50%。
在一個實施例中，菌株BT2013用於改良個體之腸道微生物群。
如本文所用之術語「腸道微生物群」係指生活在宿主動物之消化道中的微生物。此等微生物發揮多種代謝、結構、保護及其他受益功能。
如本文所用，術語「改良腸道微生物群」係指增加存在於個體(例如宿主)之腸道中之所需微生物的數目及/或類型，及/或增加該等所需微生物在其代謝、結構、保護及其他受益功能方面之活性。術語「改良腸道微生物群」亦可指減少存在於個體(例如宿主)之腸道中之不需要之微生物的數目及/或類型，及/或降低該等不需要之微生物在其代謝、結構、保護及其他受益功能方面之活性。
宿主腸道中所需之微生物為具有保護及受益功能之彼等微生物。厚壁菌門及擬桿菌門細菌為宿主腸道中之所需微生物的實例。
宿主腸道中不需要之微生物為可能妨礙腸道中具有保護及受益功能之所需微生物之代謝、結構、保護及其他受益功能之彼等微生物。或者或另外，不需要之微生物為引起例如炎症及/或腹瀉之彼等。大腸桿菌(E. coli
)為宿主腸道中不需要之微生物的實例。
舉例來說，一旦已向個體投與菌株BT2013，在具有炎性腸道疾病(IBD)之個體中，即可產生腸道內所需微生物(諸如厚壁菌門及擬桿菌門細菌)與不需要之微生物(諸如大腸桿菌：ETEC、EPEC、EIEC、EHEC及EAEC)之間的微生物群平衡之變化。
在一個實施例中，存在於個體(例如宿主)之腸道中的所需微生物(諸如厚壁菌門及擬桿菌門細菌)之數目增加，使得與在投與之前個體中之水準相比，在投與菌株BT2013之後，微生物之數目高至少10%、20%、30%、40%或50%，或高大於100%。或者或另外，存在於個體(例如宿主)之腸道中之所需微生物(諸如厚壁菌門及擬桿菌門)的類型增加，使得當與在投與之前個體中之類型相比時，在投與菌株BT2013之後，微生物之類型多至少2%、5%、10%或15%。
在一個實施例中，存在於個體(例如宿主)之腸道中之不需要之微生物(諸如大腸桿菌ETEC、EPEC、EIEC、EHEC及EAEC)的數目降低，使得當與在投與之前個體中之水準相比時，在投與菌株BT2013之後，微生物之數目低至少10%、20%、30%、40%或50%。或者或另外，存在於個體(例如宿主)之腸道中之不需要之微生物(諸如大腸桿菌ETEC、EPEC、EIEC、EHEC及EAEC)的類型減少，使得當與在投與之前個體中之類型相比時，在投與菌株BT2013之後，不需要之微生物的類型少至少1%、2%、5%或10%。 囊封
在一個實施例中，多形擬桿菌菌株BT2013為囊封的。
在另一實施例中，包含菌株BT2013之醫藥組合物為囊封的。
在另一個實施例中，包含菌株BT2013之營養補充物為囊封的。
在另一實施例中，如本文所描述之飼料、食物產品、膳食補充物或食物添加劑為囊封的。
如本文所用術語「囊封」係指用於藉由物理分離以使得菌株BT2013可遞送至目標位點(例如腸道)而不會降解或顯著降解以使其可對目標位點產生影響來保護菌株BT2013不受到不相容環境影響之手段。一實例為腸溶包衣膠囊或腸道耐性膠囊。
即使當囊封之目的為使菌株自其環境中分離時，在所需作用時保護性包衣或外殼亦必須破裂。保護性包衣或外殼之破裂係典型地通過施加化學及物理刺激(諸如壓力、酶攻擊、化學反應及物理崩解)而引起。
舉例來說，囊封確保可攝入菌株以使得微生物可以在目標位點有效產生作用之量遞送至目標位點(例如腸道)。藥物組合物
在一個實施例中，醫藥組合物包含菌株BT2013之微生物及視情況存在之醫藥學上可接受之賦形劑、載劑或稀釋劑。
醫藥組合物可為任何醫藥組合物。在一個態樣中，醫藥組合物有待於經口、腸內或直腸投與。舉例來說，組合物可為可食用組合物。「可食用」意謂材料被批准供人類或動物消耗。
醫藥組合物可在人類及獸醫學中用於人類或動物用途。
此類適合用於本文所描述之各種不同形式之醫藥組合物之賦形劑的實例可見於A Wade及PJ Weller編之「Handbook of Pharmaceutical Excipients」, 第2版, (1994)中。
治療性用途可接受之載劑或稀釋劑為醫藥技術中熟知的，且描述於例如Remington's Pharmaceutical Sciences, Mack Publishing Co. (A. R. Gennaro編1985)中。
適合之載劑的實例包括乳糖、澱粉、葡萄糖、甲基纖維素、硬脂酸鎂、甘露糖醇、山梨糖醇及類似物。
適合之稀釋劑的實例包括以下中之一或多者：水、乙醇、丙三醇、丙二醇及甘油及其組合。
醫藥載劑、賦形劑或稀釋劑之選擇可考慮預期投藥途徑及標準醫藥實踐來進行選擇。醫藥組合物可包含作為載劑、賦形劑或稀釋劑或除載劑、賦形劑或稀釋劑之外的任何適合之黏合劑、潤滑劑、懸浮劑、包衣劑、增溶劑。
適合之黏合劑的實例包括澱粉、明膠、天然糖(諸如葡萄糖)、無水乳糖、自由流動乳糖、β-乳糖、玉米甜味劑、天然及合成樹膠(諸如阿拉伯膠、黃蓍膠或海藻酸鈉)、羧甲基纖維素及聚乙二醇。
適合之潤滑劑的實例包括油酸鈉、硬脂酸鈉、硬脂酸鎂、苯甲酸鈉、乙酸鈉、氯化鈉及類似物。
防腐劑、穩定劑、染料及甚至調味劑可提供於醫藥組合物中。防腐劑之實例包括苯甲酸鈉、山梨酸及對羥基苯甲酸之酯。亦可使用抗氧化劑及懸浮劑。
在一個態樣中，菌株BT2013醫藥組合物之微生物為囊封的。
醫藥可呈溶液形式或呈固體形式，此取決於用途及/或施加模式及/或投與模式。
如本文所用，術語「藥劑」涵蓋在人類及獸醫學中用於人類與動物用途兩者之藥劑。此外，如本文所用之術語「藥劑」意謂提供治療及/或有益作用之任何物質。如本文所用之術語「藥劑」未必限於需要上市批准之物質，而是可包括可用於化妝品、營養品、食物(包括例如飼料及飲料)、益生菌培養物、營養補充物及天然療法之物質。此外，如本文所用之術語「藥劑」涵蓋經設計用於摻入動物飼料(例如牲畜飼料及/或寵物食物)之產品。營養補充物
營養學上可接受之載劑、稀釋劑及賦形劑包括適合於人類或動物消耗且在食品工業中用作標準之彼等。典型營養學上可接受之載劑、稀釋劑及賦形劑將為此項技術中之熟練人員所熟悉的。
在一個實施例中，營養補充物包含菌株BT2013之微生物或包含含有該多核苷酸序列之表現載體的宿主細胞以及營養學上可接受之賦形劑、載劑或稀釋劑。
在一個實例中，菌株BT2013之微生物為囊封的。飼料 / 產品
本發明之另一態樣係關於包含菌株BT2013之微生物的飼料、食物產品、膳食補充物及食物添加劑。
如本文所用之術語「飼料」、「食物產品」、「食物添加劑」及「膳食補充物」旨在覆蓋可為固體、果凍狀或液體之所有可消耗產品。
術語「食物產品」以廣義意義使用，且覆蓋人類之食物以及動物之食物(即飼料)。在一個態樣中，食物產品係供人類消耗。食物產品之實例包括乳製品(諸如奶、乳酪、包含乳清蛋白之飲料、奶飲品、乳酸菌飲品、酸凝酪、飲用酸凝酪)、焙烤產品、飲料及飲料粉。
「飼料」、「食物產品」、「食物添加劑」及「膳食補充物」可呈溶液形式或呈固體形式，此取決於用途及/或施加模式及/或投與模式。
如本文所用，術語「膳食補充物」包括為或可添加至食物產品或飼料中作為營養補充物之調配物。如在此所用之術語「膳食補充物」亦指可以低含量用於多種需要膠凝、紋理化、穩定化、懸浮、成膜及結構化、保持多汁及改良口感而不增加黏度之產品中之調配物。
適合之食物產品可包括例如功能性食物產品、食物組合物、寵物食物、牲畜飼料、健康食品、飼料及類似物。在一個態樣中，食物產品為健康食品。
如本文所用，術語「功能性食物產品」意謂不僅能夠提供營養作用而且能夠為消費者遞送另一有益作用之食物。因此，功能性食品為普通食物，其具有摻入其中從而除了單純營養作用之外賦予食物特定功能(例如醫學或生理益處)的組分或成分(諸如本文所描述之彼等)。
適用於本發明之特定食物產品之實例包括供人類使用之基於奶之產品、即食甜點、用於用例如奶或水複水之粉末、巧克力奶飲品、麥芽飲品、即食盤裝菜、速食盤裝菜或飲品或者代表旨在供寵物或牲畜使用之全部或部分膳食的食物組合物。
在一個態樣中，根據本發明之飼料、食物產品、膳食補充物或食物添加劑旨在供人類、寵物或牲畜(諸如單胃動物)使用。飼料、食物產品、膳食補充物或食物添加劑可旨在供選自由以下組成之群的動物使用：犬、貓、豬、馬或禽類。在另一實施例中，食物產品、膳食補充物或食物添加劑旨在供成年物種，尤其成年人類使用。
如本文所用之術語「基於奶之產品」意謂具有不同脂肪含量之任何液體或半固體之基於奶或乳清之產品。基於奶之產品可為例如奶牛奶、山羊奶、綿羊奶、脫脂乳、全脂奶、奶粉再製奶及未經任何加工之乳清，或經加工產品，諸如酸凝酪、凝結奶、凝乳、優酪乳、酸全脂奶、白脫乳及其他優酪乳產品。另一重要群包括奶飲料，諸如乳清飲料、發酵奶、濃縮奶、嬰兒或寶寶奶；調味奶、霜淇淋；含奶食物，諸如甜食。
本發明之飼料、食物產品、膳食補充物或食物添加劑可為或可添加至食物補充物中，該等食物補充物在本文中亦稱為膳食或營養補充物或食物添加劑。
根據本發明之飼料、食物產品、膳食補充物或食物添加劑亦可用於動物營養中(例如豬營養中)，尤其在早期斷奶期及生長增肥期中。飼料、食物產品、膳食補充物或食物添加劑預期增強免疫功能，減輕及預防感染性疾病，有利地改變微生物群組成，且改良動物之生長及表現，例如通過增加之飼料轉化效率。
在一個實施例中，飼料、食物產品、膳食補充物或食物添加劑為囊封的。活性生物治療產品
菌株BT2013之微生物可用於或用作活性生物治療產品(LBP)。
在一個態樣中，LBP為具有代謝活性之經口可管理之組合物，即活的及/或凍乾的或無活性熱滅活、照射或溶解之細菌。LBP可含有其他成分。LBP可經口投與，即呈片劑、膠囊或粉末形式。LBP可另外包含其他細菌種類，例如細菌種類人羅氏菌(R. hominis
)。囊封產品有助於人羅氏菌，因為其為厭氧菌。可包括其他成分(諸如維生素C)作為除氧劑及受質(諸如此等物質改良定殖及活體內存活率)。或者，本發明之LBP可作為食物或營養產品(諸如基於奶或乳清之發酵乳製品)或作為藥物產品經口投與。
LBP中之細菌之適合日劑量為約1 x 103
至約1 x 1012
菌落形成單位(CFU)；例如約1 x 107
至約1 x 1010
CFU；在另一實例中，約1 x 106
至約1 x 1010
CFU。
在一個態樣中，LBP含有以相對於組合物之重量約1×106
至約1×1012
CFU/g；例如約1×108
至約1×1010
CFU/g之量的細菌種類及/或其細胞組分作為活性成分。典型地，LBP視情況與至少一種適合之益生元化合物組合。益生元通常為不易消化之碳水化合物，諸如寡醣或多醣，或糖醇，其在上部消化道中不降解或吸收。已知益生元包括諸如菊粉及轉半乳-寡醣之商業產品。
在一個態樣中，本說明書之LBP包括呈相對於組合物總重量約1至約30重量%(例如5至20重量%)之量的益生元。碳水化合物可選自由以下組成之群：果糖-寡醣(或FOS)、短鏈果糖-寡醣、菊粉、異麥芽糖醇-寡醣、果膠、木糖-寡醣(或XOS)、殼聚糖-寡醣(或COS)、β-葡聚糖、經阿拉伯膠修飾且具耐性之澱粉、聚糊精、D-塔格糖、阿拉伯膠纖維、角豆、燕麥及柑桔纖維。在一個態樣中，益生元為短鏈果糖-寡醣(為簡單起見在下文中顯示為FOSs-c.c)；該FOSs-c.c.不為可消化之碳水化合物，通常藉由甜菜糖轉化而獲得且包括三種葡萄糖分子所鍵結之蔗糖分子。投藥
本發明之醫藥組合物、營養補充物、飼料、食物產品、膳食補充物或食物添加劑可適合於經口、直腸、陰道、非經腸、肌肉內、腹膜內、動脈內、鞘內、支氣管內、皮下、皮內、靜脈內、鼻內、頰內或舌下投藥途徑。
在一個態樣中，本發明之醫藥組合物、營養補充物、飼料、食物產品、膳食補充物或食物添加劑適合於經口、直腸、陰道、非經腸、鼻內、頰內或舌下投藥途徑。
在另一態樣中，本發明之醫藥組合物、營養補充物、飼料、食物產品、膳食補充物或食物添加劑適合於經口投與。
對於經口投與，特定用途由壓製錠劑、丸劑、錠劑、膠囊劑、滴劑及膠囊構成。
其他投藥形式包括溶液或乳液，其可為靜脈、動脈內、鞘內、皮下、皮內、腹膜內或肌肉內注射，且其由無菌或可無菌化溶液製備。本發明之醫藥組合物亦可呈栓劑、陰道栓及懸浮液形式。醫藥組合物、營養補充物、飼料、食物產品、膳食補充物或食物添加劑可調配成單位劑型，亦即呈含有單位劑量或單位劑量之多個單位或子單位元之離散部分的形式。劑量
一般熟習此項技術者可在未經過度實驗之情況下容易地確定向個體投與菌株BT2013之適當劑量。典型地，醫師將確定將最適合於個別患者之實際劑量且其將取決於包括以下之多種因素：所使用菌株之活性、該菌株之代謝穩定性及作用長度、年齡、體重、總體健康、性別、膳食、投與模式及時間、排泄速率、藥物組合、特定病狀之嚴重性及經歷治療之個體。本文所揭示之劑量例示一般情況。當然可存在值得更高或更低劑量範圍之個別情況且此類情況在本發明之範疇內。組合
在一個態樣中，菌株BT2013之微生物係與一或多種其他活性劑組合投與。在此類情況下，菌株BT2013之微生物可與一或多種其他活性劑連續、同時或依序投與。功能分析： 活體內模型
C57BL/6小鼠(6週齡)用於評估多形擬桿菌菌株E1、E2及BT2013在DSS誘導型結腸炎期間之治療作用。使小鼠中定殖多形擬桿菌菌株中之一者，然後用DSS治療。將動物安樂死且進行腸道組織取樣。收集小腸用於藉由流式細胞術進行之免疫分析及髓過氧化物酶(MPO)之酶活性量測。將升結腸分成相等份且轉移至中性緩衝福爾馬林(NBF；Sigma-Aldrich)中用於組織分析或RNAlater (Ambion)中用於分子分析。
對小腸固有層中之T細胞群體進行流式細胞術分析(圖1及圖2)。單獨DSS及多形擬桿菌治療不影響CD3+CD4+CD8群體之總百分比。受單獨DSS及多形擬桿菌影響之群體為Treg (CD25+FoxP3+*及FR4hi
CD25+*)及Teff細胞(FR4lo
CD25+*)(圖1及2)。與DSS單獨相比，在用多形擬桿菌菌株BT2013處理之小鼠中，Treg之百分比增加。菌株E1W似乎不對Treg具有任何影響(圖1)。BT2013對Treg之影響僅在用DSS共處理之小鼠中明顯。在未處理之小鼠中菌株對Treg沒有影響，但影響Teff細胞群(圖2)。
測定迴腸及盲腸中MPO之酶活性(圖3a及3b)。MPO為儲存於嗜中性粒細胞之嗜苯胺藍顆粒中之促炎性酶。MPO為用作炎症，尤其嗜中性粒細胞募集及累積之指示物。與單獨DSS相比，在多形擬桿菌/DSS處理之小鼠的迴腸或盲腸組織樣品中偵測到MPO活性水準更低指示嗜中性粒細胞募集減少且因此炎症減輕。
對升結腸進行組織分析(圖4及5及表1)。組織病理學分級流程係基於Berg等人1996之準則，其概括如下：
=隱窩淺，無或很少浸潤炎性細胞，上皮完整，杯狀細胞呈現為充滿黏蛋白。亦即無病變。
=隱窩可略微展現上皮細胞增生，在隱窩之間可見一些擴散浸潤炎性細胞，腔上皮呈現為完整，杯狀細胞可呈現為黏蛋白略微減少。
2=隱窩呈現為更深且具有上皮細胞增生之明顯證據，杯狀細胞之黏蛋白耗盡，浸潤炎性細胞明顯且性質上可為多灶性的，不過在黏膜下層中未見到浸潤。
3=與等級2中所見相比，病變涉及更大區域之黏膜及/或更頻繁。病變不涉及黏膜下層。腔上皮細胞展現小規模侵蝕。病變不為透壁的。
4=隱窩上皮呈現為被腐蝕狀。可存在膿腫。腔上皮細胞呈現為不規則，有時完全損失。觀測到透壁浸潤-此往往與上皮細胞完全損失進入腔中相關。
藉由用多形擬桿菌菌株E1、E2及BT2013治療小鼠，因DSS誘導型結腸炎而對結腸產生之破壞顯著降低。與用單獨DSS處理之小鼠相比，在定殖有多形擬桿菌之小鼠中，炎症相關基因於升結腸中之表現降低。與菌株E2相比，菌株E1及BT2013極大地降低IL1B及IL6炎性基因表現。(圖6)表 1 T檢驗 對照 BT E1 BT 2013 BT E2
DSS 0.000 0.032 0.041 0.089
活體外模型
在多形擬桿菌菌株E1、E2及BT2013存在下，調節在PMA暴露之後在腸道上皮細胞中白介素-8誘導之炎性基因的表現(圖7)。
菌株BT2013基因組定序
在MiSeq (v2 nano 2x250bp)上對來自菌株BT2013之DNA樣品進行定序，對於快速斷裂使用Nextera XT文庫且用定序銜接子標記，得到總共4605120個讀長(1115615927個鹼基)。
以下概括資料分析：
a. 使用bowtie2 (2.2.2)映射至參考序列(NC_004663及NC_004703)
b. 使用VarScan (2.3.7)及SNVer (0.5.3)進行SNV及小InDel探測(calling)，從而進行共同性探測，以避免假陽性
c. 使用參考gff對變異加以注釋
d. 使用pindel (0.2.5a3)進行大InDel探測
e. 使用SOAPdenovo (2.04)進行未映射讀長之從頭組裝
f. 將經組裝之重疊群與NCBI核苷酸資料庫進行Blast比對
g. 對樣品之所有讀長二次抽樣達到50%
h. 使用SOAPdenovo (2.04)對二次抽樣讀長進行從頭組裝
使用bowtie2 (2.2.2)將序列映射至參考序列(NC_004663及NC_004703)。在定序期間，使用VarScan (2.3.7)及SNVer (0.5.3)鑑別核苷酸變異及小插入及/或缺失，以避免假陽性，且將變異使用參考序列加以注釋。大插入及缺失係使用pindel (0.2.5a3)鑑別。使用SOAPdenovo (2.04)將未映射讀長從頭組裝。將定序片段再組裝成重疊群，將該等重疊群與NCBI核苷酸資料庫進行blast比對。將所有樣品讀長二次抽樣達到50%且然後使用SOAPdenovo (2.04)從頭組裝以提供BT2013從頭序列組裝之串聯型式。序列
SEQ ID NO:1 (BT2013從頭序列組裝之串聯型式)-參見序列表。The present invention is based on the discovery that the BT strain BT2013 has a more potent anti-inflammatory effect compared to the control BT strain. BT strain BT2013 has been deposited in National Collections of Industrial, Food and Marine Bacteria (NCIMB) with accession number 42341 on December 3, 2014, which is located at NCIMB Ltd, Ferguson Building, Craibstone Estate, Bucksburn, Aberdeen, UK, AB21 9YA. This deposit is made under the terms of the Budapest Treaty. The deposit was made by GT Biologics Ltd. (Life Sciences Innovation Building, Aberdeen, AB25 2ZS, Scotland). GT Biologics Ltd. later changed its name to 4D Pharma Research Limited. Derivatives The present invention covers derivatives of the deposited strains. The term "derivative" includes progeny strains (progeny) or strains grown from the original strain (subculture) but modified in some way (including at the genetic level) without negatively altering the biological activity, i.e. the derivative strain will be at least Has the same immunomodulatory activity as the original BT2013 strain. The genome sequence of biotype strain BT2013 is provided in SEQ ID NO:1. Bacterial strains which are biotypes of the bacteria deposited under accession number NCIMB 42341 are also expected to be effective in the treatment or prophylaxis of inflammatory and/or autoimmune and/or allergic disorders. Biotypes are closely related strains with identical or very similar physiological and biochemical characteristics. In certain embodiments, the bacterial strains used in the present invention have at least 95%, 96%, 97%, 98%, 99%, 99.5% or 99.9% of the 16s rRNA sequence of the bacteria deposited under accession number NCIMB 42341 Consensus 16s rRNA sequence. Alternatively, strains suitable for use in the present invention that are biotypes of the bacterium deposited under Accession No. NCIMB 42341 can be identified by sequencing other nucleotide sequences of the bacterium deposited under Accession No. NCIMB 42341. For example, substantially the entire genome can be sequenced, and the biotype strains used in the present invention can have sequences in at least 80% (e.g., at least 85%, 90%, 95%, or 99%) of their entire genomes , or throughout its genome) have at least 95%, 96%, 97%, 98%, 99%, 99.5%, or 99.9% sequence identity. Other suitable sequences for identifying biotype strains may include hsp60 or repeat sequences such as BOX, ERIC, (GTG) 5 or REP (Masco et al. (2003) Systematic and Applied Microbiology, 26:557-563). A biotype strain may have a sequence with at least 95%, 96%, 97%, 98%, 99%, 99.5% or 99.9% sequence identity to the corresponding sequence of the bacterium deposited under accession number NCIMB 42341. In certain embodiments, the bacterial strain used in the present invention has a genome with sequence identity to SEQ ID NO:1. In a preferred embodiment, the bacterial strains used in the present invention have at least 60% (for example at least 65%, 70%, 75%, 80%, 85%, 95%, 96%, 97%, 98%, 99% or 100%) have at least 90% sequence identity (e.g., at least 92%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity). For example, the genome of the bacterial strain used in the present invention may have at least 90% sequence identity to SEQ ID NO: 1 at 70% of SEQ ID NO: 1, or at least 80% of SEQ ID NO: 1 having at least 90% sequence identity with SEQ ID NO: 1, or having at least 90% sequence identity with SEQ ID NO: 1 in 90% of SEQ ID NO: 1, or having at least 90% sequence identity with SEQ ID NO: 1 in having at least 90% sequence identity to SEQ ID NO: 1 in 100%, or at least 95% sequence identity to SEQ ID NO: 1 in 70% of SEQ ID NO: 1, or in SEQ ID NO: 1 1 has at least 95% sequence identity with SEQ ID NO:1 in 80%, or has at least 95% sequence identity with SEQ ID NO:1 in 90% of SEQ ID NO:1, or has at least 95% sequence identity with SEQ ID NO:1 in 90%, or in SEQ ID NO:1 NO: 1 has at least 95% sequence identity with SEQ ID NO: 1 in 100%, or has at least 98% sequence identity with SEQ ID NO: 1 in 70% of SEQ ID NO: 1, or in SEQ ID NO:1 has at least 98% sequence identity with SEQ ID NO:1 in 80%, or has at least 98% sequence identity with SEQ ID NO:1 in 90% of SEQ ID NO:1, or having at least 98% sequence identity to SEQ ID NO: 1 in 100% of SEQ ID NO: 1. Alternatively, strains suitable for use in the present invention which are biotypes of bacteria deposited under accession number NCIMB 42341 may be identified by depositing with accession number NCIMB 42341 and restriction fragment analysis and/or PCR analysis, for example by using fluorescent Amplified fragment length polymorphism (FAFLP) and repetitive DNA element (rep)-PCR fingerprinting or protein expression profiling or partial 16S or 23s rDNA sequencing. In certain embodiments, a strain suitable for use in the present invention as a biotype of the bacterium deposited under accession number NCIMB 42341 is when analyzed by amplified ribosomal DNA restriction analysis (ARDRA), for example when using Sau3AI restriction Enzymes (see eg Srůtková et al. (2011) J. Microbiol. Methods, 87(1):10-6 for exemplary methods and guidance) provide strains of the same pattern as the bacteria deposited under accession number NCIMB 42341. Alternatively, biotype strains are identified as strains having the same carbohydrate fermentation pattern as the bacteria deposited under accession number NCIMB 42341. Bacterial strains that are biotypes of the bacteria deposited under Accession No. NCIMB 42341 and suitable for use in the compositions and methods of the invention may be identified using any suitable method or strategy. For example, bacterial strains having a similar growth pattern, metabolic type and/or surface antigens to the bacteria deposited under accession number NCIMB 42341 may be suitable for use in the present invention. The biotype strain will have comparable immunomodulatory activity to the NCIMB 42341 strain. For example, biotypic strains elicited comparable effects on the DSS-induced colitis model and on Treg levels, MPO enzyme activity, inflammation-related gene expression, and colonic histopathology compared to the effects shown in functional assays A comparable effect of , which can be identified by using the protocol described in Functional Analysis. Disorders Bacteroides polymorpha strain BT2013 is useful for treating and/or preventing a disorder in a subject, wherein the disorder is an inflammatory disorder and/or an autoimmune disorder. In one embodiment, the disorder affects the digestive tract, a portion of the digestive tract, the liver, hepatocytes, immune cells, epithelial cells, epidermal cells, neuronal cells, endothelial cells, fibroblasts, pancreas, and/or pancreatic cells (such as pancreatic islets ). Examples of portions (ie, components) of the digestive tract include the esophagus, stomach, and intestinal tract, such as the small intestine (eg, duodenum, jejunum, and ileum) and/or the large intestine (eg, cecum, ascending colon, transverse colon, descending colon, and sigmoid colon). Examples of epithelial cells include intestinal epithelial cells. Examples of immune cells include dendritic cells, monocytes/macrophages, T cells and neutrophils. In one embodiment, the disorder is selected from the group consisting of: organ-related disorders such as irritable bowel syndrome (IBS), inflammatory bowel disease (including Crohn's disease and ulcerative colitis), Necrotizing enterocolitis, bursitis, celiac disease, multiple sclerosis (brain), type 1 diabetes, Goodpasture's syndrome, Hashimoto's thyroiditis, chronic active hepatitis, Cardiomyopathy, uveitis and rhinitis. Systemic disorders such as rheumatoid arthritis, systemic lupus erythematosus, scleroderma, psoriasis, atopic dermatitis, leukoplakia, multiple sclerosis, alopecia areata, sarcoidosis, polymyositis, and combinations thereof. In one aspect, the disorder affects the gut. In one aspect, the disorder is an inflammatory disorder. For example, the disorder is an inflammatory bowel disorder (IBD), such as Crohn's disease. In one aspect, the disorder is an autoimmune disorder. For example, the autoimmune disorder is selected from the group consisting of ulcerative colitis, bursitis, rheumatoid arthritis, psoriasis, multiple sclerosis, type 1 diabetes, allergies (including celiac disease), idiopathic Atopic dermatitis and rhinitis. Subject In one embodiment, the subject is a monogastric animal. Examples of monogastric animals include birds, humans, rats, pigs, dogs, cats, horses and rabbits. In another embodiment, the individual is a mammal, such as a monogastric mammal. Examples of monogastric mammals include omnivores such as humans, rats and pigs, carnivores such as dogs and cats, and herbivores such as horses and rabbits. Preferably, the individual is human. In one aspect, the individual has a disorder selected from the group consisting of: inflammatory bowel disease (IBD), colitis, rheumatoid arthritis, psoriasis, multiple sclerosis, type 1 diabetes, celiac disease, idiopathic Atopic dermatitis, rhinitis, irritable bowel syndrome (IBS), ulcerative colitis, bursitis, Crohn's disease, functional dyspepsia, atopic disease, necrotizing enterocolitis, nonalcoholic fatty liver disease , gastrointestinal infections and combinations thereof. For example, an individual has IBD. Regulation / Regulation The terms "modulation" and "regulation" may be used interchangeably herein. In one embodiment, Bacteroides polymorpha strain BT2013 is used to modulate inflammation in cells, tissues or organs of an individual. In one embodiment, the term "modulate" means to increase and/or induce and/or facilitate and/or activate. In an alternative embodiment, the term "modulate" refers to lowering and/or reducing and/or inhibiting. In one embodiment, the term "modulate" refers to upregulation. In an alternative embodiment, the term "modulate" refers to downregulation. In one embodiment, Bacteroides polymorpha strain BT2013 as described herein reduces inflammation of a cell, tissue or organ. For example, relief of alimentary canal, a portion (i.e., part) of the alimentary canal (such as the intestine), liver, hepatocytes, epithelial cells, epidermal cells, neuronal cells, endothelial cells, fibroblasts, pancreas, and/or pancreatic cells (such as pancreatic islets) inflammation. In one example, inflammation of the digestive tract or a part thereof, such as the intestine, is reduced. In another example, inflammation caused by immune cells of a tissue or organ is reduced. In another example, inflammation caused by epithelial cells of a tissue or organ is reduced. The term "inflammation" as used herein refers to one or more of redness, swelling, pain, tenderness, fever, and cells, tissues or organs due to an inflammatory process triggered by an overreaction of the immune system Disruption of function. In one embodiment, after administration of a polypeptide or polynucleotide or host cell as described herein, when compared to the number of inflamed cells in an individual prior to administration of a strain BT2013 as described herein to the individual, The number of inflamed cells in the individual is at least 10%, 20%, 30%, 40% or 50% lower. In one embodiment, the amount of inflamed tissue or organ in the individual is at least 10% lower after administration of strain BT2013 when compared to the amount of inflamed tissue or organ in the individual prior to administration of strain BT2013 to the individual, 20%, 30%, 40% or 50%. In one embodiment, strain BT2013 reduces inflammation caused by epithelial cells of a tissue or organ. For example, an epithelial cell is an epithelial cell of the digestive tract or a part thereof, such as the intestinal tract. Without wishing to be bound by theory, strain BT2013 increases the production of T cells, such as regulatory T cells, which may also be referred to as Tregs, in an individual. This increase in Treg numbers counteracts the effects of other effector T cells (also known as Teff, such as Th1, Th17 and Th2) that drive inflammation, autoimmunity and allergic/atopic conditions. In Crohn's disease and ulcerative colitis, Teff/Treg cell balance is lost. In one embodiment, the production of T cells in the individual is increased such that when compared to the number of T cells in the individual prior to administration of strain BT2013 to the individual, upon administration of a polypeptide or polynucleotide or host as described herein The cells are followed by at least 10%, 20%, 30%, 40% or 50% more T cells, or more than 100% more T cells. Intestinal Barrier Integrity In one embodiment, strain BT2013 is used to improve intestinal barrier integrity in a subject. The term "improved intestinal barrier integrity" as used herein refers to the number and/or type of microorganisms that spread from the intestinal tract into other cells in an individual prior to administration of the strain BT2013 as described herein, Following administration of strain BT2013, the number and/or type of microorganisms that spread from the intestinal tract to other cells in the individual is reduced. In one embodiment, the number of microorganisms that have diffused from the intestinal tract to other cells in the individual after administration of strain BT2013 when compared to the number of microorganisms that have diffused from the intestinal tract to other cells in the individual prior to administration The number is at least 10%, 20%, 30%, 40% or 50% lower. In one embodiment, after administration of strain BT2013, the individual has fewer types of microorganisms that have diffused from the intestinal tract to other cells when compared to the types of microorganisms that have diffused from the intestinal tract to other cells in the individual prior to administration At least 5%, 10%, 15% or 20%. Intestinal Disruption In one embodiment, strain BT2013 is used to reduce disruption to the intestinal tract (e.g., large intestine) of an individual, such as an individual with IBD. As used herein, the term "disruption of an individual's intestinal tract" refers to an effect on the integrity of the mucosal epithelium and/or an effect on the number of goblet cells in the epithelium and/or an effect on the number of immune cells infiltrating the lamina propria influences. In one embodiment, strain BT2013 reduces or prevents disruption of the integrity of the mucosal epithelium and/or reduces or prevents a reduction in the number of goblet cells in the epithelium and/or reduces or prevents immune cell infiltration into the lamina propria. In one embodiment, the disruption to the integrity of the mucosal epithelium is reduced when compared to the number of bacteria penetrating into intestinal cells from the intestinal lumen in an individual prior to administration, after administration of strain BT2013, bacteria from the intestinal lumen The number of bacteria penetrating intestinal cells is reduced by at least 5%, 10%, 15% or 20%. In one embodiment, the reduction in the number of goblet cells in the epithelium is the number of goblet cells in the epithelium of the individual after administration of strain BT2013 when compared to the number of goblet cells in the epithelium of the individual prior to administration A reduction of at least 2%, 5%, 10%, 15% or 20%. In one embodiment, immune cell infiltration into the lamina propria is reduced such that after administration of strain BT2013, when compared to the number of immune cells (e.g., T cells) penetrating into the lamina propria cells in the subject prior to administration, , the number of immune cells (eg, T cells) penetrating into cells of the lamina propria is reduced by at least 5%, 10%, 15%, 20%, or 30% over a fixed period of time, such as 24 hours. Pro- inflammatory genes and barrier integrity genes In one embodiment, strain BT2013 is used to modulate the expression of one or more pro-inflammatory genes and/or one or more barrier integrity genes in cells of an individual. In one embodiment, the term "modulation" refers to the upregulation of the expression of one or more pro-inflammatory genes. In an alternative embodiment, the term "modulation" refers to down-regulation of the expression of one or more pro-inflammatory genes. In one embodiment, the strain BT2013 down-regulates the expression of one or more pro-inflammatory genes in cells of the subject. The term "pro-inflammatory gene" as used herein refers to a gene that, when expressed, promotes inflammation. Examples of proinflammatory genes include, but are not limited to, genes encoding IL1-β, IL4, IL5, IL6, IL8, IL12, IL13, IL17, IL21, IL22, IL23, IL27, IFN, CCL2, CCL3, CCL5, CCL20, CXCL5, CXCL10, CXCL12, CXCL13, and TNF-α. In one embodiment, the pro-inflammatory gene is selected from the group consisting of: IL1-β, IL6, and IL8. In one embodiment, the expression level (e.g., mRNA level) of one or more pro-inflammatory genes is reduced (i.e., down-regulated) such that after administration of strain BT2013, the level is lower when compared to the level in the individual prior to administration. At least 10%, 20%, 30%, 40% or 50%. The term "barrier integrity gene" as used herein refers to a gene that, when expressed, plays a role in the barrier function of the intestinal tract, such as repairing the barrier and preventing passage of microorganisms through the barrier. Examples of barrier integrity genes include genes encoding Retnlg|Retnlb, Si, Defa24, Hsd11b2, Hsd17b2, and Nrld1|Thra. In one embodiment, the term "modulation" refers to the upregulation of the expression of one or more barrier integrity genes. In an alternative embodiment, the term "modulation" refers to the downregulation of the expression of one or more barrier integrity genes. In one embodiment, strain BT2013 up-regulates the expression of barrier integrity genes in cells of an individual. In one embodiment, the barrier integrity genes are selected from the group consisting of: Retnlg|Retnlb, Si, Defa24, Hsd11b2, Hsd17b2, and Nr1d1 |Thra. In one embodiment, the expression level (e.g., mRNA level) of one or more barrier integrity genes is increased (i.e., upregulated) such that after administration of strain BT2013, the level is increased when compared to the level in an individual prior to administration. At least 10%, 20%, 30%, 40% or 50% higher. Digestive canal Components of the alimentary canal include the esophagus, stomach, and intestinal tract such as the small intestine (eg, duodenum, jejunum, and ileum) and/or the large intestine (eg, cecum, ascending colon, transverse colon, descending colon, and sigmoid colon). Herein, the term "large intestine" may be used interchangeably with the term "colon". In one embodiment, strain BT2013 is used to improve the digestive tract health of an individual. The term "improving digestive tract health" as used herein refers to reducing the level of inflammation in the digestive tract or parts thereof and/or improving the gut microbiota. In one embodiment, after administration of strain BT2013, the level of inflammation in the alimentary tract of the individual is at least 10%, 20%, 30%, 40%, or 50% lower when compared to the level of inflammation in the alimentary tract of the subject prior to administration %. In one embodiment, strain BT2013 is used to improve the gut microbiota of an individual. The term "gut microbiota" as used herein refers to microorganisms living in the digestive tract of a host animal. These microorganisms perform a variety of metabolic, structural, protective and other beneficial functions. As used herein, the term "modified gut microbiota" refers to increasing the number and/or types of desired microorganisms present in the intestinal tract of an individual (e.g., a host), and/or increasing the number and/or types of desired microorganisms in their metabolism, structure, , protection, and other beneficial functions. The term "modifying gut microbiota" may also refer to reducing the number and/or types of unwanted microorganisms present in the intestinal tract of an individual (e.g., a host), and/or reducing the metabolism, structure, Activity in terms of protection and other beneficial functions. Desired microbes in the gut of the host are those with protective and beneficial functions. Firmicutes and Bacteroidetes are examples of desired microorganisms in the gut of a host. Undesirable microorganisms in the gut of a host are those microorganisms that may interfere with the metabolic, structural, protective and other beneficial functions of desired microorganisms in the gut that have protective and beneficial functions. Alternatively or additionally, unwanted microorganisms are those that cause, for example, inflammation and/or diarrhea. Escherichia coli ( E. coli ) is an example of an unwanted microorganism in the gut of a host. For example, once strain BT2013 has been administered to an individual, in individuals with inflammatory bowel disease (IBD), desired microorganisms in the gut (such as Firmicutes and Bacteroidetes bacteria) and different Changes in microbiota balance among desired microorganisms such as E. coli: ETEC, EPEC, EIEC, EHEC and EAEC. In one embodiment, the number of desired microorganisms (such as Firmicutes and Bacteroidetes bacteria) present in the intestinal tract of an individual (e.g., a host) is increased such that in After administration of strain BT2013, the number of microorganisms is at least 10%, 20%, 30%, 40% or 50% higher, or higher than 100%. Alternatively or additionally, the types of desired microorganisms (such as Firmicutes and Bacteroidetes) present in the intestinal tract of an individual (e.g., a host) are increased such that when compared to the types in the individual prior to administration, After strain BT2013, the types of microorganisms were at least 2%, 5%, 10% or 15% more. In one embodiment, the number of unwanted microorganisms (such as Escherichia coli ETEC, EPEC, EIEC, EHEC, and EAEC) present in the gut of an individual (e.g., a host) is reduced such that when compared to the level in the individual prior to administration In comparison, the number of microorganisms is at least 10%, 20%, 30%, 40% or 50% lower after administration of strain BT2013. Alternatively or additionally, the types of unwanted microorganisms (such as Escherichia coli ETEC, EPEC, EIEC, EHEC and EAEC) present in the gut of an individual (e.g., a host) are reduced such that when compared to the type in the individual prior to administration , the types of unwanted microorganisms are at least 1%, 2%, 5% or 10% less after administration of strain BT2013. Encapsulation In one embodiment, Bacteroides polymorpha strain BT2013 is encapsulated. In another embodiment, the pharmaceutical composition comprising strain BT2013 is encapsulated. In another embodiment, the nutritional supplement comprising strain BT2013 is encapsulated. In another embodiment, the feed, food product, dietary supplement or food additive as described herein is encapsulated. The term "encapsulation" as used herein refers to protection by physical separation such that strain BT2013 can be delivered to a target site (e.g., intestinal tract) without degradation or significantly degraded so that it can affect the target site. Means that strain BT2013 is not affected by an incompatible environment. An example is enteric coated capsules or enteric resistant capsules. Even when the purpose of encapsulation is to isolate the strain from its environment, the protective coating or shell must be ruptured for the desired effect. Rupture of the protective coating or shell is typically induced by the application of chemical and physical stimuli such as pressure, enzymatic attack, chemical reaction and physical disintegration. For example, encapsulation ensures that an ingestible strain is delivered to a target site (eg, the intestinal tract) in an amount effective for the microorganism to produce an effect at the target site. Pharmaceutical Compositions In one embodiment, a pharmaceutical composition comprises a microorganism of strain BT2013 and optionally a pharmaceutically acceptable excipient, carrier or diluent. The pharmaceutical composition can be any pharmaceutical composition. In one aspect, the pharmaceutical composition is to be administered orally, enterally or rectally. For example, the composition can be an edible composition. "Edible" means that the material is approved for human or animal consumption. Pharmaceutical compositions can be used in human or veterinary medicine for human or animal use. Examples of such excipients suitable for use in the various forms of the pharmaceutical compositions described herein can be found in "Handbook of Pharmaceutical Excipients", 2nd Ed., (1994), edited by A Wade and PJ Weller. Carriers or diluents acceptable for therapeutic use are well known in the pharmaceutical art and are described, for example, in Remington's Pharmaceutical Sciences, Mack Publishing Co. (ed. AR Gennaro 1985). Examples of suitable carriers include lactose, starch, glucose, methylcellulose, magnesium stearate, mannitol, sorbitol and the like. Examples of suitable diluents include one or more of water, ethanol, glycerol, propylene glycol, and glycerin, and combinations thereof. The choice of pharmaceutical carrier, excipient or diluent can be selected taking into account the intended route of administration and standard pharmaceutical practice. The pharmaceutical composition may comprise any suitable binder, lubricant, suspending agent, coating agent, solubilizing agent as or in addition to a carrier, excipient or diluent. Examples of suitable binders include starch, gelatin, natural sugars such as glucose, anhydrous lactose, free-flowing lactose, beta-lactose, corn sweeteners, natural and synthetic gums such as acacia, tragacanth, or sodium alginate. ), carboxymethylcellulose and polyethylene glycol. Examples of suitable lubricants include sodium oleate, sodium stearate, magnesium stearate, sodium benzoate, sodium acetate, sodium chloride, and the like. Preservatives, stabilizers, dyes and even flavoring agents can be provided in pharmaceutical compositions. Examples of preservatives include sodium benzoate, sorbic acid, and esters of p-hydroxybenzoic acid. Antioxidants and suspending agents may also be used. In one aspect, the microorganisms of the strain BT2013 pharmaceutical composition are encapsulated. The medicine may be in solution or in solid form, depending on the use and/or mode of administration and/or administration. As used herein, the term "medicament" encompasses medicaments used in human and veterinary medicine for both human and animal use. Furthermore, the term "medicament" as used herein means any substance that provides a therapeutic and/or beneficial effect. The term "pharmaceutical" as used herein is not necessarily limited to substances that require marketing approval, but may include substances that can be used in cosmetics, nutritional products, food (including, for example, feed and beverages), probiotic cultures, nutritional supplements, and natural remedies. Furthermore, the term "medication" as used herein encompasses products designed for incorporation into animal feed, such as livestock feed and/or pet food. Nutritional Supplements Nutritionally acceptable carriers, diluents and excipients include those suitable for human or animal consumption and used as standards in the food industry. Typical nutritionally acceptable carriers, diluents and excipients will be familiar to those skilled in the art. In one embodiment, the nutritional supplement comprises a microorganism of strain BT2013 or a host cell comprising an expression vector comprising the polynucleotide sequence and a nutritionally acceptable excipient, carrier or diluent. In one example, the microorganisms of strain BT2013 are encapsulated. Feed / Products Another aspect of the present invention relates to feed, food products, dietary supplements and food additives comprising microorganisms of strain BT2013. The terms "feed", "food product", "food additive" and "dietary supplement" as used herein are intended to cover all consumable products which may be solid, jelly-like or liquid. The term "food product" is used in a broad sense and covers food for humans as well as food for animals (ie feed). In one aspect, the food product is for human consumption. Examples of food products include dairy products (such as milk, cheese, beverages containing whey protein, milk beverages, lactic acid bacteria beverages, curd cheese, curdled drinking), bakery products, beverages, and beverage powders. "Feed", "food product", "food additive" and "dietary supplement" may be in solution form or in solid form, depending on the use and/or mode of application and/or mode of administration. As used herein, the term "dietary supplement" includes formulations that are or can be added to food products or feed as nutritional supplements. The term "dietary supplement" as used herein also refers to products that can be used at low levels in a variety of products that require gelling, texturing, stabilizing, suspending, film-forming and structuring, maintaining juiciness and improving mouthfeel without increasing viscosity The concoction. Suitable food products may include, for example, functional food products, food compositions, pet food, livestock feed, health food, feed, and the like. In one aspect, the food product is a health food. As used herein, the term "functional food product" means a food that not only provides a nutritional effect but also delivers another beneficial effect to the consumer. Thus, a functional food is a common food that has components or ingredients (such as those described herein) incorporated therein to impart a specific function (eg, medical or physiological benefit) to the food other than a purely nutritional effect. Examples of specific food products suitable for use in the present invention include milk-based products for human consumption, ready-to-eat desserts, powders for reconstitution with e.g. milk or water, chocolate milk drinks, malt drinks, ready-to-eat dishes, instant meals A dish or drink or a food composition representing all or part of a meal intended for pets or livestock. In one aspect, the feed, food product, dietary supplement or food additive according to the invention is intended for use by humans, pets or livestock such as monogastric animals. The feed, food product, dietary supplement or food additive may be intended for use with animals selected from the group consisting of: dogs, cats, pigs, horses or poultry. In another embodiment, the food product, dietary supplement or food additive is intended for adult species, especially adult humans. The term "milk-based product" as used herein means any liquid or semi-solid milk or whey-based product with varying fat content. Milk-based products may be, for example, cow's milk, goat's milk, sheep's milk, skimmed milk, whole milk, reconstituted milk powder and whey without any processing, or processed products such as curdled cheese, curdled milk, curdled milk , yogurt, sour whole milk, buttermilk and other yogurt products. Another important group includes milk drinks, such as whey drinks, fermented milk, concentrated milk, infant or infant milk; flavored milk, ice cream; milk-containing foods, such as sweets. The feedstuffs, food products, dietary supplements or food additives of the present invention may be or may be added to food supplements, also referred to herein as dietary or nutritional supplements or food additives. The feedstuffs, food products, dietary supplements or food additives according to the invention can also be used in animal nutrition, for example in pig nutrition, especially in the early weaning and growing-finishing periods. Feeds, food products, dietary supplements or food additives are expected to enhance immune function, reduce and prevent infectious diseases, favorably alter microbiota composition, and improve animal growth and performance, for example through increased feed conversion efficiency. In one embodiment the feed, food product, dietary supplement or food additive is encapsulated. Active Biotherapeutic Products Microorganisms of strain BT2013 can be used or used as active biotherapeutic products (LBP). In one aspect, the LBP is an orally administrable composition with metabolic activity, ie, live and/or lyophilized or inactive heat-inactivated, irradiated or lysed bacteria. LBP may contain other ingredients. LBP can be administered orally, ie in tablet, capsule or powder form. The LBP may additionally comprise other bacterial species, such as the bacterial species R. hominis . Encapsulated products help Rothia hominis because it is anaerobic. Other ingredients such as vitamin C may be included as oxygen scavengers and substrates (such substances improve colonization and in vivo survival). Alternatively, the LBP of the present invention may be administered orally as a food or nutritional product, such as a milk or whey based fermented dairy product, or as a pharmaceutical product. A suitable daily dose of bacteria in LBP is about 1 x 103 to about 1 x 1012 colony forming units (CFU); for example about 1 x 107 to about 1 x 1010 CFU; in another example, about 1 x 106 to about 1 x 1010 CFU. In one aspect, the LBP contains bacterial species in an amount of about 1×10 6 to about 1×10 12 CFU/g; for example, about 1×10 8 to about 1×10 10 CFU/g by weight of the composition and/or its cellular components as active ingredients. Typically, LBP is optionally combined with at least one suitable prebiotic compound. Prebiotics are generally non-digestible carbohydrates, such as oligo- or polysaccharides, or sugar alcohols, which are not degraded or absorbed in the upper digestive tract. Known prebiotics include commercial products such as inulin and transgalacto-oligosaccharides. In one aspect, the LBP of the present specification includes a prebiotic in an amount of about 1 to about 30% by weight (eg, 5 to 20% by weight) relative to the total weight of the composition. The carbohydrate may be selected from the group consisting of: fructo-oligosaccharides (or FOS), short chain fructo-oligosaccharides, inulin, isomalt-oligosaccharides, pectin, xylose-oligosaccharides (or XOS), shell Glycan-oligosaccharides (or COS), β-glucan, starch modified and resistant to acacia, polydextrin, D-tagatose, acacia fiber, carob, oat and citrus fiber. In one aspect, the prebiotics are short-chain fructo-oligosaccharides (shown below as FOSs-cc for simplicity); the FOSs-cc are non-digestible carbohydrates, usually obtained by conversion of beet sugar and Consists of sucrose molecules bonded to three glucose molecules. Administration The pharmaceutical composition, nutritional supplement, feed, food product, dietary supplement or food additive of the present invention may be suitable for oral, rectal, vaginal, parenteral, intramuscular, intraperitoneal, intraarterial, intrathecal, bronchial Intradermal, subcutaneous, intradermal, intravenous, intranasal, buccal or sublingual routes of administration. In one aspect, the pharmaceutical composition, nutritional supplement, feed, food product, dietary supplement or food additive of the present invention is suitable for oral, rectal, vaginal, parenteral, intranasal, buccal or sublingual administration way. In another aspect, the pharmaceutical composition, nutritional supplement, feed, food product, dietary supplement or food additive of the invention is suitable for oral administration. For oral administration, particular uses consist of compressed tablets, pills, lozenges, capsules, drops, and capsules. Other forms of administration include solutions or emulsions, which can be injected intravenously, intraarterially, intrathecally, subcutaneously, intradermally, intraperitoneally or intramuscularly, and which are prepared from sterile or sterilizable solutions. The pharmaceutical compositions of the present invention may also be in the form of suppositories, pessaries and suspensions. A pharmaceutical composition, nutritional supplement, feed, food product, dietary supplement or food additive may be formulated in unit dosage form, that is, in the form of discrete portions containing a unit dose or units or subunits of a unit dose. Dosages Appropriate dosages for administering strain BT2013 to individuals can be readily determined by one of ordinary skill in the art without undue experimentation. Typically, a physician will determine the actual dosage that will be most suitable for an individual patient and will depend on a variety of factors including: activity of the strain used, metabolic stability and length of action of the strain, age, body weight, general health, sex , diet, mode and time of administration, rate of excretion, drug combination, severity of the particular condition, and individual undergoing treatment. Dosages disclosed herein are exemplary of typical situations. There may, of course, be individual cases deserving higher or lower dosage ranges and such cases are within the scope of this invention. Combinations In one aspect, microorganisms of strain BT2013 are administered in combination with one or more other active agents. In such cases, the microorganism of strain BT2013 may be administered sequentially, simultaneously or sequentially with one or more other active agents. Functional Assays: In vivo model C57BL/6 mice (6 weeks old) were used to evaluate the therapeutic effects of Bacteroides polymorpha strains E1, E2 and BT2013 during DSS-induced colitis. Mice were colonized with one of the B. polymorpha strains and then treated with DSS. Animals were euthanized and intestinal tissue samples were taken. Small intestines were collected for immunoassays by flow cytometry and for enzymatic activity measurement of myeloperoxidase (MPO). The ascending colon was divided into equal portions and transferred to neutral buffered formalin (NBF; Sigma-Aldrich) for tissue analysis or RNAlater (Ambion) for molecular analysis. Flow cytometry analysis was performed on the T cell population in the lamina propria of the small intestine (Figure 1 and Figure 2). DSS alone and B. polymorpha treatment did not affect the overall percentage of the CD3+CD4+CD8 population. The populations affected by DSS alone and B. polymorpha were Treg (CD25+FoxP3+* and FR4 hi CD25+*) and Teff cells (FR4 lo CD25+*) ( FIGS. 1 and 2 ). The percentage of Treg was increased in mice treated with B. polymorpha strain BT2013 compared to DSS alone. Strain E1W did not appear to have any effect on Tregs (Figure 1). The effect of BT2013 on Treg was only apparent in mice co-treated with DSS. In untreated mice the strain had no effect on Treg, but affected Teff cell populations (Figure 2). The enzyme activity of MPO in the ileum and cecum was determined (Figures 3a and 3b). MPO is a pro-inflammatory enzyme stored in the azurophilic granules of neutrophils. MPO is used as an indicator of inflammation, especially neutrophil recruitment and accumulation. The detection of lower levels of MPO activity in ileal or cecal tissue samples from B. polymorpha/DSS-treated mice compared to DSS alone indicated reduced neutrophil recruitment and thus reduced inflammation. Histological analysis was performed on the ascending colon (Figures 4 and 5 and Table 1). The histopathological grading algorithm is based on the guidelines of Berg et al. 1996, which are summarized as follows: = shallow crypts, few or few infiltrating inflammatory cells, intact epithelium, goblet cells appear filled with mucin. That is, no disease. =Crypts may show slight epithelial hyperplasia, some diffuse infiltrating inflammatory cells may be seen between crypts, luminal epithelium may appear intact, and goblet cells may appear slightly reduced in mucin. 2 = Crypts appear deeper with clear evidence of epithelial hyperplasia, mucin depletion of goblet cells, infiltrating inflammatory cells are evident and may be multifocal in nature, although no infiltration is seen in the submucosa. 3 = Lesions involve a larger area of mucosa and/or are more frequent than seen in grade 2. The lesion does not involve the submucosa. The luminal epithelium exhibits small scale erosions. The lesion is not transmural. 4=The crypt epithelium appears corroded. Abscesses may be present. The luminal epithelium appears irregular and sometimes completely lost. Transmural infiltration was observed - this often correlates with complete loss of epithelial cells into the lumen. By treating mice with B. polymorpha strains E1 , E2 and BT2013, damage to the colon due to DSS-induced colitis was significantly reduced. Expression of inflammation-related genes in the ascending colon was reduced in mice colonized with B. polymorpha compared with mice treated with DSS alone. Compared with strain E2, strains E1 and BT2013 greatly reduced the expression of IL1B and IL6 inflammatory genes. (Figure 6) Table 1 T test control BT E1 BT 2013 BT E2
DSS 0.000 0.032 0.041 0.089
In vitro model Modulation of interleukin-8-induced inflammatory gene expression in intestinal epithelial cells following PMA exposure in the presence of Bacteroides polymorpha strains El, E2 and BT2013 (Figure 7). Strain BT2013 Genome Sequencing DNA samples from strain BT2013 were sequenced on a MiSeq (v2 nano 2x250bp) using the Nextera XT library for rapid breaks and tagged with sequencing adapters resulting in a total of 4605120 reads (1115615927 bases ). The following summary data analysis: a. Use bowtie2 (2.2.2) to map to the reference sequence (NC_004663 and NC_004703) b. Use VarScan (2.3.7) and SNVer (0.5.3) for SNV and small InDel detection (calling), so that Perform consensus detection to avoid false positives c. Annotate variants using reference gff d. Use pindel (0.2.5a3) for large InDel detection e. Use SOAPdenovo (2.04) for de novo assembly of unmapped reads f. The assembled contigs were compared with the NCBI nucleotide database by Blast. g. All the read lengths of the sample were subsampled to 50% h. Use SOAPdenovo (2.04) to de novo assemble the subsampled read lengths using bowtie2 (2.2. 2) Map the sequences to reference sequences (NC_004663 and NC_004703). During sequencing, nucleotide variations and small insertions and/or deletions were identified using VarScan (2.3.7) and SNVer (0.5.3) to avoid false positives, and variations were annotated with reference sequences. Large insertions and deletions were identified using pindel (0.2.5a3). Unmapped reads were assembled de novo using SOAPdenovo (2.04). The sequenced fragments were reassembled into contigs, and these contigs were blasted against the NCBI nucleotide database. All sample reads were subsampled to 50% and then assembled de novo using SOAPdenovo (2.04) to provide a tandem version of the BT2013 de novo sequence assembly. Sequence SEQ ID NO: 1 (tandem version of BT2013 de novo sequence assembly) - see Sequence Listing.