Use of the Gram stain in microbiology

The Gram stain differentiates bacteria into two fundamental varieties of cells. Bacteria that retain the initial crystal violet stain (purple) are said to be ''Gram-positive,'' whereas those that are decolorized and stain red with carbol fuchsin (or safranin) are said to be ''Gram-negative.'' This staining response is based on the chemical and structural makeup of the cell walls of both varieties of bacteria. Gram-positives have a thick, relatively impermeable wall that resists decolorization and is composed of peptidoglycan and secondary polymers. Gram-negatives have a thin peptidoglycan layer plus an overlying lipid-protein bilayer known as the outer membrane, which can be disrupted by decolorization. Some bacteria have walls of intermediate structure and, although they are officially classified as Gram-positives because of their linage, they stain in a variable manner. One prokaryote domain, the Archaea, have such variability of wall structure that the Gram stain is not a useful differentiating tool.     

The characterization and ultrastructure of two new strains of Butyrivibrio

Strains B-385-1 and 2-33 are numerically important components rumen bacterial populations , but they have remained (taxonomically) undefined. In spite of some resemblance to Selenomonas ruminantium in their cell size and in their formation of tufts of flagella, they more closely resemble Butyrivibrio fibrisolvens in the subpolar location of their flagella, in their guanine + cytosine content, and in most biochemical characteristics, including butyrate formation. Cells of these strains stain Gram negative, as do both Selenomonas and Butyrivibrio, but their cell walls closely resemble those of Butyrivibrio in their Gram-positive type of molecular architecture and in their cleavage pattern in freeze-etching. Cells of these strains and of B. fibrisolvens have a very thin (ca. 12 nm) peptidoglycan cell wall; thus, they fail to retain the crystal violet complex of the Gram stain and stain Gram negative. This important structural characteristic of their cell walls places strains B-385-1 and 2-33 within the genus Butyrivibrio and certain morphological and biochemical characteristics distinguish them from B. fibrisolvens.     

革兰氏染色三步法与质量控制

革兰氏染色(Gram stain),是细菌学中一个经常使用和十分重要的方法,自从1884年微生物学家Gram氏发明著名的革兰氏染色法以后,100多年来虽然经过后来学者的几次改进,但都仍然沿用着Gram氏原来的四步法,基本原理也没有改变。最近Allen氏对Ziehl-Neelsen抗酸菌染色法的改进,是一个良好的启示,使我们开始了革兰氏染色三步法的研究并取得了成功。现将我们建立的革兰氏染色三步法与质量控制报告如下。 1 材料和方法 1.1 结晶紫染色液 甲液:结晶紫2g;95％乙醇20ml。 乙液:草酸铵0.8g;蒸馏水80ml。 甲乙二液先分别溶解,然后混合在一起,过滤除去残渣后装入滴瓶中备用。     

Peptidoglycan turnover and recycling in Gram-positive bacteria

Bacterial cells are protected by an exoskeleton, the stabilizing and shape-maintaining cell wall, consisting of the complex macromolecule peptidoglycan. In view of its function, it could be assumed that the cell wall is a static structure. In truth, however, it is steadily broken down by peptidoglycan-cleaving enzymes during cell growth. In this process, named cell wall turnover, in one generation up to half of the preexisting peptidoglycan of a bacterial cell is released from the wall. This would result in a massive loss of cell material, if turnover products were not be taken up and recovered. Indeed, in the Gram-negative model organism Escherichia coli, peptidoglycan recovery has been recognized as a complex pathway, named cell wall recycling. It involves about a dozen dedicated recycling enzymes that convey cell wall turnover products to peptidoglycan synthesis or energy pathways. Whether Gram-positive bacteria also recover their cell wall is currently questioned. Given the much larger portion of peptidoglycan in the cell wall of Gram-positive bacteria, however, recovery of the wall material would provide an even greater benefit in these organisms compared to Gram-negatives. Consistently, in many Gram-positives, orthologs of recycling enzymes were identified, indicating that the cell wall may also be recycled in these organisms. This mini-review provides a compilation of information about cell wall turnover and recycling in Gram-positive bacteria during cell growth and division, including recent findings relating to muropeptide recovery in Bacillus subtilis and Clostridium acetobutylicum from our group. Furthermore, the impact of cell wall turnover and recycling on biotechnological processes is discussed.     

Photometric Application of the Gram Stain Method To Characterize Natural Bacterial Populations in Aquatic Environments

The Gram stain method was applied to the photometric characterization of aquatic bacterial populations with a charge-coupled device camera and an image analyzer. Escherichia coli and Bacillus subtilis were used as standards of typical gram-negative and gram-positive bacteria, respectively. A mounting agent to obtain clear images of Gram-stained bacteria on Nuclepore membrane filters was developed. The bacterial stainability by the Gram stain was indicated by the Gram stain index (GSI), which was applicable not only to the dichotomous classification of bacteria but also to the characterization of cell wall structure. The GSI spectra of natural bacterial populations in water with various levels of eutrophication showed a distinct profile, suggesting possible staining specificity that indicates the presence of a particular bacterial population in the aquatic environment.Gram’s method is the most important and fundamental orthodox method for bacterial identification. It classifies bacteria into two groups, gram-negative and gram-positive. The mechanism of Gram staining is based on the fundamental structural and chemical attributes of bacterial cell walls. The cell walls of gram-positive bacteria have a high percentage of peptidoglycan, while those of gram-negative bacteria have only a thin peptidoglycan layer (1–3, 6). In Gram’s method, an insoluble dye-iodine complex is formed inside bacterial cells and is extracted by alcohol from gram-negative but not gram-positive bacteria (6, 12, 16). There are taxonomically gram-variable species, but some cells of gram-negative or gram-positive species may show gram-variable characteristics due to environmental stress, such as unsuitable nutrients, temperature, pH, or electrolytes (3).Functional differences between gram-positive and gram-negative cell walls have been studied with special emphasis on nutrient uptake from the ambient environment. Gram-negative bacteria have a periplasmic space between the lipopolysaccharide layer and the plasma membrane. In this space, binding proteins initially attach to nutrients and take them to a membrane carrier. Gram-positive bacteria lack the periplasmic space and are believed to have no binding proteins (9). Therefore, nutrient uptake from the environment is easier for gram-negative bacteria than for gram-positive bacteria. Because of this difference, the population density of gram-negative bacteria in more oligotrophic environments could be higher than that of gram-positive bacteria (20).Gram staining is commonly used only to reflect cell wall structure. If Gram staining characterizes not only simple taxonomical dichotomy but also multiple biological functions, it may also be used to correlate bacterial cell wall structure with related physiological responses to the environment. In particular, Gram staining could supply ecological information on natural bacterial populations that are difficult to culture by the present technology.Membrane filter methods are widely used for microscopy in aquatic microbiology because of the low population densities of bacteria in many aquatic environments (4, 11, 16). However, these methods sometimes have problems associated with microscopic observations, causing unclear images of bacterial cells on Nuclepore filters when used with the conventional mounting medium (immersion oil; refractive index [nd] = 1.514). Hence, a suitable mounting agent must be applied to obtain precise image analyses of Gram-stained bacteria on Nuclepore filters.In this study, we have established a distinct method to characterize photometric Gram stain images; it involves the Gram stain index (GSI) for specifying natural bacterial populations in various aquatic environments. For this purpose, we have standardized the GSI of typical gram-negative and gram-positive bacteria by using Escherichia coli and Bacillus subtilis, respectively, and compared these GSI values to those of natural bacterial populations of several freshwater environments. The natural waters we investigated were Hyoutaro-ike pond, Matsumi-ike bog, and Lake Kasumigaura, which are oligotrophic, mesotrophic, and eutrophic water bodies, respectively, as previously determined (8, 10, 13, 18, 22, 23).     

Cell wall structure and function in lactic acid bacteria

The cell wall of Gram-positive bacteria is a complex assemblage of glycopolymers and proteins. It consists of a thick peptidoglycan sacculus that surrounds the cytoplasmic membrane and that is decorated with teichoic acids, polysaccharides, and proteins. It plays a major role in bacterial physiology since it maintains cell shape and integrity during growth and division; in addition, it acts as the interface between the bacterium and its environment. Lactic acid bacteria (LAB) are traditionally and widely used to ferment food, and they are also the subject of more and more research because of their potential health-related benefits. It is now recognized that understanding the composition, structure, and properties of LAB cell walls is a crucial part of developing technological and health applications using these bacteria. In this review, we examine the different components of the Gram-positive cell wall: peptidoglycan, teichoic acids, polysaccharides, and proteins. We present recent findings regarding the structure and function of these complex compounds, results that have emerged thanks to the tandem development of structural analysis and whole genome sequencing. Although general structures and biosynthesis pathways are conserved among Gram-positive bacteria, studies have revealed that LAB cell walls demonstrate unique properties; these studies have yielded some notable, fundamental, and novel findings. Given the potential of this research to contribute to future applied strategies, in our discussion of the role played by cell wall components in LAB physiology, we pay special attention to the mechanisms controlling bacterial autolysis, bacterial sensitivity to bacteriophages and the mechanisms underlying interactions between probiotic bacteria and their hosts.     

Mechanism of gram variability in select bacteria.

Gram stains were performed on strains of Actinomyces bovis, Actinomyces viscosus, Arthrobacter globiformis, Bacillus brevis, Butyrivibrio fibrisolvens, Clostridium tetani, Clostridium thermosaccharolyticum, Corynebacterium parvum, Mycobacterium phlei, and Propionibacterium acnes, using a modified Gram regimen that allowed the staining process to be observed by electron microscopy (J. A. Davies, G. K. Anderson, T. J. Beveridge, and H. C. Clark, J. Bacteriol. 156:837-845, 1983). Furthermore, since a platinum salt replaced the iodine mordant of the Gram stain, energy-dispersive X-ray spectroscopy could evaluate the stain intensity and location by monitoring the platinum signal. These gram-variable bacteria could be split into two groups on the basis of their staining responses. In the Actinomyces-Arthrobacter-Corynebacterium-Mycobacterium-Propionibacterium group, few cells became gram negative until the exponential growth phase; by mid-exponential phase, 10 to 30% of the cells were gram negative. The cells that became gram negative were a select population of the culture, had initiated septum formation, and were more fragile to the stress of the Gram stain at the division site. As cultures aged to stationary phase, there was a relatively slight increase toward gram negativity (now 15 to 40%) due to the increased lysis of nondividing cells by means of lesions in the side walls; these cells maintained their rod shape but stained gram negative. Those in the Bacillus-Butyrivibrio-Clostridium group also became gram negative as cultures aged but by a separate set of events. These bacteria possessed more complex walls, since they were covered by an S layer. They stained gram positive during lag and the initial exponential growth phases, but as doubling times increased, the wall fabric underlying the S layer became noticeably thinner and diffuse, and the cells became more fragile to the Gram stain. By stationary phase, these cultures were virtually gram negative.     

Visualizing the production and arrangement of peptidoglycan in Gram‐positive cells

Decades of study have revealed the fine chemical structure of the bacterial peptidoglycan cell wall, but the arrangement of the peptidoglycan strands within the wall has been challenging to define. The application of electron cryotomography (ECT) and new methods for fluorescent labelling of peptidoglycan are allowing new insights into wall structure and synthesis. Two articles in this issue examine peptidoglycan structures in the model Gram‐positive species Bacillus subtilis. Beeby et al. combined visualization of peptidoglycan using ECT with molecular modelling of three proposed arrangements of peptidoglycan strands to identify the model most consistent with their data. They argue convincingly for a Gram‐positive wall containing multiple layers of peptidoglycan strands arranged circumferentially around the long axis of the rod‐shaped cell, an arrangement similar to the single layer of peptidoglycan in similarly shaped Gram‐negative cells. Tocheva et al. examined sporulating cells using ECT and fluorescence microscopy to demonstrate the continuous production of a thin layer of peptidoglycan around the developing spore as it is engulfed by the membrane of the adjacent mother cell. The presence of this peptidoglycan in the intermembrane space allows the refinement of a model for engulfment, which has been known to include peptidoglycan synthetic and lytic functions.     

Architecture and assembly of the Gram‐positive cell wall

The bacterial cell wall is a mesh polymer of peptidoglycan – linear glycan strands cross‐linked by flexible peptides – that determines cell shape and provides physical protection. While the glycan strands in thin ‘Gram‐negative’ peptidoglycan are known to run circumferentially around the cell, the architecture of the thicker ‘Gram‐positive’ form remains unclear. Using electron cryotomography, here we show that Bacillus subtilis peptidoglycan is a uniformly dense layer with a textured surface. We further show it rips circumferentially, curls and thickens at free edges, and extends longitudinally when denatured. Molecular dynamics simulations show that only atomic models based on the circumferential topology recapitulate the observed curling and thickening, in support of an ‘inside‐to‐outside’ assembly process. We conclude that instead of being perpendicular to the cell surface or wrapped in coiled cables (two alternative models), the glycan strands in Gram‐positive cell walls run circumferentially around the cell just as they do in Gram‐negative cells. Together with providing insights into the architecture of the ultimate determinant of cell shape, this study is important because Gram‐positive peptidoglycan is an antibiotic target crucial to the viability of several important rod‐shaped pathogens including Bacillus anthracis, Listeria monocytogenes, and Clostridium difficile.     

Partial functional redundancy of MreB isoforms, MreB, Mbl and MreBH, in cell morphogenesis of Bacillus subtilis

MreB proteins are bacterial actin homologues thought to have a role in cell shape determination by positioning the cell wall synthetic machinery. Many bacteria, particularly Gram-positives, have more than one MreB isoform. Bacillus subtilis has three, MreB, Mbl and MreBH, which colocalize in a single helical structure. We now show that the helical pattern of peptidoglycan (PG) synthesis in the cylindrical part of the rod-shaped cell is governed by the redundant action of the three MreB isoforms. Single mutants for any one of mreB isoforms can still incorporate PG in a helical pattern and generate a rod shape. However, after depletion of MreB in an mbl mutant (or depletion of all three isoforms) lateral wall PG synthesis was impaired and the cells became spherical and lytic. Overexpression of any one of the MreB isoforms overcame the lethality as well as the defects in lateral PG synthesis and cell shape. Furthermore, MreB and Mbl can associate with the peptidoglycan biosynthetic machinery independently. However, no single MreB isoform was able to support normal growth under various stress conditions, suggesting that the multiple isoforms are used to allow cells to maintain proper growth and morphogenesis under changing and sometimes adverse conditions.     

The Phenomenon of Gram-Positivity; Its Definition and Some Negative Evidence on the Causative Role of Sulfhydryl Groups

It has been accepted for many decades that a Gram-positive organism is one which retains the primary dye when stained by accepted Gram stain procedures. It has also been known that the iodine step is essential if Gram differentiation is to be obtained. If bacterial cells are treated in such a way that they will retain the primary dye following a Gram staining procedure, regardless of whether or not the iodine step is included, then the mechanism of this dye retention must differ from that which normally is responsible for a Gram-positive state. Similarly, when both the iodine and decolorization steps are omitted, the counter-stain should always replace the primary stain. If it does not, then the mechanism of dye retention would not be normal, and any such dye retention would not be related to the Gram phenomenon. In such cases one is not studying the Gram reaction, but is studying chemical affinities or physical states which produce visually similar but actually unrelated phenomena. Failure to appreciate this has resulted in papers appearing under the guise of studies of the Gram reaction which have little or no relationship to the Gram phenomenon.

In the interest of consistency, these criteria of true Gram-positivity (the necessity of iodine for Gram-positivity with a normal Gram procedure, and the ability of the counterstain to replace the primary dye when both the iodine and decolorization steps are omitted) should be applied to both intact cells and cell-free substances, even though their mechanism of Gram-positivity may differ.

The above criteria have been applied in a study of the sulfhydryl concept of the mecharism of Gram-positivity as proposed by Fischer and Larose. It was found that while the experimental work of Fischer and Larose was reproducible, the supposedly Gram-positive states produced did not possess the characteristics which would identify them as true Gram-positive states. Our results would not support the sulfhydryl concept concerning the mechanism of Gram-positivity.     

The fine structure of Micrococcus radiophilus and Micrococcus radioproteolyticus

The radiation resistant bacteria Micrococcus radiophilus and M. radioproteolyticus were studied by thin sectioning and freeze-etching techniques and the two species were found to be similar in the fine structure. The only significant difference was in the appearance of the surfaces of the cell walls in freeze-etched preparations.Since the two species, together with M. radiodurans, possess a unique cell wall structure and a cell wall peptidoglycan, which is different from that of other micrococci and Gram-positive cocci, it is recommended that they be reclassified into a new genus.     

Alterations in the composition and bacteriophage-binding properties of walls of Staphylococcus aureus H grown in continuous culture in simplified defined media.

A nutritional mutant of Staphylococcus aureus H has been isolated and grown in media in which the only amino acids are arginine, cysteine, glutamic acid and proline. Walls of the bacteria grown in such media in continuous culture under potassium limitation differ in composition from walls of the bacteria grown in batch culture in rich nutrient broth in that they contain less glycine, the peptidoglycan component is less highly cross-linked and the teichoic acid component contains a reduced proportion of N-acetylglucosaminyl substituents. Walls of the potassium-limited bacteria retain the ability to bind bacteriophage 52a but are more susceptible to the action of lytic peptidases than are wall samples in which the peptidoglycan is more highly cross-linked. Teichoic acid was present in walls of the bacteria grown under phosphate limitation in the defined medium and these walls were also able to absorb bacteriophage 52a.     

Protein secretion and surface display in Gram-positive bacteria

The cell wall peptidoglycan of Gram-positive bacteria functions as a surface organelle for the transport and assembly of proteins that interact with the environment, in particular, the tissues of an infected host. Signal peptide-bearing precursor proteins are secreted across the plasma membrane of Gram-positive bacteria. Some precursors carry C-terminal sorting signals with unique sequence motifs that are cleaved by sortase enzymes and linked to the cell wall peptidoglycan of vegetative forms or spores. The sorting signals of pilin precursors are cleaved by pilus-specific sortases, which generate covalent bonds between proteins leading to the assembly of fimbrial structures. Other precursors harbour surface (S)-layer homology domains (SLH), which fold into a three-pronged spindle structure and bind secondary cell wall polysaccharides, thereby associating with the surface of specific Gram-positive microbes. Type VII secretion is a non-canonical secretion pathway for WXG100 family proteins in mycobacteria. Gram-positive bacteria also secrete WXG100 proteins and carry unique genes that either contribute to discrete steps in secretion or represent distinctive substrates for protein transport reactions.     

Variations in the Gram Staining Results Caused by Air Moisture

The exposure of heat-fixed bacterial smears to relative humidities of 0, 52 and 98%, following the iodine step in a dry Gram stain procedure, markedly influenced the rate of decolorization upon exposure to 95% ethyl alcohol. If a single decolorization time were used to give a proper Gram differentiation after exposure to 98% relative humidity, this decolorization time might not result in proper Gram differentiation following exposure to 0% relative humidity. Different organisms varied in the degree of their response to changes in humidity. Hence the “degree of Gram-positivity,” as compared with other organisms, differed with changes in relative humidity. When Neisseria catarrhalis was compared with strongly Gram-positive and Gram-negative organisms, it was always found to be in an intermediate position in its Gram characteristics regardless of the relative humidity used. Because of the intermediate position of this organism, its proper Gram differentiation would require a precise definition of both the decolorization time and the decolorization procedure to be used. The results for all organisms studied clearly indicated that the control of wetness or dryness of the smear before decolorization would be essential in any Gram procedure where a single decolorization time is to be used.     

The Effect of the Chemical Nature of a Decolorizer on its Functioning. i. the Gram Classification

Decolorizers which are distinctly acidic or basic in their chemical nature give abnormally high decolorization in the Gram stain for bacteria. Acidic substances yield more regular results. Ideally an “inert” decolorizer should be used, but ordinarily such substances will not dissolve the dye or dye-mordant precipitate from the smear. The most practical substances seem to be those so very slightly acidic in character as to be practically inert, such as acetone or alcohol, or a mixture of such substances.     

Alterations in the composition and bacteriophage-binding properties of walls of Staphylococcus aureus H grown in continuous culture in simplified defined media

A nutritional mutant of Staphylococcus aureus H has been isolated and grown in media in which the only amino acids are arginine, cysteine, glutamic acid and proline. Walls of the bacteria grown in such media in continuous culture under potassium limitation differ in composition from walls of the bacteria grown in batch culture in rich nutrient broth in that they contain less glycine, the peptidoglycan component is less highly cross-linked and the teichoic acid component contains a reduced proportion of $\text{N-}\text{acetylglucosaminyl}$ substituents. Walls of the potassium-limited bacteria retain the ability to bind bacteriophage 52a but are more susceptible to the action of lytic peptidases than are wall samples in which the peptidoglycan is more highly cross-linked. Teichoic acid was present in walls of the bacteria grown under phosphate limitation in the defined medium and these walls were also able to absorb bacteriophage 52a.     

Progress in the Standardization of Stains the Standardization of Eosin and Related Dyes

Decolorizers which are distinctly acidic or basic in their chemical nature give abnormally high decolorization in the Gram stain for bacteria. Acidic substances yield more regular results. Ideally an “inert” decolorizer should be used, but ordinarily such substances will not dissolve the dye or dye-mordant precipitate from the smear. The most practical substances seem to be those so very slightly acidic in character as to be practically inert, such as acetone or alcohol, or a mixture of such substances.     

Electromechanical Interactions in Cell Walls of Gram-Positive Cocci

Isolated cell walls of Staphylococcus aureus and Micrococcus lysodeikticus were found to expand and contract in response to changes in environmental pH and ionic strength. These volume changes, which could amount to as much as a doubling of wall dextran-impermeable volume, were related to changes in electrostatic interactions among fixed, ionized groups in wall polymers, including peptidoglycans. S. aureus walls were structurally more compact in the hydrated state and had a higher maximum charge density than M. lysodeikticus walls. However, they were less responsive to changes in electrostatic interactions, apparently because of less mechanical compliance. In media of nearly neutral pH, S. aureus walls had a net positive charge whereas M. lysodeikticus walls had a net negative charge. These charge differences were reflected in Donnan distributions of mobile ions between wall phases and bulk medium phases. Cell walls of unfractionated cocci also could be made to swell and contract, and wall tonus in intact cells appeared to be set partly by electrostatic interactions and partly by mechanical tension in the elastic structures due to cell turgor pressure. The experimental results led to the conclusions that bacterial cell walls have many of the properties of polyelectrolyte gels and that peptidoglycans are flexible polymers. A reasonable mechanical model for peptidoglycan structure might be a sort of three-dimensional rope ladder with relatively rigid, polysaccharide rungs and relatively flexible polypeptide ropes. Thus, the peptidoglycan network surrounding cocci appeared to be predominantly an elastic restraining structure rather than a rigid shell.     

The Mechanism of the Gram Reaction. II. The Function of Iodine in the Gram Stain

Fifty-five reagents were studied as to their ability to replace iodine in the Gram stain. None gave results as good as iodine. Eight gave usable Gram preparations, and forty-seven gave negative results. Omission of the counterstain resulted in increasing to thirty-three the number of reagents giving differentiation, but this, was not considered a true Gram differentiation. Many oxidizing agents were shown not to be substitutes for iodine; therefore the function of iodine must be more than to serve as an oxidizing agent. Many reagents which formed precipitates with the dye could not replace iodine; therefore factors other than precipitate formation must be involved. However, all agents which were good substitutes for iodine were both good oxidizing and dye precipitating agents. Experiments involving the study of cell membrane permeability showed that Gram-positive cells were less permeable to iodine in alcoholic solution than Gram-negative cells. This difference could not be demonstrated for iodine in aqueous solution. It was concluded that iodine served to form a dye-iodine precipitate (or complex) in the cell. Since Gram-positive cells were less permeable to iodine in alcohol than Gram-negative cells, this resulted in a slower dissolving out of this complex from Gram-positive cells during de-colorization and hence a slower decolorization time. The relative solubilities of dye precipitates in alcohol and in aqueous safranin solution were also indicated as an important factor influencing decolorization. Dyes which formed highly soluble precipitates with iodine could not be used in the Gram stain. It is not proposed that the mechanism of the Gram stain is entirely one of membrane permeability; chemical factors are undoubtedly important and will be discussed in a later paper. However, it is proposed that the chemical and physical factors are closely interrelated in the Gram stain mechanism.