Lecture 26: Gut microbiome

“The wrong mic of gut bacteria, not just starvation, could contribute to severe malnutrition” In Malawi, 10s of thousands of children have this, with 15% being fatal

~3000 bacterial species in gut. Also contains yeast fungi (“mycobiome”) and viruses (“virome”). The “bacteriome” makes up >99% of the microbiome what is the bacteriology of different regions of the human gastrointestinal tract: • Small intestine: 10^4-6g • Stomach: 10^3g • Large intestine: 10^12g

• Bacteriome • Mycobiome (fungi) • Virome

1. Commensal fungi coexisting with other 'bugs' 2. Can be positive or negative 3. Low diversity compared to bacteriome 4. Dominated by yeast, making up 8 of the top 15 most abundant genera a. Saccharomyces b. Malassezia c. Candida

1. Human faeces contain at least 10^9 virus- like particle per gram 2. Highly individualised 3. Vast majority of viral particles unidentified 4. Viruses important to them carrying antibiotic resistance genes as well as virulence genes 5. Can modulate the microbiome composition

• Firmicutes. E.g; a. Lactobacillus b. Clostridium c. Staphylococcus etc • Bacteroidetes. E.g; a. Bacteroides b. Prevotella • Proteobacteria. E.g; a. Escherichia b. Pseudomonas • Actinobacteria. E.g; a. Bifidobacterium 90% of gut = Firmicutes and Bacteroidetes

Different animals have unique microbiomes. These include: • Persissodactyla: a. Elephant b. Rhino c. Horse d. Zebra • Primates: a. Monkeys b. Chimpanzees • Carnivora: a. Lions b. Hyena • Artiodactyla: a. Sheep b. Cow c. Giraffe

1. Vaginally delivered infants - microbiota is dominated by mothers vaginal and faecal bacteria 2. C-section infants - microbiota dominated by skin and bacteria from hospital environment (LESS MICROBIOTA DIVERSITY THAN VAGINAL) 3. Microbiota changes with weaning

• Genetics • Ageing • Diet • Stress • Infection • Antibiotics

Beneficial: • Stim of host immune system • aids digestion • Prod short chain FAs and vitamins • Inhibition of pathogenic bacteria • Transformation of bioactive compounds • Provide fixed nitrogen Harmful: • Prod of carcinogens • Role in obesity and diabetes • Involvement in inflammatory diseases

• Microbiome provides health benefits • We provide a home: a. free food b. free water c. constant temperature

• Pathogen exclusion • Brain development • biotransformation of dietary components • asthma • cancer • liver function • obesity • diabetes • mucosal immunity • inflammatory bowel disease

• Microbial community. From: a. GI tract b. Seawater c. biofilm d. soil • DNA isolation • Sequence all bacterial DNA (“metagenomic” shotgun sequencing) OR PCR variable region of genome - 16S rRNA (“metataxonomic”) • Next gen sequencing • Bioinformatics

• > 50% of humans share 75 species • > 90% of humans share 57 species “GREATER SIMILARITY BETWEEN INDIVIDUALS ON A FUNCTIONAL LEVEL”

• Form of inflammatory bowel disease (IBD) • Specifically in large intestine • 1/1000 un UK and western world affected Different factors include: a. Genetics b. Environmental c. Gut bacteria

• 64% of Americans overweight or obese • Factors affecting obesity: a. high calorie intake b. genetic predisposition c. Microbial metabolism

“Obese mice have 50% less Bacteroidetes (major phyla in gut microbiome) than lean mice, the reverse is true for Firmicutes” CAUSE OR EFFECT??? Another study transplanted the gut microbiome from an obese mice into a normal mice. This lead to a greater percentage increase in total body fat compared to donation of microbiota from lean donors.

• new species found in human stool: “D. diazotrophicus sp. nov” • Ability to fix nitrogen (N2 to NH3 via nifHDK) may be an advantage in survival in complex gut microbiome if nitrogen becomes limited particularly in people with low protein diet

1. A superbug-major cause of hospital acquired infections 2. Spores can persist in the hospital environment: hands, floor, clothing, bedding 3. Produce toxins 4. Possible food borne pathogen 5. 20,000 cases of CDI ("Closridium difficile infection") in UK

• Mild = severe diarrhoea, abdominal pain, fever • Severe = bowel inflammation (1500 deaths in UK) • Elderly patients who have taken broad spectrum antibiotics and immuno- compromised patients are at most risk (>80% of CDI reported in people >65 YO) • Clear association between disruption of normal gut biota by antibiotic

• Currently treatable via: a. Metronidazole b. oral vancomycin • Relapse occurs 20-30% • Potential risk of antibiotic resistance

• Treatment for CDI • Procedure: a. patient stops taking antibiotics b. patient given enema to empty the bowels c. Nasjejunal (NJ) tube is inserted through by gastroenterologist d. Fresh faecal slurry is prepared e. Transported to hospital and delivered to patient via NJ tube f. Takes 20 minutes • 92% success rate in norwich

+ Cheap + high success rate + Easy to administer + Very few side effects • Risk transferring unknown pathogens • Public acceptance • Long-term impact of foreign microbiome unknown

• Frozen donor faecal matter • Freeze dried donor faecal capsules • Defined mix of gut bacteria instead of whole faecal microbiome