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

  • Paul H. Patterson 2003 Paul H. Patterson 2002 paywall 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 Furusawa Nature 2013 Smith Science 2013

• p130 prehistory nursing mothers swap infants and bugs

• p131 WEIRD: Western, Educated, Industrialized, Rich, and Democratic.

• p133 Jonathan Eisen, UC Davis: Overselling the Microbiome Award - also see 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 Kohl 2014

• p186 mountain pine beetle, fungus make nutrients, microbes disable protective terpines 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, 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 Kembel 2012 Kembel 2014 TED 2013 talk TED 2011 talk

• p260 Chicago's Karen Weigert, antifungal plastics