Honor thy symbionts

Xu, Jian; Gordon, Jeffrey I.

doi:10.1073/pnas.1734063100

Cited by 761 publications

(416 citation statements)

References 99 publications

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“…However, in terms of cell numbers, we are about 10% human and 90% bacterial (308)! Further, the number of genes in our microbiome may exceed the number of human genes by two orders of magnitude (264,308), making us genetically 1% human and 99% bacterial! Consequently, bacteria play a major role in bodily functions, including immunity, digestion, and protection against disease (208).…”

Section: Introductionmentioning

confidence: 99%

“…Bacteroides may be passed from mother to child during vaginal birth and thus become part of the human flora in the earliest stages of life (208). The bacteria maintain a complex and generally beneficial relationship with the host when retained in the gut, and their role as commensals has been extensively reviewed (308). A quote in a recent publication captured this attribute: ".…”

Section: Introductionmentioning

confidence: 99%

“…First, there is an unusually low gene content for their genome size, which reflects a large number of proteins containing Ͼ1,000 amino acids (308); many of these predicted proteins were assigned putative functions based on homology with known bacterial proteins (ϳ60% in B. thetaiotaomicron). Second, in both B. fragilis and B. thetaiotaomicron, extensive DNA inversions may control expression of a large number of genes.…”

Section: Introductionmentioning

confidence: 99%

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Bacteroides: the Good, the Bad, and the Nitty-Gritty

2007

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SUMMARY Summary: Bacteroides species are significant clinical pathogens and are found in most anaerobic infections, with an associated mortality of more than 19%. The bacteria maintain a complex and generally beneficial relationship with the host when retained in the gut, but when they escape this environment they can cause significant pathology, including bacteremia and abscess formation in multiple body sites. Genomic and proteomic analyses have vastly added to our understanding of the manner in which Bacteroides species adapt to, and thrive in, the human gut. A few examples are (i) complex systems to sense and adapt to nutrient availability, (ii) multiple pump systems to expel toxic substances, and (iii) the ability to influence the host immune system so that it controls other (competing) pathogens. B. fragilis, which accounts for only 0.5% of the human colonic flora, is the most commonly isolated anaerobic pathogen due, in part, to its potent virulence factors. Species of the genus Bacteroides have the most antibiotic resistance mechanisms and the highest resistance rates of all anaerobic pathogens. Clinically, Bacteroides species have exhibited increasing resistance to many antibiotics, including cefoxitin, clindamycin, metronidazole, carbapenems, and fluoroquinolones (e.g., gatifloxacin, levofloxacin, and moxifloxacin).

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Bacteroides: the Good, the Bad, and the Nitty-Gritty

2007

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“…This view has led some scientists to declare that we should not think anymore of ourselves (and of other organisms) as individuals (Gilbert, Sapp, & Tauber 2013) but as communities or ecosystems (Xu & Gordon 2003;Bäckhed & al 2005;Gordon & Klaenhammer, 2011;Williams 2013). While individuation remains a conceptual tool for making sense of the world since it helps us describes the ways in which we identify an entity or ecosystem as being different from other things, the ecosystem view concerning our biological constitution denies the deeper ontological view about ourselves, as being individual (single & indivisible).…”

Section: Autonomy 20mentioning

confidence: 99%

The Porosity of Autonomy: Social and Biological Constitution of the Patient in Biomedicine

Beever

Morar²

2016

The American Journal of Bioethics

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The nature and role of the patient in biomedicine are issues central to bioethical inquiry. Given its developmental history grounded firmly in a backlash against 20 th century cases of egregious human subjects abuse, contemporary medical bioethics has come to rely on a fundamental assumption: the unit of care (and the unit of value) is the autonomous self-directing patient. In this paper we examine first the structure of the feminist social critique of autonomy. Then, we show that a parallel argument can be made against relational autonomy as well, demonstrating how this second concept of autonomy fails to take sufficiently into account an array of biological determinants, particularly those from microbial biology. Finally, in light of this biological critique, we question whether or to what extent any relevant and meaningful view of autonomy can be recovered in the contemporary landscape of bioethics.

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“…Most importantly, the binding can be examined with living bacteria. As in the study of DNA-protein interactions, CL EMSA is expected to be widely used for heparin-bacteria interaction studies complementing existing methods specially for the study of heparin binding of the commensal microorganisms as their huge diversity (500-1000 species in human gut) [19] requires a fast method. …”

mentioning

confidence: 99%

Characterization of heparin–living bacteria interactions by chemiluminescence electrophoretic mobility shift assay

Kang

Lee

Gorenstein

2007

Analytical Biochemistry

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Keywordschemiluminescence; nonradioisotopic detection; EMSA; heparin-bacteria interactions; heparin; bacteriaThe electrophoretic mobility shift assay [EMSA]1 is one of the most sensitive methods for studying DNA-protein interactions. Chemiluminescence [CL]1 has been used as an alternative to radioisotopic detection of samples in the EMSA [1,2], as it has advantages such as safety and stability (no isotopic decay) of the sample. In this study, we examined the feasibility of the application of CL EMSA to studying heparin-living bacteria interactions. As an example, binding of biotinylated heparin to Escherichia coli was examined.The pathogenesis of most infections is initiated by microbial adhesion to host tissue. This adhesion is, therefore, a promising target for the development of new antimicrobial therapeutics [3]. In the adhesion, heparin or heparin-related oligosaccharides are one of the extracellular matrix molecules of the host recognized by cell surface proteins of bacteria [4][5][6][7][8].Due to the lack of appropriate techniques for the study of the interactions of heparin-living bacteria, most heparin-bacteria binding studies have been conducted with isolated bacterial proteins [9,10]. Although useful information can be obtained from such studies, one potential drawback is the exclusion of membrane phenomena such as ligand-induced receptor oligomerization that can affect the overall binding affinity [11]. Therefore, it is desirable to examine the adhesion process using bacteria in the intact state to include the membrane phenomena. With this purpose, scintillation counting of radioisotope radiation [12] and sodium dodecyl sulfate-polyacrylamide gel electrophoresis [8] were used to assess the binding of heparin to living bacteria. More recently, atomic force microscopy was successfully used to investigate heparin-living bacteria interactions and producing quantitative data [13]. However, these methods are qualitative [8], require radioisotope labeling [12], an instrument, which may not be readily available in common laboratories [13].EMSA has been widely employed to detect DNA-protein interactions since its first application [14]. In this study, CL EMSA is introduced to complement the existing methods to study heparin-bacteria interactions. CL has advantages such as safety and sample stability (no

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Honor thy symbionts

Cited by 761 publications

References 99 publications

Bacteroides: the Good, the Bad, and the Nitty-Gritty

Bacteroides: the Good, the Bad, and the Nitty-Gritty

The Porosity of Autonomy: Social and Biological Constitution of the Patient in Biomedicine

Characterization of heparin–living bacteria interactions by chemiluminescence electrophoretic mobility shift assay

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