Biology subjects

Aalvink, S.

Publications and source records attributed to Aalvink, S..

3 recordsLinked to original sources

bioRxiv2019

Growth rate alterations of human colorectal cancer cells by 157 gut bacteria

Several bacteria in the human gut microbiome have been associated with colorectal cancer (CRC) by high-throughput screens. In some cases, molecular mechanisms have been elucidated that drive tumorigenesis, including bacterial membrane proteins or secreted molecules that interact with the human cancer cells. For most gut bacteria, however, it remains unknown if they enhance or inhibit cancer cell growth. Here, we screened bacteria-free supernatants (secretomes) and inactivated cells of over 150 cultured bacterial strains for their effect on CRC cell growth. We observed family-level and strain-level effects that often differed between bacterial cells and secretomes, suggesting that different molecular mechanisms are at play. Secretomes of Bacteroidaceae, Enterobacteriaceae, and Erysipelotrichaceae bacteria enhanced CRC cell growth, while most Fusobacteriaceae cells and secretomes inhibited growth, contrasting prior findings. In some bacteria, the presence of specific functional genes was associated with CRC cell growth rates, including the virulence genes TcdA in Clostridiales and FadA in Fusobacteriaceae, which both inhibited growth. Bacteroidaceae cells that enhanced growth were enriched for genes of the cobalamin synthesis pathway, while Fusobacteriaceae cells that inhibit growth were enriched for genes of the ethanolamine utilization pathway. Together, our results reveal how different gut bacteria have wide-ranging effects on cancer cells, contribute a better understanding of the effects of the gut microbiome on the human host, and provide a valuable resource for identifying candidate target genes for potential microbiome-based diagnostics and treatment strategies.

microbiology↗

bioRxiv2018

Bacterial Zombies And Ghosts: Production Of Inactivated Gram-Positive And Gram-Negative Species With Preserved Cellular Morphology And Cytoplasmic Content

There are many approaches available to inactivate bacteria, each with a different efficacy, impact on cell integrity, and potential for application in high-throughput. The aim of this study was to compare these approaches and develop a standardized protocol for generation of intact Gram-positive as well as on Gram-negative \"bacterial zombies\", i.e. cells that are metabolically dead with retained cellular integrity. Here, we introduce the term \"bacterial zombies\" in addition to \"bacterial ghosts\" to differentiate inactivated bacteria with preserved cellular integrity from those with perforated membranes, where DNA and cytoplasmic contents have been released. This differentiation of inactivated bacteria is important if the cell content is the subject of study, or if cell contents in the media may cause unwanted effects in downstream applications. We inactivated eight different bacterial species by treatment with beta-propiolactone, ethanol, formalin, sodium hydroxide, and pasteurization. Inactivation efficacy was determined by culturing, and cell wall integrity assessed by quantifying released DNA and visualization by scanning electron microscopy. Based on these results, we discuss the choice of bacterial inactivation methods, and conclude that beta-propiolactone and ethanol are the most promising approaches for standardized generation of bacterial zombies.\n\nIMPORTANCEFor applications such as vaccination or analyses that are sensitive to bacterial growth, inactivated bacteria are preferred because they simplify the analyses and the interpretation of results. This study compared various bacterial inactivation treatments that maintain cell integrity and may be used in high-throughput. Our results demonstrated that beta-propiolactone and 70% ethanol were the best techniques to achieve these goals.

microbiology↗

bioRxiv2018

Cross-feeding between Bifidobacterium infantis and Anaerostipes caccae on lactose and human milk oligosaccharides

The establishment of the gut microbiota immediately after birth is a dynamic process that may impact lifelong health. At this important developmental stage in early life, human milk oligosaccharides (HMOS) serve as specific substrates to promote the growth of gut microbes, particularly the group of Actinobacteria (bifidobacteria). Later in life, this shifts to the colonisation of Firmicutes and Bacteroidetes, which generally dominate the human gut throughout adulthood. The well-orchestrated transition is important for health, as an aberrant microbial composition and/or SCFA production are associated with colicky symptoms and atopic diseases in infants. Here, we study the trophic interactions between an HMOS-degrader, Bifidobacterium longum subsp. infantis and the butyrogenic Anaerostipes caccae using carbohydrate substrates that are relevant in this early life period, i.e. lactose and HMOS. Mono-and co-cultures of these bacterial species were grown at pH 6.5 in anaerobic bioreactors supplemented with lactose or total human milk carbohydrates (containing both lactose and HMOS). A cac was not able to grow on these substrates except when grown in co-culture with B. inf, leading concomitant butyrate production. Cross-feeding was observed, in which A. cac utilised the liberated monosaccharides as well as lactate and acetate produced by B. inf. This microbial cross-feeding is indicative of the key ecological role of bifidobacteria in providing substrates for other important species to colonise the infant gut. The symbiotic relationship between these key species contributes to the gradual production of butyrate early in life that could be important for host-microbial cross-talk and gut maturation.\n\nImportanceThe establishment of a healthy infant gut microbiota is crucial for the immune, metabolic and neurological development of infants. Recent evidence suggests that an aberrant gut microbiota early in life could lead to discomfort and predispose infants to the development of immune related diseases. This paper addresses the ecosystem function of two resident microbes of the infant gut. The significance of this research is the proof of cross-feeding interactions between HMOS-degrading bifidobacteria and a butyrate-producing microorganism. Bifidobacteria in the infant gut that support the growth and butyrogenesis of butyrate-producing bacteria, could orchestrated an important event of maturation for both the gut ecosystem and physiology of infant.

microbiology↗