The document is a poem describing the various microhabitats within the human body that are suitable for commensal microbes to colonize, including pores, arm pits, and scalp. It welcomes microbes to build colonies and supplies them warmth, moisture, and nutrients, on the condition they do not cause issues like acne or athlete's foot. The poem acknowledges microbes as guests in the body on this new year's day.

1. The Commensal Flora For creatures your size I offer a free choice of habitat, so settle yourselves in the zone that suits you best, in the pools of my pores or the tropical forests of arm-pit and crotch, in the deserts of my fore-arms, or the cool woods of my scalp. Build colonies: I will supply adequate warmth and moisture, the sebum and lipids you need, on condition you never do me annoywith your presence, but behave as good guests should, not rioting into acne or athlete's-foot or a boil..” W.H. Auden “A New Year Greeting After an article by Mary J. Marples in Scientific American, January, 1969 On this day tradition allots to taking stock of our lives, my greetings to all of you, Yeasts, Bacteria, Viruses, Aerobics and Anaerobics:A Very Happy New Yearto all for whom my ectoderm is as Middle-Earth to me.

2. Very few microbes are always pathogenic Many microbes are potentially pathogenic Most microbes are never pathogenic Introduction Microbes and human

3. Why care about the normal flora? They may be good

4. great majority of commensal bacteria Rich in microbial biodiversity Most fairly permanent. Composition varies from individual. Difficult to alter composition of the normal flora of gut in a healthy individual.

5. Anaerobes stomach 103-104bacteria/g Streptococcus C O L O N Duodenum 105 -106 bacteria/g Streptococcus Caecum and colon 1010 - 1014 bacteria/g Bacteroides Eubacterium Bifidobacterium Peptostreptococcus Fusobacterium Ruminococcus Clostridium Streptococcus Lactobacillus Enterobacteria gp Jejunum and ileum 107 -108 bacteria/g mainly Streptococcus Lactobacillus Bacteroides and other facultatives Facultative Aerobes Anaerobes Distribution of flora

7. biochemical identification.

8. Laborious and time consuming.

11. Less mutationsConserved regions:universal Variable regions: genus Hyper-variable regions:species

12. Molecular inventory Dot blot hybridization, FISH FACS Sequencing Denaturing gradient gel electrophoresis Temporal temperature gradient gel electrophoresis Competitive PCR Real time PCR Yes/no If yes, how much?? ultimate choice Quantification Diversity

13. COMMENSAL FECAL ANAEROBIC FLORA IN HEALTH AND DISEASE Ramadass Balamurugan

15. Bacteroides-Prevotella-Porphyromonas Gp

16. Bacteroides fragilis

17. Bifidobacterium genera

18. Bifidobacterium longum

19. Lactobacillus acidophilus

20. Escherichia coli

21. Clostridium difficile

22. Clostridium perfringens

23. Enterococcus faecalis

26. Age groups of 2 – 17 yrs

28. gender,

29. mode of delivery,

30. Weaned,

31. socio economic status,

32. source of drinking water,

33. Drug/antibiotic intake and Worm infestations

34. 24 hour recall food frequency.Homogenous group in terms of diet

35. Groups Age Expt n°1 Results Succession study Group 1 2+3years Group 2 4+ 5years Group 3 6+7 years Group 4 8+9 years Group 5 10+11 years Group 6 12+13 years Group 7 14+15 years Group 8 16+17 years parents were farmers/manual labourers and belonged to the lower class/lower middle class of the socio-economic scale. The population was found to be predominantly vegetarian, with meat intake once a week, they primarily consumed carbohydrates and small quantities of dairy products including milk.

36. Expt n°1 Results Succession study

38. Suggestive of succession of bacterial groups with increasing age

39. Perhaps stabilize,during late teens and reach the adult patterns.R. Balamurugan et al, 2008 AJCN.

40. Molecular studies of fecal anaerobic commensal bacteria in acute diarrhea in children. Expt n°2 Introduction Antibiotics 20 villages- CHAD Infection Children with acute diarrhea First assessment health worker ORS dispensed No or mild dehydration Stool collected WHO-ORS 10 villages HAMS-ORS Base team telephoned Investigating team takes over. Alteration of gut flora ongoing ORS acceptability Trail

42. SE status-IV (range III-V)

43. 13 were rota viral +ve

45. Bifidobacterial diversity in children with acute diarrhea and effect of ORS. M D1 wO1 H1 D2 wO2 H2 D3 hO3 H3 D4 hO4 H4 MD5 hO5 H5 D6 wO6 H6 D7 wO7 H7 M Expt n°2a Results D-Diarrheal wO- WHO-ORS hO-HAMS-ORS H_-Healthy Unpublished data

46. Expt n°2b Results Neonates & Rotaviral Diarrhea M R+1R+1R-1R-1 M R+2R+2R-2R-2 M R+3R+3R-3 M H1 H2 C M B.longum subs infantis Subjects: 12 neonates rotaviral +ve & 12 healthy neonates. Sample:fecal samples. samples collected on 1,6,11and 16 were studied. Methods: TTGE, qPCR. Quality of Bifidobacterium never changed. Unpublished data

48. Walls of the living quarters are plastered with dilute cow dung.

49. Sun dried cow dung patties are used as a source of fuel. Methanogens & Butyrivibrios are predominant in rumens.

52. Suggesting that a Commensal bacterium found in the environment can colonize human intestine.R. Balamurugan et al, Micro Ecol Heal & Dis. 2009; 21: 3843

53. Detection of Clostridium difficile in feces of patients with UC. Expt n°4 results R. Balamurugan et al, 2008IJMR.

55. Butyrate - protective against cancer

56. H2S and oxygen free radicals can be toxic.

57. To quantitate E.rectale,F.prausnitzii (BPB), Desulfovibrios (srb), and E. faecalis (produce extracellular superoxide) R. Balamurugan et al, 2008 JGH.

59. increases both Enterobacteria and Bifidobacterial colonic populations.

60. increased thickness of the colonic mucus layer.

61. Links between mucus layer thickness, colonic microbiota and oxidative stress remain to be clarified.R. Balamurugan et al, communicated FEMS M&ECOL , 2010

63. Bacterial alteration

64. Host-Bacterial interactions-inflammation

68. Urine was collected for 5 hours, and the concentration of lactulose and mannitol was measured by an enzymatic method.

74. SIBO Model

75. Quick

76. Easy

77. Reproducible

78. Dietary toxicity

81. Commonly found on intestinal epithelial surface.We chose sucrose….Why sucrose?? Aim: To test the hypotheses that sucrose may rescue toxic effects of PHA- containing crude red kidney beans. sucrose may reduce PHA-induced loss in trans-epithelial resistance (TER) in Caco-2 cell lines.

86. Sucrose rescues Lectin effectDoes this legume lectin enters intestinal epithelium? 3 h 1 h 48 h 24 h

89. P=0.0001 Bacterial density: RRKB>CFD+RRKB>Control>CFD

90. P=0.0002 Bacterial Activity: RRKB>Control> CFD+RRKB>CFD

92. -1.0 Controls Antibiotic Antibiotic+RRKB -1.5 Median relative bacteria load (log) -2.0 -2.5 -3.0 Proximal Mid Distal Colon Region Increased Bacterial density in Antibiotic+RRKB treated group followed by Antibiotic treated group when compared to control group.

96. Post diet Antibiotic + RKB fed Baseline Antibiotic+RKB- overgrowth of bacteria, abnormal to the site

97. -3.5 Controls Antibiotic Antibiotic+RRKB -4.0 Median relative ICAM expression (log) -4.5 -5.0 Proximal Mid Distal Colon Cecum Region ICAM expression in Proximal SI Decreased significantly compared to controls.

100. They bind normally to FXR (farnesoid X Receptor) in order to initiate a cascade of antimicrobial actions.

102. iNOS

104. (FXR knock-out mice)