Background:The success of different species of ruminants in the colonization of a diverse range of environments is due to their ability to digest and absorb nutrients from cellulose,a complex polysaccharide found in l...Background:The success of different species of ruminants in the colonization of a diverse range of environments is due to their ability to digest and absorb nutrients from cellulose,a complex polysaccharide found in leaves and grass.Ruminants rely on a complex and diverse microbial community,or microbiota,in a unique compartment known as the rumen to break down this polysaccharide.Changes in microbial populations of the rumen can affect the host’s development,health,and productivity.However,accessing the rumen is stressful for the animal.Therefore,the development and use of alternative sampling methods are needed if this technique is to be routinely used in cattle breeding.To this end,we tested if the fecal microbiome could be used as a proxy for the rumen microbiome due to its accessibility.We investigated the taxonomic composition,diversity and inter-relations of two different GIT compartments,rumen and feces,of 26 Nelore(Bos indicus)bulls,using Next Generation Sequencing(NGS)metabarcoding of bacteria,archaea and ciliate protozoa.Results:We identified 4265 Amplicon Sequence Variants(ASVs)from bacteria,571 from archaea,and 107 from protozoa,of which 143(96 bacteria and 47 archaea)were found common between both microbiomes.The most prominent bacterial phyla identified were Bacteroidetes(41.48%)and Firmicutes(56.86%)in the ruminal and fecal microbiomes,respectively,with Prevotella and Ruminococcaceae UCG-005 the most relatively abundant genera identified in each microbiome.The most abundant archaeal phylum identified was Euryarchaeota,of which Methanobrevibacter gottschalkii,a methanogen,was the prevalent archaeal species identified in both microbiomes.Protozoa were found exclusively identified in the rumen with Bozasella/Triplumaria being the most frequent genus identified.Co-occurrence among ruminal and fecal ASVs reinforces the relationship of microorganisms within a biological niche.Furthermore,the co-occurrence of shared archaeal ASVs between microbiomes indicates a dependency of the predominant fecal methanogen population on the rumen population.Conclusions:Co-occurring microorganisms were identified within the rumen and fecal microbiomes,which revealed a strong association and inter-dependency between bacterial,archaeal and protozoan populations of the same microbiome.The archaeal ASVs identified as co-occurring between GIT compartments corresponded to the methanogenic genera Methanobrevibacter and Methanosphaera and represented 26.34%of the overall archaeal sequencesdiversity in the rumen and 42.73%in feces.Considering that these archaeal ASVs corresponded to a significant part of the overall diversity of both microbiomes,which is much higher if one includes the interactions of these co-occurring with other rumen archaea ASVs,we suggest that fecal methanogens could be used as a proxy of ruminal methanogens.展开更多
Erhualian and Landrace breeds are typical genetically obese and lean pigs, respectively. To compare the fecal methanogenic Archaeal community between these two pig breeds, fecal samples from different growth phase pig...Erhualian and Landrace breeds are typical genetically obese and lean pigs, respectively. To compare the fecal methanogenic Archaeal community between these two pig breeds, fecal samples from different growth phase pigs were collected and used for PCR-denaturing gradient gel electrophoresis （DGGE） with two primer pairs （344fGC/519r and 519f/915rGC） and real-time PCR analysis. Results showed that a better separation and higher quality of bands pattern were obtained in DGGE proifles using primers 344fGC/519r as compared with primers 519f/915rGC. Sequencing of DGGE bands showed that the predominant methanogens in the feces of Erhualian and Landrace pigs belonged to Methanobrevibacter spp. and Methanosphaera spp. Real-time PCR analysis revealed that there was no signiifcant difference in the numbers of fecal total methanogens between Erhualian and Landrace pigs;however, pig growth phase affected the numbers of 16S rRNA genes of total methanogens and Methanobrevibacter smithii. Dissociation curves of methyl coenzyme-M reductase subunit A （mcrA） gene fragments ampliifed with real-time PCR showed all samples possessed a single peak at 82＆#176;C, which might be associated with M. smithii. Samples from the same growth phase of each breed showed good replicative dissociation curves. The results suggest that the growth phase （including diet factor） other than genotype of pig may affect the fecal methanogenic Archaeal community of pigs.展开更多
Archaea are an understudied component of the human microbiome.In this study,the gut archaeome and bacteriome of 60 healthy adults from different region were analyzed by whole-genome shotgun sequencing.Archaea were ubi...Archaea are an understudied component of the human microbiome.In this study,the gut archaeome and bacteriome of 60 healthy adults from different region were analyzed by whole-genome shotgun sequencing.Archaea were ubiquitously found in a wide range of abundances,reaching up to 7.2%.The dominant archaeal phylum was Methanobacteriota,specifically the family Methanobacteriaceae,encompassing more than 50%of Archaea in 50 samples.The previously underestimated Thermoplasmatota,mostly composed of Methanomassiliicoccaceae,dominated in 10 subjects(>50%)and was present in all others except one.Halobacteriota,the sole other archaeal phylum,occurred in negligible concentration,except for two samples(4.6-4.8%).This finding confirmed that the human gut archaeome is primarily composed of methanogenic organisms and among the known methanogenic pathway:i)hydrogenotrophic reduction of CO_(2) is the predominant,being the genus Methanobrevibacter and the species Methanobrevibacter smithii the most abundant in the majority of the samples;ii)the second pathway,that involved Methanomassiliicoccales,was the hydrogenotrophic reduction of methyl-compounds;iii)dismutation of acetate or methyl-compounds seemed to be absent.Co-occurrence analysis allowed to unravel correlations between Archaea and Bacteria that shapes the overall structure of the microbial community,allowing to depict a clearer picture of the human gut archaeome.展开更多
基金This study was conducted with funding from EMBRAPA,São Paulo Research Foundation scholarship to BGNA(grant number:2017/12642–8)the National Council for Scientific and Technological Development(CNPq,grant number:428153/2018)and fellowships to LCAR and LLC.
文摘Background:The success of different species of ruminants in the colonization of a diverse range of environments is due to their ability to digest and absorb nutrients from cellulose,a complex polysaccharide found in leaves and grass.Ruminants rely on a complex and diverse microbial community,or microbiota,in a unique compartment known as the rumen to break down this polysaccharide.Changes in microbial populations of the rumen can affect the host’s development,health,and productivity.However,accessing the rumen is stressful for the animal.Therefore,the development and use of alternative sampling methods are needed if this technique is to be routinely used in cattle breeding.To this end,we tested if the fecal microbiome could be used as a proxy for the rumen microbiome due to its accessibility.We investigated the taxonomic composition,diversity and inter-relations of two different GIT compartments,rumen and feces,of 26 Nelore(Bos indicus)bulls,using Next Generation Sequencing(NGS)metabarcoding of bacteria,archaea and ciliate protozoa.Results:We identified 4265 Amplicon Sequence Variants(ASVs)from bacteria,571 from archaea,and 107 from protozoa,of which 143(96 bacteria and 47 archaea)were found common between both microbiomes.The most prominent bacterial phyla identified were Bacteroidetes(41.48%)and Firmicutes(56.86%)in the ruminal and fecal microbiomes,respectively,with Prevotella and Ruminococcaceae UCG-005 the most relatively abundant genera identified in each microbiome.The most abundant archaeal phylum identified was Euryarchaeota,of which Methanobrevibacter gottschalkii,a methanogen,was the prevalent archaeal species identified in both microbiomes.Protozoa were found exclusively identified in the rumen with Bozasella/Triplumaria being the most frequent genus identified.Co-occurrence among ruminal and fecal ASVs reinforces the relationship of microorganisms within a biological niche.Furthermore,the co-occurrence of shared archaeal ASVs between microbiomes indicates a dependency of the predominant fecal methanogen population on the rumen population.Conclusions:Co-occurring microorganisms were identified within the rumen and fecal microbiomes,which revealed a strong association and inter-dependency between bacterial,archaeal and protozoan populations of the same microbiome.The archaeal ASVs identified as co-occurring between GIT compartments corresponded to the methanogenic genera Methanobrevibacter and Methanosphaera and represented 26.34%of the overall archaeal sequencesdiversity in the rumen and 42.73%in feces.Considering that these archaeal ASVs corresponded to a significant part of the overall diversity of both microbiomes,which is much higher if one includes the interactions of these co-occurring with other rumen archaea ASVs,we suggest that fecal methanogens could be used as a proxy of ruminal methanogens.
基金funding from the National Basic Research Program of China (2012CB124705,2013CB127603)the European Community’s Seventh Framework Programme (FP7/2007-2013) under the grant agreement n° 227549+1 种基金the Royal Dutch Academy of Sciences (KNAW) through Project 09CDP006the Fundamental Research Funds for the Central Universities,China (KYZ201153)
文摘Erhualian and Landrace breeds are typical genetically obese and lean pigs, respectively. To compare the fecal methanogenic Archaeal community between these two pig breeds, fecal samples from different growth phase pigs were collected and used for PCR-denaturing gradient gel electrophoresis （DGGE） with two primer pairs （344fGC/519r and 519f/915rGC） and real-time PCR analysis. Results showed that a better separation and higher quality of bands pattern were obtained in DGGE proifles using primers 344fGC/519r as compared with primers 519f/915rGC. Sequencing of DGGE bands showed that the predominant methanogens in the feces of Erhualian and Landrace pigs belonged to Methanobrevibacter spp. and Methanosphaera spp. Real-time PCR analysis revealed that there was no signiifcant difference in the numbers of fecal total methanogens between Erhualian and Landrace pigs;however, pig growth phase affected the numbers of 16S rRNA genes of total methanogens and Methanobrevibacter smithii. Dissociation curves of methyl coenzyme-M reductase subunit A （mcrA） gene fragments ampliifed with real-time PCR showed all samples possessed a single peak at 82＆#176;C, which might be associated with M. smithii. Samples from the same growth phase of each breed showed good replicative dissociation curves. The results suggest that the growth phase （including diet factor） other than genotype of pig may affect the fecal methanogenic Archaeal community of pigs.
基金partially funded by PIANO NAZIONALE DI RIPRESA E RESILIENZA(PNRR)-MISSIONE 4 COMPONENTE 2,“Dalla ricerca all’impresa”INVESTIMENTO 1.3,Creazione di“Partenariati estesi alle universita,ai centri di ricerca,alle aziende per il finanziamento di progetti di ricerca di base”,finanziato dall’Unione europea-NextGenerationEU”-Progetto identificato con codice PE00000019,Titolo“HEAL ITALIA”-Spoke 5-CUP E93C22001860006 Avviso MUR DD.341 del 15.03.2022.
文摘Archaea are an understudied component of the human microbiome.In this study,the gut archaeome and bacteriome of 60 healthy adults from different region were analyzed by whole-genome shotgun sequencing.Archaea were ubiquitously found in a wide range of abundances,reaching up to 7.2%.The dominant archaeal phylum was Methanobacteriota,specifically the family Methanobacteriaceae,encompassing more than 50%of Archaea in 50 samples.The previously underestimated Thermoplasmatota,mostly composed of Methanomassiliicoccaceae,dominated in 10 subjects(>50%)and was present in all others except one.Halobacteriota,the sole other archaeal phylum,occurred in negligible concentration,except for two samples(4.6-4.8%).This finding confirmed that the human gut archaeome is primarily composed of methanogenic organisms and among the known methanogenic pathway:i)hydrogenotrophic reduction of CO_(2) is the predominant,being the genus Methanobrevibacter and the species Methanobrevibacter smithii the most abundant in the majority of the samples;ii)the second pathway,that involved Methanomassiliicoccales,was the hydrogenotrophic reduction of methyl-compounds;iii)dismutation of acetate or methyl-compounds seemed to be absent.Co-occurrence analysis allowed to unravel correlations between Archaea and Bacteria that shapes the overall structure of the microbial community,allowing to depict a clearer picture of the human gut archaeome.
