Recent research on the genome of Bifidobacterium bifidum has mainly focused on the isolation sources(intestinal tract niche)recently,but reports on the isolation region are limited.This study analyzed the differences ...Recent research on the genome of Bifidobacterium bifidum has mainly focused on the isolation sources(intestinal tract niche)recently,but reports on the isolation region are limited.This study analyzed the differences in the genome of B.bifidum isolated from different geographical populations by comparative genomic analysis.Results at the genome level indicated that the GC content of American isolates was significantly higher than that of Chinese and Russian isolates.The phylogenetic tree,based on 919 core genes showed that B.bifidum might be related to the geographical characteristics of isolation region.Furthermore,functional annotation analysis demonstrated that copy numbers of carbohydrate-active enzymes(CAZys)involved in the degradation of polysaccharide from plant and host sources in B.bifidum were high,and 18 CAZys showed significant differences across different geographical populations,indicating that B.bifidum had adapted to the human intestinal environment,especially in the groups with diets rich in fiber.Dietary habits were one of the main reasons for the differences of B.bifidum across different geographical populations.Additionally,B.bifidum exhibited high diversity,evident in glycoside hydrolases,the CRISPR-Cas system,and prophages.This study provides a genetic basis for further research and development of B.bifidum.展开更多
Microorganisms plays an important role in the growth of Pyropia haitanensis.To understand the structural and functional diversity of the microorganism community of P.haitanensis(PH40),the associated metabolic pathway ...Microorganisms plays an important role in the growth of Pyropia haitanensis.To understand the structural and functional diversity of the microorganism community of P.haitanensis(PH40),the associated metabolic pathway network in cluster of orthologous groups(COG)and Kyoto Encyclopedia of Genes and Genomes(KEGG),and carbohydrate-active enzymes(CAZymes)were explored in metagenomic analysis.DNA extraction from gametophytes of P.haitanensis was performed first,followed by library construction,sequencing,preprocessing of sequencing data,taxonomy assignment,gene prediction,and functional annotation.The results show that the predominant microorganisms of P.haitanensis were bacteria(98.98%),and the phylum with the highest abundance was Proteobacteria(54.64%),followed by Bacteroidetes(37.92%).Erythrobacter(3.98%)and Hyunsoonleella jejuensis(1.56%)were the genera and species with the highest abundance of bacteria,respectively.The COG annotation demonstrated that genes associated with microbial metabolism was the predominant category.The results of metabolic pathway annotation show that the ABC transport system and two-component system were the main pathways in the microbial community.Plant growth hormone biosynthesis pathway and multi-vitamin biosynthesis functional units(modules)were the other important pathways.The CAZyme annotation revealed that the starch might be an important carbon source for microorganisms.Glycosyl transferase family 2(GT2)and glycosyl transferase family 3(GT3)were the highly abundant families in glucoside transferase superfamily.Six metagenome-assembled genomes containing enzymes involved in the biosynthesis of cobalamin(vitamin B 12)and indole-3-acetic acid were obtained by binning method.They were confirmed to belong to Rhodobacterales and Rhizobiales,respectively.Our findings provide comprehensive insights into the microorganism community of Pyropia.展开更多
Green macroalgae,e.g.,Ulva lactuca,are valuable bioactive sources of nutrients;but algae recalcitrant cell walls,composed of a complex cross-linked matrix of polysaccharides,can compromise their utilization as feedstu...Green macroalgae,e.g.,Ulva lactuca,are valuable bioactive sources of nutrients;but algae recalcitrant cell walls,composed of a complex cross-linked matrix of polysaccharides,can compromise their utilization as feedstuffs for monogastric animals.This study aimed to evaluate the ability of pre-selected Carbohydrate-Active enZymes(CAZymes)and sulfatases to degrade U.lactuca cell walls and release nutritive compounds.A databank of 199 recombinant CAZymes and sulfatases was tested in vitro for their action towards U.lactuca cell wall polysaccharides.The enzymes were incubated with the macroalga,either alone or in combination,to release reducing sugars and decrease fluorescence intensity of Calcofluor White stained cell walls.The individual action of a polysaccharide lyase family 25(PL25),an ulvan lyase,was shown to be the most efficient in cell wall disruption.The ulvan lyase treatment,in triplicate measures,promoted the release of 4.54 g/L(P<0.001)reducing sugars,a mono-and oligosaccharides release of 11.4 and 11.2 mmol/100 g of dried alga(P<0.01),respectively,and a decrease of 41.7%(P<0.001)in cell wall fluorescence,in comparison to control.The ability of ulvan lyase treatment to promote the release of nutritional compounds from alga biomass was also evaluated.A release of some monounsaturated fatty acids was observed,particularly the health beneficial 18:1c9(P<0.001).However,no significant release of total fatty acids(P>0.05),proteins(P?0.861)or pigments(P>0.05)was found.These results highlight the capacity of a single recombinant ulvan lyase(PL25 family)to incompletely disrupt U.lactuca cell walls.This enzyme could enhance the bioaccessibility of U.lactuca bioactive products with promising utilization in the feed industry.展开更多
基金the National Key R&D Program of China(2022YFD21007002)the National Natural Science Foundation of China(32325040)+1 种基金Inner Mongolia Science&Technology planning project(2022YFSJ0017)the earmarked fund for CARS36.
文摘Recent research on the genome of Bifidobacterium bifidum has mainly focused on the isolation sources(intestinal tract niche)recently,but reports on the isolation region are limited.This study analyzed the differences in the genome of B.bifidum isolated from different geographical populations by comparative genomic analysis.Results at the genome level indicated that the GC content of American isolates was significantly higher than that of Chinese and Russian isolates.The phylogenetic tree,based on 919 core genes showed that B.bifidum might be related to the geographical characteristics of isolation region.Furthermore,functional annotation analysis demonstrated that copy numbers of carbohydrate-active enzymes(CAZys)involved in the degradation of polysaccharide from plant and host sources in B.bifidum were high,and 18 CAZys showed significant differences across different geographical populations,indicating that B.bifidum had adapted to the human intestinal environment,especially in the groups with diets rich in fiber.Dietary habits were one of the main reasons for the differences of B.bifidum across different geographical populations.Additionally,B.bifidum exhibited high diversity,evident in glycoside hydrolases,the CRISPR-Cas system,and prophages.This study provides a genetic basis for further research and development of B.bifidum.
基金Supported by the National Key R&D Program of China(Nos.2018YFC1406704,2018YFD0900106,2018YFC1406700)the Marine S&T Fund of Shandong Province for Pilot National Laboratory for Marine Science and Technology(Qingdao)(No.2018SDKJ0302-4)the MOA Modern Agricultural Talents Support Project。
文摘Microorganisms plays an important role in the growth of Pyropia haitanensis.To understand the structural and functional diversity of the microorganism community of P.haitanensis(PH40),the associated metabolic pathway network in cluster of orthologous groups(COG)and Kyoto Encyclopedia of Genes and Genomes(KEGG),and carbohydrate-active enzymes(CAZymes)were explored in metagenomic analysis.DNA extraction from gametophytes of P.haitanensis was performed first,followed by library construction,sequencing,preprocessing of sequencing data,taxonomy assignment,gene prediction,and functional annotation.The results show that the predominant microorganisms of P.haitanensis were bacteria(98.98%),and the phylum with the highest abundance was Proteobacteria(54.64%),followed by Bacteroidetes(37.92%).Erythrobacter(3.98%)and Hyunsoonleella jejuensis(1.56%)were the genera and species with the highest abundance of bacteria,respectively.The COG annotation demonstrated that genes associated with microbial metabolism was the predominant category.The results of metabolic pathway annotation show that the ABC transport system and two-component system were the main pathways in the microbial community.Plant growth hormone biosynthesis pathway and multi-vitamin biosynthesis functional units(modules)were the other important pathways.The CAZyme annotation revealed that the starch might be an important carbon source for microorganisms.Glycosyl transferase family 2(GT2)and glycosyl transferase family 3(GT3)were the highly abundant families in glucoside transferase superfamily.Six metagenome-assembled genomes containing enzymes involved in the biosynthesis of cobalamin(vitamin B 12)and indole-3-acetic acid were obtained by binning method.They were confirmed to belong to Rhodobacterales and Rhizobiales,respectively.Our findings provide comprehensive insights into the microorganism community of Pyropia.
基金Fundaçao para a Ciencia e Tecnologia(FCT,Lisbon,Portugal)through grant PTDC/CAL-ZOO/30238/2017 associated post-doc contract to MMC,CIISA(Project UIDB/00276/2020)a PhD fellowship to DFC(SFRH/BD/126198/2016).
文摘Green macroalgae,e.g.,Ulva lactuca,are valuable bioactive sources of nutrients;but algae recalcitrant cell walls,composed of a complex cross-linked matrix of polysaccharides,can compromise their utilization as feedstuffs for monogastric animals.This study aimed to evaluate the ability of pre-selected Carbohydrate-Active enZymes(CAZymes)and sulfatases to degrade U.lactuca cell walls and release nutritive compounds.A databank of 199 recombinant CAZymes and sulfatases was tested in vitro for their action towards U.lactuca cell wall polysaccharides.The enzymes were incubated with the macroalga,either alone or in combination,to release reducing sugars and decrease fluorescence intensity of Calcofluor White stained cell walls.The individual action of a polysaccharide lyase family 25(PL25),an ulvan lyase,was shown to be the most efficient in cell wall disruption.The ulvan lyase treatment,in triplicate measures,promoted the release of 4.54 g/L(P<0.001)reducing sugars,a mono-and oligosaccharides release of 11.4 and 11.2 mmol/100 g of dried alga(P<0.01),respectively,and a decrease of 41.7%(P<0.001)in cell wall fluorescence,in comparison to control.The ability of ulvan lyase treatment to promote the release of nutritional compounds from alga biomass was also evaluated.A release of some monounsaturated fatty acids was observed,particularly the health beneficial 18:1c9(P<0.001).However,no significant release of total fatty acids(P>0.05),proteins(P?0.861)or pigments(P>0.05)was found.These results highlight the capacity of a single recombinant ulvan lyase(PL25 family)to incompletely disrupt U.lactuca cell walls.This enzyme could enhance the bioaccessibility of U.lactuca bioactive products with promising utilization in the feed industry.
