Comparative transcriptomics reveals key differences in the response to milk oligosaccharides of infant gut-associated bifidobacteria.
Breast milk enhances the predominance of Bifidobacterium species in the infant gut, probably due to its large concentration of human milk oligosaccharides (HMO). Here we screened infant-gut isolates of Bifidobacterium longum subsp. infantis and Bifidobacterium bifidum using individual HMO, and compared the global transcriptomes of representative isolates on major HMO by RNA-seq. While B. infantis displayed homogeneous HMO-utilization patterns, B. bifidum were more diverse and some strains did not use fucosyllactose (FL) or sialyllactose (SL). Transcriptomes of B. bifidum SC555 and B. infantis ATCC 15697 showed that utilization of pooled HMO is similar to neutral HMO, while transcriptomes for growth on FL were more similar to lactose than HMO in B. bifidum. Genes linked to HMO-utilization were upregulated by neutral HMO and SL, but not by FL in both species. In contrast, FL induced the expression of alternative gene clusters in B. infantis. Results also suggest that B. bifidum SC555 does not utilize fucose or sialic acid from HMO. Surprisingly, expression of orthologous genes differed between both bifidobacteria even when grown on identical substrates. This study highlights two major strategies found in Bifidobacterium species to process HMO, and presents detailed information on the close relationship between HMO and infant-gut bifidobacteria.
Department of Viticulture &Enology, One Shields Ave. Davis, CA 95616, United States.|Foods for Health Institute, One Shields Ave. Davis, CA 95616, United States.|Department of Chemical and Bioprocess Engineering, School of Engineering, Av. Vicuña Mackenna 4860, Santiago, Chile.|Programa ASIS, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna 4860, Santiago, Chile.
Daniel
D
Garrido
Department of Viticulture &Enology, One Shields Ave. Davis, CA 95616, United States.|Foods for Health Institute, One Shields Ave. Davis, CA 95616, United States.
Santiago
S
Ruiz-Moyano
Foods for Health Institute, One Shields Ave. Davis, CA 95616, United States.|Genome Center, University of California, One Shields Ave. Davis, CA 95616, United States.
Danielle G
DG
Lemay
Department of Viticulture &Enology, One Shields Ave. Davis, CA 95616, United States.|Foods for Health Institute, One Shields Ave. Davis, CA 95616, United States.|Department of Food Science, University of Massachusetts, Amherst, MA 01003.
David A
DA
Sela
Food Science &Technology, One Shields Ave. Davis, CA 95616, United States.|Foods for Health Institute, One Shields Ave. Davis, CA 95616, United States.
J Bruce
JB
German
Department of Viticulture &Enology, One Shields Ave. Davis, CA 95616, United States.|Food Science &Technology, One Shields Ave. Davis, CA 95616, United States.|Foods for Health Institute, One Shields Ave. Davis, CA 95616, United States.
David A
DA
Mills
D000818:Animals; D001644:Bifidobacterium / Q000378:metabolism*; D000069196:Gastrointestinal Microbiome / Q000502:physiology; D006801:Humans; D007413:Intestinal Mucosa / Q000378:metabolism*; D007422:Intestines / Q000382:microbiology*; D008895:Milk, Human / Q000737:chemistry* / Q000382:microbiology; D009844:Oligosaccharides / Q000378:metabolism*; D014157:Transcription Factors / Q000378:metabolism*; D059467:Transcriptome / Q000502:physiology
D009844:Oligosaccharides; D014157:Transcription Factors