Microbial Metabolism In The Digestive Tract

M. J. Hill

• Publisher: CRC Press
• Year: 2018
• Print ISBN:
  9781315895444
• eBook ISBN:
  9781351091442
• Topic: Biological Sciences
• Subtopic: Biology
• Index: Biological Sciences

In this book an attempt has been made to give an update on the flora of the human digestive tract and its role in disease. This is a subject that has implications in many disciplines and therefore is aimed at not only microbiologists, but also clinicians, dentists, medical researchers, biochemists, and toxicologists who have a background knowledge of bacteriology but are not necessarily directly involved in research into the metabolic actions of gut bacteria.

Chapter 1

Microbial Flora Of The Gastrointestinal Tract

S. P. Borriello

TABLE OF CONTENTS

I. Introduction

II. Limitations to the Study of the Flora of the Gastrointestinal Tract

A. Sampling, Transport, and Storage

B. Cultivation, Enumeration, and Identification

III. Microbial Flora of the Mouth

IV. Microbial Flora of the Stomach

V. Microbial Flora of the Biliary Tract

VI. Microbial Flora of the Proximal Small Bowel

VII. Microbial Flora of the Distal Small Bowel

VIII. Microbial Flora of the Large Bowel

A. Microbial Flora of the Cecum and Appendix

B. Fecal Flora

C. Mucosal Flora

D. Protozoa in the Large Bowel

IX. Conclusions

References

I. Introduction

The microbial flora of the gastrointestinal tract forms an extremely complex ecosystem. There are at least 17 families of bacteria yielding at least 50 different genera. There are then countless species, subspecies, and biotypes, with at least 400 to 500 different bacterial species thought to be present in the fecal flora of a single person.^1-3 Each gram of gut content contains up to 10¹² organisms and these massive numbers of bacteria in feces would account for up to 40% of the total fecal mass. We each of us harbor more bacteria within our gastrointestinal tract than there are (or have been) people in the world. Obviously, the biochemical and disease causing potential of this complex ecosystem is immense. In many ways the gut flora could be viewed as an organ of the body in its own right.

Identifying the components of the gut flora and investigating their biochemical activities has occupied the mind of microbiologists from the very earliest days of this branch of science. What this chapter will try to do will be to give an overview of the components of the gut flora at different sites within the gastrointestinal tract in health and disease. This will be done after outlining the difficulties involved in studies of the gut flora to allow for better interpretation of the results presented.

II. Limitations to the Study of the Flora of the Gastrointestinal Tract

In order to interpret correctly the qualitative and quantitative data generated from studies on the flora of the gastrointestinal tract it is important to be aware of the limitations imposed on such studies. The major problems are those of the extreme complexity of the ecosystem under investigation and the inaccessibility of many parts of that ecosystem in a healthy subject. The difficulties that may influence the results fall into two major groups, sampling transport and storage, and cultivation, enumeration, and identification.

A. Sampling, Transport, and Storage

One of the major problems encountered is that of obtaining specimens from any site other than the mouth and anus. However, even at these two sites problems may arise. For example, in analysis of fecal material in swine it has been shown that there are differences in the recoverable flora, dependent on where the stool specimen sample is taken from.⁴ Also, in the mouth there are a number of sites where it is difficult to perform quantitative bacteriological investigations. For parts of the gastrointestinal tract other than these sites, invasive techniques are employed. This means either intubation or collection of material at operation. In both cases there will be associated factors that could be expected to influence the results. There may be contamination of the specimen due to bacteria from other sites. For example, salivary contamination of juice collected when intubating the jejunum. In most cases the subject was anesthetized and had fasted. These factors will obviously have an effect on the flora, especially the reduction of peristalsis induced by anesthetics which will have an effect on the flora of the small bowel. It must also be remembered that in many cases the subjects studied will have been abnormal and will have received antibiotics and/or bowel washout.

Having collected the specimen the nature of the collection vessel could influence the results. Obviously, the optimal collection vessel would be one in which an anaerobic atmosphere could be maintained. In addition, the length of time in which the specimen remains in the collection vessel during transport will also influence the results. Further details of sampling and transport techniques are given in the review by Borriello et al.⁵ If the specimen is not to be analyzed immediately then the length of time that it is stored prior to examination and the method of storage will also greatly affect the results obtained. Even with a recommended storage method⁶ it can be seen that there are qualitative and quantitative changes in the flora even after a relatively short storage time.⁶ If frozen the rate of freezing and thawing of the specimen will also affect the bacteria present.⁷

B. Cultivation, Enumeration, and Identification

One of the major problems in defining the flora of the gastrointestinal tract is that of being able to cultivate the microorganisms present. In many cases the cultivation media used may not be able to support the growth of certain bacteria. So although present and surviving the transport and storage systems used they will not form colonies visible to the naked eye. Some organisms may be able to grow under the conditions used, but will do so only very slowly, therefore the length of incubation is also an important variable. In addition to the type of media used the degree of anaerobiosis will also be an important factor influencing recovery. The major problem with respect to cultivation, enumeration, and identification is that of the complexity of the flora. If only nonselective media are employed then the less dominant bacteria will be masked by the dominant organisms that can grow under the in vitro conditions used. The relative numers of bacteria present in the samples from two different subjects may not only give different findings because of differences between the samples but may in themselves result in apparent differences. For example, we could envisage in one population 10⁹ per gram or milliliter of specimen of organism A and only 10⁵ of organism B, where organism A is the major component of the flora. The situation in the other population may be that there are 10⁵ of organism B but only 10' of organism A and organism B is the major component. If no selective methods exist for these organisms then the findings would indicate that one population harbors only organism A and the other only organism B because the dominant organism outnumbers the other by 10⁴:1 and would be overgrown on agar media. In reality both groups carry both types of organism and more significantly both have the same number of organism B. The relative limits of detection of different organism imposed by their relative numbers are rarely stated or discussed. Although selective media or procedures can sometimes be employed to overcome this problem there are two major drawbacks to the use of selective media that must be borne in mind. First, few selective media are totally selective. Some unwanted organisms may be isolated by this method and some desired organisms will not be isolated and will fail to grow. For example, vancomycin, an antibiotic active against Gram-positive organisms, is frequently a component of selective media used for the isolation of Bacteroides. However, some species of Bacter-oides are sensitive to this antibiotic.⁸ Second, from a quantitative point of view selective media will give an underestimate of the true number. Despite the drawbacks selective media have been extremely useful in helping to define the flora of the gastrointestinal tract and in some cases have helped to isolate organisms for which the medium was not originally designed (e.g., the isolation of anaerobiospirillum using selective media and procedures designed for the isolation of Campylobacter).⁹ The optimal methods for cultivating the bacteria present would be a combination of the Hungate roll-tube technique using a selection of selective and nons...

Table of contents

• Cover Page
• Title Page
• Copyright Page
• Preface
• Editor
• Contributors
• Table of Contents
• Chapter 1 Microbial Flora of the Gastrointestinal Tract
• Chapter 2 Factors Affecting Bacterial Metabolism
• Chapter 3 Metabolism of Carbohydrates and Glycosides
• Chapter 4 Bacterial Metabolism of Dietary Fiber
• Chapter 5 The Metabolism of Bile Acids
• Chapter 6 Metabolism of Neutral Steroids
• Chapter 7 Metabolism of Ammonia, Urea, and Amino Acids, and Their Significance in Liver Disease
• Chapter 8 Gut Bacteria and the Metabolism of Aromatic Amino Acids
• Chapter 9 Nitrate Metabolism
• Chapter 10 Gut Bacteria and the Enterohepatic Circulation of Foreign Compounds
• Chapter 11 The Metabolism of Oral Bacteria in Health and Disease
• Chapter 12 Bacterial Metabolism and Acute Enteric Infection
• Chapter 13 Bacterial Metabolism and the Diagnosis of Small Bowel and Gastric Overgrowth
• Chapter 14 Interrelationship Between Bacteria and Mucosa of the Gastrointestinal Tract
• Chapter 15 Bacteria and Inflammatory Bowel Disease
• Chapter 16 Bacterial Metabolism and Human Cancer
• Index