= I Contain Multitudes = === Ed Yong, 2016, Bvtn 579.17 YON === ---- Repetitive, some factoids unsourced ---- .p10 30e9 human, 39e9 microbe cells no source . 10T WAG Dwayne Savage :100T WAG by Thomas Luckey in 1979 .p11 100 species can cause infections, McFall-Ngai 2007 Nature 446, thousands in gut .p27 exceptionally large bacteria: ''Epulopscium fishelsoni'' is size of period .p28 draper '''Leeuwenhoek''' "door hinge" single lens microscope 270x, repeated observations, documented everything . 1665 ''Micrographia'', 1680 Fellow of the Royal Society, 1723 died age 90 .p35 Theodor Escherich discovered E. coli .p38 Theodor Rosebury ''Microorganisms Indigenous to Man'' 1962 .p40 Carl Woese studied 16S rRNA, 30 species profiled by 1976, 1977 ''archaea'' .p42 Norman Pace sequenced "whole buckets of microbes' 1984 .p43 1998 Jo Handelsman - ''metagenomics'', the genomics of communities .p44 Jeff Gordon ... mcrobes control storage of fat and the creation of new blood vessels .p45 Amsterdam microbe museum Micropia .p54 Scott Gilbert: co-development, microbes turn on genes in host, i.e. ''Bacteroides thetaiotaomicron'' or ''B-theta'' .p59 biofouling of navy ship hulls by ''Hydroides elegans'', larvae attracted and metamorphosed by ''Pseudoalteromanas luteoviolacea'' .p64 ''Bacteroides fragilis'' polysaccharide A (PSA) restores 'helper T cells', quells inflammation, Sarkis Mazmanian .p68 Paul Patterson 2001 (no ref) viral infection substance (4-ethylphenylsulfate 4EPS), autism and schizophrenia, B-frag helps . [[ http://www.jneurosci.org/content/23/1/297.full-text.pdf | Paul H. Patterson 2003 ]] [[ http://link.springer.com/article/10.1023/A:1015337611258 | Paul H. Patterson 2002 paywall ]] [[ http://www.sciencedirect.com/science/article/pii/S0959438802002994 | Paul H. Patterson 2002 paywall ]] .p73 John Cryan Ted Dinan U.Cork ''Lactobacillus rhamnosus'' JB-1 in yogurt -> timid mice overcome anxiety .p77 1936 ''Wolbachia pipientis'' (Simeon Burt Wolbach) .p79 infects 40% of arthropods, helps and hurts .p80 ''Heliobacter pylori'' causes ulcers and stomach cancers, protective against oesophageal cancer .p80 ''Bacillus thuringeiensis'' Bt punctures insect guts, gut bacteria trigger immune system .p81 Mitochondria in blood dan trigger immune system, systemic inflammatory response syndrome (SIRS) .p84 Acacia sugars feed ants, also enzymes that prevent digestion of other sugars .p86 ''Propionibacterium acnes'' microbe causes acne .p87 Insect bacteriocytes contain/control bacterial symbionts .p88 Mucas molecule mucin, protein backbone with thousands of sugar branches, interlinked layer with bacteriophage viruses .p90 Antimicrobial peptides AMP .p92 Baby 6mo immune systems suppressed to allow microbiome to establish, antibodies in mother's milk (Elahi Nature 2013) .p93 200 human milk oligosaccharides HMO, bagies can't digest, microbes can, cows milk doesn't feed ''Bifidobacterium longum infantis'' . ''B. infantis'' stimulates adhesive that seals gut, and anti-inflammatory molecules, makes sialic acid that stimulates brain growth . HMO 500x cows milk, 5x more species, resemble intestinal glycans that pathogens attach to .p96 UC Davis Milk Research Bruce German, David Mills, Daniela Barile .p99 microbes absorbed into cells as sybmiont, Nasuia is 112,000 codons .p103 Kingman reef healthy, Kiritimati reef dying, overfishing led to algae blooms which create '''dissolved organic carbon''' which feeds coral pathogens. Iron whipwrecks also feed algae .p110 '''dysbiosis''' when harmless or helpful bacteria change state to pathogens .p111 WUSTL Jeff Gordon isolation labs for microbe-free mice .p114 Obese people have more ''Firmicutes'' and fewer ''Bacteriodetes'', ''Akkermansia muciniphilia'' less common in obese mice .p116 Malawi malnourishment, either marasmus (skeletal) or kwashiorkor, bloating from leaking blood vessels. . Treated with peanut paste, sugar, vegetable oil, milk, only temporary effect for kwashiorkor .p119 Inflammatory bowel disease '''IBD''' ulcerative colitis and Crohn's disease . fewer antiinflammatory microbes, more invasive '''E.coli''' and ''Faecalibacterium prausnitzii'' .p122 Dogs and older siblings, less hay fever (''but perhaps higher family income? KHL'') .p123 Vaginal birth provides microbes, Caesarean does not (30% in US) .p124 Sat, fats feed inflammatory microbes (Devkota 2015), additives CMC and P80 suppress anti-inflammatory microbes (Chassaing 2015) .p124 microbes make Short Chain Fatty Acids from dietary fiber [[ http://www.academia.edu/download/45233876/Commensal_microbe-derived_butyrate_induc20160430-16478-1e01elo.pdf | Furusawa Nature 2013 ]] [[ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3807819/pdf/nihms-518169.pdf | Smith Science 2013 ]] .p130 prehistory nursing mothers swap infants and bugs .p131 '''WEIRD:''' '''Western''', '''Educated''', '''Industrialized''', '''Rich''', and '''Democratic'''. .p133 [[ https://phylogenomics.me/|Jonathan Eisen]], UC Davis: [[https://phylogenomics.blogspot.com/p/blog-page.html|Overselling the Microbiome Award]] - also see [[ http://www.theallium.com/ | The Allium ]] .p145 ''Sodalis praecaptivus'' like insced symbionts .p147 ''Streptomyces'' on beewolf antennae protects cocoons from fungus and infection .p156 Dawkins ''Extended Phenotype:'' dams, nests, books .p156 Margulis '''endosymbiosis:''' paper rejected 15 times before 1976 publication. '''holobiont''' 1991 "whole unit of life" .p166 Hemiptera feed exclusively on sap, aphid ''Buchnera'' makes essential amino acids .p172 Colleen Cavanaugh Harvard ''Riftia pachyptila'' rift work, troposomes packed with sulfur from bacterial chemosynthesis .p177 fermenters: '''Hindgut''' elephants horses rabbits '''Foregut''' cow sheep hippos, digest bacteria after those digest .p179 termite protists half of body weight. Macrotermites: wood → fungus → gut bacteria → worker termites → queen (palm sized) .p184 creosote bush → (which bug??) → woodrat [[ http://biologylabs.utah.edu/dearing/lab/pdf/2014_kohl_facilitate_toxins.pdf | Kohl 2014 ]] .p186 mountain pine beetle, fungus make nutrients, microbes disable protective terpines [[ http://static.springer.com/sgw/documents/1419317/application/pdf/art%25253A10.1007%25252Fs10886-013-0318-8.pdf | Diane L. Six, 2013]] .p191 Horizontal gene transfer HGT .p193 Japanese Porphyra seaweed,nori - ocean bacteria ''Zobellia galactanivorans'' transferred porphyranases to gut ''Bacteroides plebeius'' Jan-Hendrick Hehemann .p199 Braconid wasps make(?) symbiotic viruses which paralyze caterpillar immune systems, larvae grow in them, [[http://rstb.royalsocietypublishing.org/content/368/1626/20130051.full.pdf | Herniou 2013 ]] .p200 Mealybug contains ''Tremblaya'' contains ''Moranella'', together make 9 enzymes to make amino acid phenylalanine .p204 Aphids attacked by braconid wasp ''Aphidius ervi'', available by mail order .p213 filariasis (elephantiasis, river blindness) caused by nematodes with ''Wolbachia'' symbionts, doxycycline kills symbiont and nematodes die. A-WOL Anti-Wolbachia Consortium, Gates funded .p216 ''Bactrachochytrium dendrobatis'' Bd attacks amphibians, Reid Harris found protective bacteria on eastern US salamanders, also ''Janthinobacterium lividum'' J-liv on Sierra Nevada Mount Conness frogs. .p222 Activa probiotic bacteria do not colonize gut, Cochrane (!AlFaleh 2014, Goldenberg 2013, Allen 2010) .p228 Kenya Honda 2013, 17 ''Clostridia'' strains reduce gut inflammation, Vedanta !BioSciences probiotic in clinical trials .p229 Fecal microbiota transplant for untreatable ''Clostridium difficle'' C-diff .p231 Dutch Josbert Keller randomized trial, vancomycin 27% cure, FMT 94% cure .p234 Elaine Petroff and Emma Allen-Vercoe, cultured 33 strain FMT called RePOOpulate .p237 gut bacteria make TMAO, slows cholesterol breakdown .p238 Harvard's Pamela Silver 2014 tetracycline sensor in E. coli, engineered bugs could sense and generate specific antibiotics. .p240 MIT's Jim Collins suggests B-theta instead .p242 Australian Scott O'Neill, ''Wolbachia'' in stops dengue in ''Aedes'' mosquitos .p257 Oregon's Jessica Green bioinformed hospital design [[http://www.nature.com/ismej/journal/v6/n8/pdf/ismej2011211a.pdf | Kembel 2012 ]] [[http://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0087093&type=printable | Kembel 2014 ]] [[ https://www.ted.com/talks/jessica_green_good_germs_make_healthy_buildings | TED 2013 talk ]] [[ https://www.ted.com/talks/jessica_green_are_we_filtering_the_wrong_microbes | TED 2011 talk ]] .p260 Chicago's Karen Weigert, antifungal plastics