复旦大学：《人体的社交网络——共生微生物》课程教学资源（课件讲义）共栖微生物——人体微生物组学研究方法（谢幼华）

2016.7.8 暑期裸程:共粞徼生物 微生物组的研究方法 谢幼华 病原生物系 54237973 hxie@fudan edu cn

微生物组的研究方法 暑期课程：共栖微生物 2016.7.8 谢幼华 病原生物系 54237973 yhxie@fudan.edu.cn

Human as A Super-organism o Microorganisms are all over the earth Less than 1% of all microorganisms present in diverse natural habitats have been cultured o ahuman is a super-organism comprising the human body and its dwelling microbiota(normal flora Skin, Nose, Oral cavity Throat, Gut(Colon), Vagina, Uretha Super organism

 Microorganisms are all over the Earth  Less than 1% of all microorganisms present in diverse natural habitats have been cultured  A human is a super-organism comprising the human body and its dwelling microbiota (normal flora)  Skin, Nose, Oral cavity, Throat, Gut (Colon), Vagina, Uretha Super￾organism Human as A Super-organism

Human Gut microbiota Micro biome o the human gut microbiota is a complex ecosystem composed of approximately 1014 bacteria and archaea, as well as fungI and viruses >10 times larger than the human cell complement o The human gut microbiome is the collective genome capacity( genes) of the gut microbiota 150 times larger than the human gene complement with an estimated 3. 3 million microbial genes

Human Gut Microbiota & Microbiome  The human gut microbiota is  a complex ecosystem composed of approximately 1014 bacteria and archaea, as well as fungi and viruses  10 times larger than the human cell complement  The human gut microbiome is  the collective genome capacity (genes) of the gut microbiota  150 times larger than the human gene complement, with an estimated 3.3 million microbial genes

The General Composition of the human gut Microbiota o Bacteria constitute the bulk of the gut microbiota o Archaea account for approximately 1% of the microbes in the human intestine o Viral and fungal abundance vary greatly Viral sequences account for between 1x10-5% and 2% of total dna in stool Fungal DNA, typically less than 1%, can be as high as 10%

The General Composition of the Human Gut Microbiota  Bacteria constitute the bulk of the gut microbiota  Archaea account for approximately 1% of the microbes in the human intestine  Viral and fungal abundance vary greatly  Viral sequences account for between 1x10–5% and 2% of total DNA in stool  Fungal DNA, typically less than 1%, can be as high as 10%

The Main Bacterial Phyla of the Human Gut Microbiota o Seven phyla constitute the bulk of the human gut bacteria Firmicutes 硬壁菌门 Bacteroidetes 拟杆菌门 Proteobacteria 变形菌门 Fusobacteria 梭杆菌门 Verrucomicrobia 疣微菌门 Cyanobacteria 蓝藻细菌门 Actinobacteria 放线菌门 o The firmicutes and bacteroidetes accommodate the most abundant species and constitute over 90% of the human gut microbiota

The Main Bacterial Phyla of the Human Gut Microbiota  Seven phyla constitute the bulk of the human gut bacteria  Firmicutes 硬壁菌门  Bacteroidetes 拟杆菌门  Proteobacteria 变形菌门  Fusobacteria 梭杆菌门  Verrucomicrobia 疣微菌门  Cyanobacteria 蓝藻细菌门  Actinobacteria 放线菌门  The Firmicutes and Bacteroidetes accommodate the most abundant species and constitute over 90% of the human gut microbiota

Challenges Facing the Human Gut Microbiome Study Who are there? Profiling the gut microbiota(bacteria, archaea, fungi, viruses)into phylum, species or operational taxonomic unit (OTU) ● What are they doing Profiling the genetic capacity of the microbiota genes pathways) How do they contribute to human health? Establish the functional connections between the gut microbiota and the host's physiological or pathological status

Challenges Facing the Human Gut Microbiome Study  Who are there?  Profiling the gut microbiota (bacteria, archaea, fungi, viruses) into phylum, species or operational taxonomic unit (OTU)  What are they doing?  Profiling the genetic capacity of the microbiota (genes, pathways)  How do they contribute to human health?  Establish the functional connections between the gut microbiota and the host’s physiological or pathological status

The road to Metagenomics Beyond Teaset a.3 Carl Woese microbial Robert Koch isolates microorganisms using as marker for 9, solid cultures taxonomy 1676 1931 1980 1998 2005 2006 2008 2011 2015 1888 1977 1990 Winogradsky Kary Mullis Handelsman et al., GA sequence PacBio Rs sequencer develops PCR experiments First NGS machin released metagenomics' oral mic Fred sange uman Microbiome develops DNA Project publication Ocean sampling Day

The Road to Metagenomics & Beyond

Profiling the Human gut Microbiota o Culture: the gold standard for identification of microbial species Qualitative and quantitative information on bacterial species and their genetic capacity Changes in the gut microbiota in relation to perturbation or disease

Profiling the Human Gut Microbiota  Culture: the gold standard for identification of microbial species  <30% of the gut microbiota has been cultured  Culture-independent techniques: offer a more representative ‘snapshot’ of the gut microbiota  Microbial diversity of the gut microbiota  Qualitative and quantitative information on bacterial species and their genetic capacity  Changes in the gut microbiota in relation to perturbation or disease

Gut Metagenome Metatranscriptome ● Metagenome宏基因组(元基因组) and metatranscriptome宏转录组(元转 录组) are derived from meta-analysis"-the process of statistically combining separate analyses genome-an organism's genetic material > transcriptome-the totoal transcription products of a genome o Shotgun metagenome and metatranscriptome sequencing the process of sequencing the entire nucleotide pool isolated from a culture-independent sample ● Metaproteome ● Metabolome

Gut Metagenome & Metatranscriptome  Metagenome 宏基因组(元基因组) and metatranscriptome 宏转录组(元转 录组) are derived from  “meta-analysis” - the process of statistically combining separate analyses  “genome” - an organism’s genetic material  “transcriptome” - the totoal transcription products of a genome  Shotgun metagenome and metatranscriptome sequencing  the process of sequencing the entire nucleotide pool isolated from a culture-independent sample  Metaproteome  Metabolome

Main Forces behind metagenomics O High-throughput sequencing technologies sequencing 1 million nucleotide bases of dna decreased from $10,000 to $o 10 uS dollars between 2001 and 2011 Sequence data of microbe reference strains o Advanced bioinformatical analytic tools and pipelines o High-throughput screening technologies

Main Forces behind Metagenomics  High-throughput sequencing technologies  sequencing 1 million nucleotide bases of DNA decreased from $10,000 to $0.10 US dollars between 2001 and 2011  Sequence data of microbe reference strains  Advanced bioinformatical analytic tools and pipelines  High-throughput screening technologies