The Impact of Antibiotics on the Gut Microbiota.docx

1、The Impact of Antibiotics on the Gut MicrobiotaThe Impact of Antibiotics on the Gut Microbiota as Revealed by High Throughput DNA SequencingPublished on March 15, 2012Author:Paul D. CotterSpecialty:Microbiology,Antimicrobials,Gut MicrobiotaInstitution: Teagasc Food Research CentreAddress: Cork, Irel

2、andInstitution: Alimentary Pharmabiotic CentreAddress: Cork, IrelandAuthor:Catherine StantonSpecialty:Microbiology,Probiotics,Prebiotics,Infant HealthInstitution: Teagasc Food Research CentreAddress: Cork, IrelandInstitution: Alimentary Pharmabiotic CentreAddress: Cork, IrelandAuthor:R. Paul RossSpe

3、cialty:Microbiology,Antimicrobials,ProbioticsInstitution: Teagasc Food Research CentreAddress: Cork, IrelandInstitution: Alimentary Pharmabiotic CentreAddress: Cork, IrelandAuthor:Colin HillSpecialty:Microbiology,Antimicrobials,Food PathogensInstitution: Department of Microbiology, University Colleg

4、e CorkAddress: Cork, IrelandInstitution: Alimentary Pharmabiotic CentreAddress: Cork, Ireland Access PDF as a Subscriber 窗体顶端窗体底端 Related Articles Email This Article Share This ArticleAbstract:Treatment with broad spectrum antibiotics can have a detrimental impact on the commensal bacteria present i

5、n the gut. The extensive nature of the collateral damage caused by such compounds has been revealed more starkly than ever before through the application of high throughput DNA sequencing-based technologies to investigate resulting microbial populations. Here we review the findings of such studies a

6、nd discuss the strategies available to minimize such negative impacts.IntroductionThe discovery ofantibioticsin the early twentieth century is arguably the single most significant breakthrough to positively impact on human health in recent history. Indeed, humanlife expectancyjumped by eight years i

7、n the period between 1944 and 1972, a fact which is mainly accredited to the introduction of antibiotics. The development of microbial resistance is the negative consequence most frequently associated with the overuse of antibiotics. However, the collateral damage which these antimicrobials inflict

8、on beneficial gut microbial populations (and other components of the human microbiota) could be a much more significant problem (Blaser, 2011). The long term health effects of antibiotic treatment in early life are not well defined but, notably, antibiotic-mediated changes to the commensal microbiot

9、a have been associated with the development ofasthma, eczema,atopic dermatitisand other allergic sensitization,autoimmune encephalitis, candidiasis, cholera, and pathogen induced colitis (Willinget al., 2011). Collateral damage to commensal microbes results from the fact that the majority of antibio

10、tics employed routinely have a broad target range. There are obvious benefits associated with the use of broad spectrum antimicrobials when treating severe infections of unknown or unclear etiology. However, even in cases when the relevant disease-causing (pathogenic) bacteria is identified, broad s

11、pectrum antibiotics are also most commonly employed as a consequence of the absence of narrow spectrum alternatives. This is at least partially due to the fact that thepharmaceutical industryfocuses primarily on the development of broad spectrum antibiotics which can be employed to treat a variety o

12、f different infections. While broad spectrum antibiotics may inhibit several pathogenic bacteria, this killing action can also extend to include commensal gut bacteria that contribute to human health. However, it is only in recent years through the advent of high throughput DNA sequencing technologi

13、es that the full extent of the impact of antibiotic use on thegut microbiotahas become apparent. Through a deeper understanding of the negative consequences of antibiotic administration, it is hoped that the mechanisms by which these changes contribute to ill health can be better understood and stra

14、tegies can be developed to ensure that the collateral damage inflicted is minimal.The Importance of the Gut MicrobiotaAlthough frequently quoted in “human microbiota”-related publications, the facts and figures relating to the numbers and functions ofcommensal bacteria, and those in the gut in parti

15、cular, remain awe-inspiring. The human microbiota consists of approximately 1014bacterial cells, 10-fold higher than the total number of cells in a human body (Leyet al., 2006). Of the microbial populations associated with the human body, the largest and most complex is that present in the gut (or g

16、astrointestinal tract). Indeed, within the gut, the large intestine alone harbors 1010-1011bacterial cells/g. A recent investigation of fecal samples of 124 Europeans revealed a microbiota-associated gene set which is approximately 150 times larger than the human host gene repertoire. It was also no

17、table that examination of the combined cohort revealed between 1,000-1,150 prevalent bacterial species (Qinet al., 2010). The investigation of these gut-associated bacteria is complicated by the fact that the majority are yet to be grown in the laboratory (Goodmanet al., 2011) and it has only been t

18、hrough the development of culture independent approaches, and most recently through the application of high throughput sequencing, that it has become possible to gain an unbiased insight into the composition of these populations.The Application of High Throughput DNA Sequencing-based Technologies to

19、 Study the Gut MicrobiotaWhile a number of high throughput DNA sequencing platforms exist (Glenn, 2011), they are typically applied to studying bacterial ecosystems in either of two ways: to determine the bacterial composition of the environment through sequencing of the 16s rRNA gene, or to determi

20、ne the functional potential of the bacterial population through shotgun (random) sequencing of DNA (Petrosinoet al., 2009). The former strategy has been used to assess the impact of antibiotics on gut bacteria. It relies on the fact that the 16s rRNA gene is present in all bacteria and contains cons

21、erved and variable regions which facilitate the generation of amplicons using degeneratePCRprimers. This allows for the subsequent identification of the bacteria present on the basis of DNA sequence differences in these amplicons. The same principle underlies the sequencing of clone libraries except

22、 that in these instances the PCR amplicons are first cloned into a vector to facilitate sequencing using traditional, low throughput (Sanger) sequencing. While there have been a number of important publications in recent years in which the impact of antibiotics on the gut microbiota has been assesse

23、d using clone libraries such as those investigating the impact of different -lactams or macrolides on the gut microbiota of adult humans (Morotomiet al., 2011) or those assessing the influence of streptomycin (Garneret al., 2009),vancomycin(Robinson and Young, 2010) or a combination of bacitracin, e

24、nrofloxacin, andneomycinsulphate on the enteric microbiota of mice (Puhlet al., 2011), here the focus will specifically be on those which have benefited from the much greater depth of sequencing information provided by high throughput approaches.High Throughput DNA Sequencing-based Insights into the

25、 Impact of Antibiotics on the Gut MicrobiotaDespite the dramatic advances that have been made in recent years due to the application of high throughput sequencing technologies to the characterization of gut microbial populations, there are relatively few instances in which this technology has been a

26、pplied to assessing the impact of antibiotic administration on the enteric microbiota (Table 1). Those which have been performed have focused on human (includingex vivo), canine, and murine microbial populations. They have also varied in that, in some instances, the focus of attention is on the impa

27、ct of a single antibiotic, while in other instances a cocktail of antibiotics is employed and, in one instance, the impact of antibiotic administration was assessed without regard for the actual therapeutic agent (Table 1).In this latter case (Claessonet al., 2011), the study involved an investigati

28、on of the general overall impact of antibiotic administration on the gut microbial composition of 43 individuals in receipt of antibiotics, relative to 118 individuals who were not. It revealed that those individuals who had received antibiotics had gut microbial populations that consisted of relati

29、vely greater proportions ofBacteroidetes(and the associatedParabacteroidesspecies) and reduced proportions ofFirmicutesandProteobacteria. The gut microbiota of 26 of the individuals who had not been in receipt of antibiotics at time 0 (T0) was subsequently reassessed following a three month interval

30、. During this period, 5 of these 26 had been administered antibiotics and comparison of the data from T0and T3monthsrevealed that antibiotic administration was associated with a significant reduction in the relative abundance of bacteria from the phylumActinobacteria(Claessonet al., 2011).Assessment

31、 of the impact of antibiotic cocktails relative to that of specific antibioticsThe other studies assessing the net impact of antibiotic administration, as assessed through the administration of a cocktail of antibiotics to mice, have also provided valuable insights. In one instance, the impact of a

32、cocktail ofmetronidazole, vancomycin, and neomycin, relative to that of vancomycin (a glycopeptide) orampicillin(-lactam) alone, on the gut microbiota of mice was examined (Ubedaet al., 2010). It was noted that all three treatments reduced the number of 16S rDNA copies (representative of total bacteria numbers) by a factor of 100 in the ileum whereas only ampicillin consistently reduced the number in the cecum. All antibiotic treatments dramatically altered the ileal and cecal microbiota. Ampicillin treatment led to incr