title: Diet influences the ecology of lactic acid bacteria and Escherichia coli along the digestive tract of cattle: neural networks and 16S rDNA.
abstract: In this manuscript, the authors have sought to gain a better understanding of the interactions between Escherichia coli and lactic acid bacteria (LAB) isolated from Rogossa MRS agar along the digestive tract of grain- and forage-fed cattle. E. coli from cattle receiving a high-grain diet were more numerous (P<0.05) than from the high-forage diet and the highest numbers were in the faeces. Isolates on Rogossa MRS agar were always greater in the high-grain diet (P<0.05) and contained a significant number of LAB. A random set of Rogossa MRS agar colonies was selected and artificial neural networks were used to develop a relationship between colony description and species which was validated using sequence analysis (16S rDNA). The neural networks correctly predicted species in more than 80 % of cases and was composed, primarily, of Lactobacillus vitulinus, Lactobacillus ruminis, Selenomonas ruminantium, Streptococcus bovis, Acidaminococcus fermentans and Megasphaera elsdenii. In conjunction with statistical diversity indices, it was demonstrated that diversity in the high-fibre diet was always lower and was a consequence of the dominance of Str. bovis. In contrast, the diversity in the high-grain diet was greater (P<0.05) and was a consequence of the decline in Str. bovis. These data demonstrate that there is a positive relationship between coliform and LAB isolates throughout the digestive tract of cattle, and diet is the major factor regulating bacterial composition.
authors.affiliation: CSIRO Livestock Industries, Long Pocket Laboratories, 120 Meiers Rd, Indooroopilly, QLD 4068, Australia. denis.krause@csiro.au
authors.forename: Denis O
authors.initials: DO
authors.lastname: Krause
authors.forename: Wendy J M
authors.initials: WJ
authors.lastname: Smith
authors.forename: Laurance L
authors.initials: LL
authors.lastname: Conlan
authors.forename: Joanne M
authors.initials: JM
authors.lastname: Gough
authors.forename: M Anna
authors.initials: MA
authors.lastname: Williamson
authors.forename: Christopher S
authors.initials: CS
authors.lastname: McSweeney
mesh_terms: D000821:Animal Feed; D000818:Animals; D001419:Bacteria / Q000145:classification / Q000235:genetics / Q000254:growth & development* / Q000302:isolation & purification; D002417:Cattle; D015169:Colony Count, Microbial; D003470:Culture Media; D004275:DNA, Ribosomal / Q000032:analysis; D004064:Digestive System / Q000382:microbiology*; D017753:Ecosystem; D004926:Escherichia coli / Q000145:classification / Q000235:genetics / Q000254:growth & development* / Q000302:isolation & purification; D019344:Lactic Acid / Q000378:metabolism*; D007778:Lactobacillus / Q000145:classification / Q000235:genetics / Q000254:growth & development / Q000302:isolation & purification; D016571:Neural Networks, Computer; D006109:Poaceae; D012150:Polymorphism, Restriction Fragment Length; D012336:RNA, Ribosomal, 16S / Q000235:genetics
chemical_list: D003470:Culture Media; D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S; D019344:Lactic Acid