Though biofilms were first described by Antonie van Leeuwenhoek, the theory describing the biofilm process was not developed until 1978. We now understand that biofilms are universal, occurring in aquatic and industrial water systems as well as a large number of environments and medical devices relevant for public health. Using tools such as the scanning electron microscope and, more recently, the confocal laser scanning microscope, biofilm researchers now understand that biofilms are not unstructured, homogeneous deposits of cells and accumulated slime, but complex communities of surface-associated cells enclosed in a polymer matrix containing open water channels. Further studies have shown that the biofilm phenotype can be described in terms of the genes expressed by biofilm-associated cells. Microorganisms growing in a biofilm are highly resistant to antimicrobial agents by one or more mechanisms. Biofilm-associated microorganisms have been shown to be associated with several human diseases, such as native valve endocarditis and cystic fibrosis, and to colonize a wide variety of medical devices. Though epidemiologic evidence points to biofilms as a source of several infectious diseases, the exact mechanisms by which biofilm-associated microorganisms elicit disease are poorly understood. Detachment of cells or cell aggregates, production of endotoxin, increased resistance to the host immune system, and provision of a niche for the generation of resistant organisms are all biofilm processes which could initiate the disease process. Effective strategies to prevent or control biofilms on medical devices must take into consideration the unique and tenacious nature of biofilms. Current intervention strategies are designed to prevent initial device colonization, minimize microbial cell attachment to the device, penetrate the biofilm matrix and kill the associated cells, or remove the device from the patient. In the future, treatments may be based on inhibition of genes involved in cell attachment and biofilm formation.

Biofilms: Survival Mechanisms of Clinically Relevant Microorganisms

The distal human intestine represents an anaerobic bioreactor programmed with an enormous population of bacteria, dominated by relatively few divisions that are highly diverse at the strain/subspecies level. This microbiota and its collective genomes (microbiome) provide us with genetic and metabolic attributes we have not been required to evolve on our own, including the ability to harvest otherwise inaccessible nutrients. New studies are revealing how the gut microbiota has coevolved with us and how it manipulates and complements our biology in ways that are mutually beneficial. We are also starting to understand how certain keystone members of the microbiota operate to maintain the stability and functional adaptability of this microbial organ.

https://science.sciencemag.org/content/sci/307/5717/1915.full.pdf

Host-Bacterial Mutualism in the Human Intestine

It has been recognized for some time that bacterial species exist in complexes in subgingival plaque. The purpose of the present investigation was to attempt to define such communities using data from large numbers of plaque samples and different clustering and ordination techniques. Subgingival plaque samples were taken from the mesial aspect of each tooth in 185 subjects (mean age 51 +/- 16 years) with (n = 160) or without (n = 25) periodontitis. The presence and levels of 40 subgingival taxa were determined in 13,261 plaque samples using whole genomic DNA probes and checkerboard DNA-DNA hybridization. Clinical assessments were made at 6 sites per tooth at each visit. Similarities between pairs of species were computed using phi coefficients and species clustered using an averaged unweighted linkage sort. Community ordination was performed using principal components analysis and correspondence analysis. 5 major complexes were consistently observed using any of the analytical methods. One complex consisted of the tightly related group: Bacteroides forsythus, Porphyromonas gingivalis and Treponema denticola. The 2nd complex consisted of a tightly related core group including members of the Fusobacterium nucleatum/periodonticum subspecies, Prevotella intermedia, Prevotella nigrescens and Peptostreptococcus micros. Species associated with this group included: Eubacterium nodatum, Campylobacter rectus, Campylobacter showae, Streptococcus constellatus and Campylobacter gracilis. The 3rd complex consisted of Streptococcus sanguis, S. oralis, S. mitis, S. gordonii and S. intermedius. The 4th complex was comprised of 3 Capnocytophaga species, Campylobacter concisus, Eikenella corrodens and Actinobacillus actinomycetemcomitans serotype a. The 5th complex consisted of Veillonella parvula and Actinomyces odontolyticus. A. actinomycetemcomitans serotype b, Selenomonas noxia and Actinomyces naeslundii genospecies 2 (A. viscosus) were outliers with little relation to each other and the 5 major complexes. The 1st complex related strikingly to clinical measures of periodontal disease particularly pocket depth and bleeding on probing.

Microbial complexes in subgingival plaque

There is good evidence that the complex microbial flora present in the gastrointestinal tract of all warm-blooded animals is effective in providing resistance to disease. However, the composition of this protective flora can be altered by dietary and environmental influences, making the host animal susceptible to disease and/or reducing its efficiency of food utilization. What we are doing with the probiotic treatments is re-establishing the natural condition which exists in the wild animal but which has been disrupted by modern trends in conditions used for rearing young animals, including human babies, and in modern approaches to nutrition and disease therapy. These are all areas where the gut flora can be altered for the worse and where, by the administration of probiotics, the natural balance of the gut microflora can be restored and the animal returned to its normal nutrition, growth and health status.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-2672.1989.tb05105.x

Probiotics in man and animals

General Issues in Clinical Microbiology Diagnostic Technologies in Clinical Microbiology Nosocomial and Community Infections: the Role of the Clinical Microbiology Laboratory Bacteria Fungi Parasites Viruses Rickettsiae and Chlamydiae Antimicrobial Agents and Susceptibility Tests Quality Control, Media, Reagents and Stains.

/pdf/manual-of-clinical-microbiology-54bqiuj7tf.pdf

Manual of Clinical Microbiology

Quantitative and qualitative examination of the fecal flora of 20 clinically healthy Japanese-Hawaiian males was carried out by using anaerobic tube culture techniques Cultural counts were 93% of the microscopic clump counts Isolated colonies were selected in a randomized manner to give an unbiased sampling of the viable bacterial types Each isolate was characterized for species identification From a total of 1,147 isolates, 113 distinct types of organisms were observed Statistical estimates indicate that these types account for 94% of the viable cells in the feces The quantitative composition of the flora of this group of people, together with differential characteristics of previously unreported species, is presented for those kinds of bacteria which each represented at least 005% of the flora

Human fecal flora: the normal flora of 20 Japanese-Hawaiians.

The bacteria of periodontal diseases

There is a perception of conflicting data and opinions among research laboratories that are studying periodontal microbiology. In response to this perception I was asked to discuss recent literature in this field at the 1986 Annual Meeting of the American Association of Dental Research. This review is based on that discussion which primarily concerned all of the relevant papers that were available to me and that had been published in the last 2 years (1984 and 1985). In order to determine what the data (rather than what our biases) may tell us, accurate comparisons of published reports in this field require an appreciation of the reasons for different results in different laboratories. Therefore, before we compare data, let's consider some of the reasons why results from different laboratories may differ. The periodontal flora is complex. We have found over 325 distinct bacterial species in the human gingival crevice (1). Many of these species have never been formally described, most of them are ignored by some laboratories, identified differently by others, or lumped together in various groups by still others. Some of the predominant species have special growth requirements and are not detected on some media that are widely used. Identification criteria differ among laboratories. Even with rigorous testing, identification of some species is questionable. With minimal testing it is even less reliable.

Microbiology of periodontal disease

Data are presented on the distribution of 101 bacterial species and subspecies among 1,442 isolates from 25 fecal specimens from three men on: (i) their normal diet and normal living conditions, (ii) normal living conditions but eating the controlled metabolic diet designed for use in the Skylab simulation and missions, and (iii) the Skylab diet in simulated Skylab (isolation) conditions. These bacteria represent the most numerous kinds in the fecal flora. Analyses of the kinds of bacteria from each astronaut during the 5-month period showed more variation in the composition of the flora among the individual astronauts than among the eight or nine samples from each person. This observation indicates that the variations in fecal flora reported previously, but based on the study of only one specimen from each person, more certainly reflect real differences (and not daily variation) in the types of bacteria maintained by individual people. The proportions of the predominant fecal species in the astronauts were similar to those reported earlier from a Japanese-Hawaiian population and were generally insensitive to changes from the normal North American diet to the Skylab diet; only two of the most common species were affected by changes in diet. However, one of the predominant species (Bacteroides fragilis subsp. thetaiotaomicron) appeared to be affected during confinement of the men in the Skylab test chamber. Evidence is presented suggesting that an anger stress situation may have been responsible for the increase of this species simultaneously in all of the subjects studied. Phenotypic characteristics of some of the less common isolates are given. The statistical analyses used in interpretation of the results are discussed.

Human fecal flora: variation in bacterial composition within individuals and a possible effect of emotional stress.

The fecal floras of polyp patients, Japanese-Hawaiians, North American Caucasians, rural native Japanese, and rural native Africans were compared. The polyp patients and Japanese-Hawaiians were considered to be groups at high risk of colon cancer, and the rural native Japanese and rural native Africans were considered to be groups at low risk. The North American Caucasians were found to have a flora composition intermediate between these two groups. Fifteen bacterial taxa from the human fecal flora were significantly associated with high risk of colon cancer, and five were significantly associated with low risk of colon cancer. Total concentrations of Bacteroides species and, surprisingly, Bifidobacterium species were generally positively associated with increased risk of colon cancer. Some Lactobacillus species and Eubacterium aerofaciens, which also produces major amounts of lactic acid, showed closest associations with low risk of colon cancer.

W. E. C. Moore

Papers

Human fecal flora: the normal flora of 20 Japanese-Hawaiians.

The bacteria of periodontal diseases

Microbiology of periodontal disease

Human fecal flora: variation in bacterial composition within individuals and a possible effect of emotional stress.

Intestinal floras of populations that have a high risk of colon cancer.