CORRELATION OF CITRATE UTILIZATION BY MEMBERS OF THE COLON-AEROGENES GROUP WITH OTHER DIFFERENTIAL CHARACTERISTICS AND WITH HABITAT

Evolution of a cross-feeding interaction following a key innovation in a long-term evolution experiment with Escherichia coli

The evolution of a novel trait can profoundly change an organism's effects on its environment, which can in turn affect the further evolution of that organism and any coexisting organisms. We examine these effects and feedbacks following the evolution of a novel function in the Long-Term Evolution Experiment (LTEE) with Escherichia coli. A characteristic feature of E. coli is its inability to grow aerobically on citrate (Cit-). Nonetheless, a Cit+ variant with this capacity evolved in one LTEE population after 31 000 generations. The Cit+ clade then coexisted stably with another clade that retained the ancestral Cit- phenotype. This coexistence was shaped by the evolution of a cross-feeding relationship based on C4-dicarboxylic acids, particularly succinate, fumarate, and malate, that the Cit+ variants release into the medium. Both the Cit- and Cit+ cells evolved to grow on these excreted resources. The evolution of aerobic growth on citrate thus led to a transition from an ecosystem based on a single limiting resource, glucose, to one with at least five resources that were either shared or partitioned between the two coexisting clades. Our findings show that evolutionary novelties can change environmental conditions in ways that facilitate diversity by altering ecosystem structure and the evolutionary trajectories of coexisting lineages.

Vibrio cholerae Alkalizes Its Environment via Citrate Metabolism to Inhibit Enteric Growth In Vitro

Vibrio cholerae is a Gram-negative pathogen, living in constant competition with other bacteria in marine environments and during human infection. One competitive advantage of V. cholerae is the ability to metabolize diverse carbon sources, such as chitin and citrate. We observed that when some V. cholerae strains were grown on a medium with citrate, the medium's chemical composition turned into a hostile alkaline environment for Gram-negative bacteria, such as Escherichia coli and Shigella flexneri. We found that although the ability to exclude competing bacteria was not contingent on exogenous citrate, V. cholerae C6706 citrate metabolism mutants ΔoadA-1, ΔcitE, and ΔcitF were not able to inhibit S. flexneri or E. coli growth. Lastly, we demonstrated that while the V. cholerae C6706-mediated increased medium pH was necessary for the enteric exclusion phenotype, secondary metabolites, such as bicarbonate (protonated to carbonate in the raised pH) from the metabolism of citrate, enhanced the ability to inhibit the growth of E. coli. These data provide a novel example of how V. cholerae outcompetes other Gram-negative bacteria. IMPORTANCE Vibrio cholerae must compete with other bacteria in order to cause disease. Here, we show that V. cholerae creates an alkaline environment, which is able to inhibit the growth of other enteric bacteria. We demonstrate that V. cholerae environmental alkalization is linked to the capacity of the bacteria to metabolize citrate. This behavior could potentially contribute to V. cholerae's ability to colonize the human intestine.

Evolutionary contingency as non-trivial objective probability: Biological evitability and evolutionary trajectories

Contingency-theorists have put forth differing accounts of evolutionary contingency. The bulk of these accounts abstractly refer to certain causal structures in which an evolutionarily contingent outcome is supposedly embedded. For example, an outcome is evolutionarily contingent if it is at the end of a 'path-dependent' or 'causally dependent' causal chain. However, this paper argues that many of these proposals fail to include a desideratum - the notion of biological evitability or that evolutionary outcomes could have been otherwise - that for good theoretical reasons ought to be part of an account of evolutionary contingency. Although an inclusion of this desideratum might seem obvious enough, under some existing accounts, an outcome can be contingent yet inevitable all the same. In my diagnosis of this issue, I develop the idea of trajectory propensity to highlight the fact that there are plausible biological scenarios in which causal structures, alone, fail to exhaustively determine the biological evitability of evolutionary forms. In the second half of the paper, I present two additional desiderata of an account of evolutionary contingency and, subsequently, proffer a novel account of evolutionary contingency as non-trivial objective probability, which overcomes the shortcomings of some previous proposals. According to this outcome-based account, contingency claims are probabilistic statements about an evolutionary outcome's objective probability of evolution within a specifically defined modal range: an outcome, O, is evolutionarily contingent in modal range, R, to the degree of objective probability, P (where P is in between 1 and 0).

Genomic and phenotypic evolution of Escherichia coli in a novel citrate-only resource environment

Evolutionary innovations allow populations to colonize new ecological niches. We previously reported that aerobic growth on citrate (Cit⁺) evolved in an Escherichia coli population during adaptation to a minimal glucose medium containing citrate (DM25). Cit⁺ variants can also grow in citrate-only medium (DM0), a novel environment for E. coli. To study adaptation to this niche, we founded two sets of Cit⁺ populations and evolved them for 2500 generations in DM0 or DM25. The evolved lineages acquired numerous parallel mutations, many mediated by transposable elements. Several also evolved amplifications of regions containing the maeA gene. Unexpectedly, some evolved populations and clones show apparent declines in fitness. We also found evidence of substantial cell death in Cit⁺ clones. Our results thus demonstrate rapid trait refinement and adaptation to the new citrate niche, while also suggesting a recalcitrant mismatch between E. coli physiology and growth on citrate.

Phenotypic characteristics contributing to the enhanced growth of Escherichia coli bloom strains

During bloom events, Escherichia coli cell counts increase to between 10,000 and 100,000 cfu/100 ml of water. The strains responsible for bloom events belong to E. coli phylogenetic groups A and B1, and all have acquired a capsule from Klebsiella. A pan-genome comparison of phylogroup A E. coli revealed that the ferric citrate uptake system (fecIRABCDE) was overrepresented in phylogroup A bloom strains compared with non-bloom E. coli. A series of experiments were carried out to investigate if the capsule together with ferric citrate uptake system could confer a growth rate advantage on E. coli. Capsulated strains had a growth rate advantage regardless of the media composition and the presence/absence of the fec operon, and they had a shorter lag phase compared with capsule-negative strains. The results suggest that the Klebsiella capsule may facilitate nutrient uptake or utilization by a strain. This, together with the protective roles played by the capsule and the shorter lag phase of capsule-positive strains, may explain why it is only capsule-positive strains that produce elevated counts in response to nutrient influx.

Absence of Global Stress Regulation in Escherichia coli Promotes Pathoadaptation and Novel c-di-GMP-dependent Metabolic Capability

Pathoadaptive mutations linked to c-di-GMP signalling were investigated in neonatal meningitis-causing Escherichia coli (NMEC). The results indicated that NMEC strains deficient in RpoS (the global stress regulator) maintained remarkably low levels of c-di-GMP, a major bacterial sessility-motility switch. Deletion of ycgG2, shown here to encode a YcgG allozyme with c-di-GMP phosphodiesterase activity, and the restoration of RpoS led to a decrease in S-fimbriae, robustly produced in artificial urine, hinting that the urinary tract could serve as a habitat for NMEC. We showed that NMEC were skilled in aerobic citrate utilization in the presence of glucose, a property that normally does not exist in E. coli. Our data suggest that this metabolic novelty is a property of extraintestinal pathogenic E. coli since we reconstituted this ability in E. coli UTI89 (a cystitis isolate) via deactivation rpoS; additionally, a set of pyelonephritis E. coli isolates were shown here to aerobically use citrate in the presence of glucose. We found that the main reason for this metabolic capability is RpoS inactivation leading to the production of the citrate transporter CitT, exploited by NMEC for ferric citrate uptake dependent on YcgG2 (an allozyme with c-di-GMP phosphodiesterase activity).

Synthesis of citramalic acid from glycerol by metabolically engineered Escherichia coli

Citramalic acid (citramalate) serves as a five-carbon precursor for the chemical synthesis of methacrylic acid. We compared citramalate and acetate accumulation from glycerol using Escherichia coli strains expressing a modified citramalate synthase gene cimA from Methanococcus jannaschii. These studies revealed that gltA coding citrate synthase, leuC coding 3-isopropylmalate dehydratase, and acetate pathway genes play important roles in elevating citramalate and minimizing acetate formation. Controlled 1.0 L batch experiments confirmed that deletions in all three acetate-production genes (poxB, ackA, and pta) were necessary to reduce acetate formation to less than 1 g/L during citramalate production from 30 g/L glycerol. Fed-batch processes using MEC568/pZE12-cimA (gltA leuC ackA-pta poxB) generated over 31 g/L citramalate and less than 2 g/L acetate from either purified or crude glycerol at yields exceeding 0.50 g citramalate/g glycerol in 132 h. These results hold promise for the viable formation of citramalate from unrefined glycerol.

A case study in evolutionary contingency

Biological evolution is a fundamentally historical phenomenon in which intertwined stochastic and deterministic processes shape lineages with long, continuous histories that exist in a changing world that has a history of its own. The degree to which these characteristics render evolution historically contingent, and evolutionary outcomes thereby unpredictably sensitive to history has been the subject of considerable debate in recent decades. Microbial evolution experiments have proven among the most fruitful means of empirically investigating the issue of historical contingency in evolution. One such experiment is the Escherichia coli Long-Term Evolution Experiment (LTEE), in which twelve populations founded from the same clone of E. coli have evolved in parallel under identical conditions. Aerobic growth on citrate (Cit(+)), a novel trait for E. coli, evolved in one of these populations after more than 30,000 generations. Experimental replays of this population's evolution from various points in its history showed that the Cit(+) trait was historically contingent upon earlier mutations that potentiated the trait by rendering it mutationally accessible. Here I review this case of evolutionary contingency and discuss what it implies about the importance of historical contingency arising from the core processes of evolution.

Rapid Evolution of Citrate Utilization by Escherichia coli by Direct Selection Requires citT and dctA

The isolation of aerobic citrate-utilizing Escherichia coli (Cit(+)) in long-term evolution experiments (LTEE) has been termed a rare, innovative, presumptive speciation event. We hypothesized that direct selection would rapidly yield the same class of E. coli Cit(+) mutants and follow the same genetic trajectory: potentiation, actualization, and refinement. This hypothesis was tested with wild-type E. coli strain B and with K-12 and three K-12 derivatives: an E. coli ΔrpoS::kan mutant (impaired for stationary-phase survival), an E. coli ΔcitT::kan mutant (deleted for the anaerobic citrate/succinate antiporter), and an E. coli ΔdctA::kan mutant (deleted for the aerobic succinate transporter). E. coli underwent adaptation to aerobic citrate metabolism that was readily and repeatedly achieved using minimal medium supplemented with citrate (M9C), M9C with 0.005% glycerol, or M9C with 0.0025% glucose. Forty-six independent E. coli Cit(+) mutants were isolated from all E. coli derivatives except the E. coli ΔcitT::kan mutant. Potentiation/actualization mutations occurred within as few as 12 generations, and refinement mutations occurred within 100 generations. Citrate utilization was confirmed using Simmons, Christensen, and LeMaster Richards citrate media and quantified by mass spectrometry. E. coli Cit(+) mutants grew in clumps and in long incompletely divided chains, a phenotype that was reversible in rich media. Genomic DNA sequencing of four E. coli Cit(+) mutants revealed the required sequence of mutational events leading to a refined Cit(+) mutant. These events showed amplified citT and dctA loci followed by DNA rearrangements consistent with promoter capture events for citT. These mutations were equivalent to the amplification and promoter capture CitT-activating mutations identified in the LTEE.IMPORTANCE E. coli cannot use citrate aerobically. Long-term evolution experiments (LTEE) performed by Blount et al. (Z. D. Blount, J. E. Barrick, C. J. Davidson, and R. E. Lenski, Nature 489:513-518, 2012, http://dx.doi.org/10.1038/nature11514 ) found a single aerobic, citrate-utilizing E. coli strain after 33,000 generations (15 years). This was interpreted as a speciation event. Here we show why it probably was not a speciation event. Using similar media, 46 independent citrate-utilizing mutants were isolated in as few as 12 to 100 generations. Genomic DNA sequencing revealed an amplification of the citT and dctA loci and DNA rearrangements to capture a promoter to express CitT, aerobically. These are members of the same class of mutations identified by the LTEE. We conclude that the rarity of the LTEE mutant was an artifact of the experimental conditions and not a unique evolutionary event. No new genetic information (novel gene function) evolved.

Replaying Evolution to Test the Cause of Extinction of One Ecotype in an Experimentally Evolved Population

In a long-term evolution experiment with Escherichia coli, bacteria in one of twelve populations evolved the ability to consume citrate, a previously unexploited resource in a glucose-limited medium. This innovation led to the frequency-dependent coexistence of citrate-consuming (Cit+) and non-consuming (Cit-) ecotypes, with Cit-bacteria persisting on the exogenously supplied glucose as well as other carbon molecules released by the Cit+ bacteria. After more than 10,000 generations of coexistence, however, the Cit-lineage went extinct; cells with the Cit-phenotype dropped to levels below detection, and the Cit-clade could not be detected by molecular assays based on its unique genotype. We hypothesized that this extinction was a deterministic outcome of evolutionary change within the population, specifically the appearance of a more-fit Cit+ ecotype that competitively excluded the Cit-ecotype. We tested this hypothesis by re-evolving the population from a frozen population sample taken within 500 generations of the extinction and from another sample taken several thousand generations earlier, in each case for 500 generations and with 20-fold replication. To our surprise, the Cit-type did not go extinct in any of these replays, and Cit-cells also persisted in a single replicate that was propagated for 2,500 generations. Even more unexpectedly, we showed that the Cit-ecotype could reinvade the Cit+ population after its extinction. Taken together, these results indicate that the extinction of the Cit-ecotype was not a deterministic outcome driven by competitive exclusion by the Cit+ ecotype. The extinction also cannot be explained by demographic stochasticity alone, as the population size of the Cit-ecotype should have been many thousands of cells even during the daily transfer events. Instead, we infer that the extinction must have been caused by a rare chance event in which some aspect of the experimental conditions was inadvertently perturbed.

Molecular Basis for Bacterial Growth on Citrate or Malonate

Environmental citrate or malonate is degraded by a variety of aerobic or anaerobic bacteria. For selected examples, the genes encoding the specific enzymes of the degradation pathway are described together with the encoded proteins and their catalytic mechanisms. Aerobic bacteria degrade citrate readily by the basic enzyme equipment of the cell if a specific transporter for citrate is available. Anaerobic degradation of citrate in Klebsiella pneumoniae requires the so-called substrate activation module to convert citrate into its thioester with the phosphoribosyl dephospho-CoA prosthetic group of citrate lyase. The citryl thioester is subsequently cleaved into oxaloacetate and the acetyl thioester, from which a new citryl thioester is formed as the turnover continues. The degradation of malonate likewise includes a substrate activation module with a phosphoribosyl dephospho-CoA prosthetic group. The machinery gets ready for turnover after forming the acetyl thioester with the prosthetic group. The acetyl residue is then exchanged by a malonyl residue, which is easily decarboxylated with the regeneration of the acetyl thioester. This equipment suffices for aerobic growth on malonate, since ATP is produced via the oxidation of acetate. Anaerobic growth on citrate or malonate, however, depends on additional enzymes of a so-called energy conservation module. This allows the conversion of decarboxylation energy into an electrochemical gradient of Na+ ions. In citrate-fermenting K. pneumoniae, the Na+ gradient is formed by the oxaloacetate decarboxylase and mainly used to drive the active transport of citrate into the cell. To use this energy source for this purpose is possible, since ATP is generated by substrate phosphorylation in the well-known sequence from pyruvate to acetate. In the malonate-fermenting bacterium Malonomonas rubra, however, no reactions for substrate level phosphorylation are available and the Na+ gradient formed in the malonate decarboxylation reaction must therefore be used as the driving force for ATP synthesis.

Model-driven discovery of underground metabolic functions in Escherichia coli

Enzyme promiscuity toward substrates has been discussed in evolutionary terms as providing the flexibility to adapt to novel environments. In the present work, we describe an approach toward exploring such enzyme promiscuity in the space of a metabolic network. This approach leverages genome-scale models, which have been widely used for predicting growth phenotypes in various environments or following a genetic perturbation; however, these predictions occasionally fail. Failed predictions of gene essentiality offer an opportunity for targeting biological discovery, suggesting the presence of unknown underground pathways stemming from enzymatic cross-reactivity. We demonstrate a workflow that couples constraint-based modeling and bioinformatic tools with KO strain analysis and adaptive laboratory evolution for the purpose of predicting promiscuity at the genome scale. Three cases of genes that are incorrectly predicted as essential in Escherichia coli--aspC, argD, and gltA--are examined, and isozyme functions are uncovered for each to a different extent. Seven isozyme functions based on genetic and transcriptional evidence are suggested between the genes aspC and tyrB, argD and astC, gabT and puuE, and gltA and prpC. This study demonstrates how a targeted model-driven approach to discovery can systematically fill knowledge gaps, characterize underground metabolism, and elucidate regulatory mechanisms of adaptation in response to gene KO perturbations.

Recursive genomewide recombination and sequencing reveals a key refinement step in the evolution of a metabolic innovation in Escherichia coli

Evolutionary innovations often arise from complex genetic and ecological interactions, which can make it challenging to understand retrospectively how a novel trait arose. In a long-term experiment, Escherichia coli gained the ability to use abundant citrate (Cit(+)) in the growth medium after ∼31,500 generations of evolution. Exploiting this previously untapped resource was highly beneficial: later Cit(+) variants achieve a much higher population density in this environment. All Cit(+) individuals share a mutation that activates aerobic expression of the citT citrate transporter, but this mutation confers only an extremely weak Cit(+) phenotype on its own. To determine which of the other >70 mutations in early Cit(+) clones were needed to take full advantage of citrate, we developed a recursive genomewide recombination and sequencing method (REGRES) and performed genetic backcrosses to purge mutations not required for Cit(+) from an evolved strain. We discovered a mutation that increased expression of the dctA C4-dicarboxylate transporter greatly enhanced the Cit(+) phenotype after it evolved. Surprisingly, strains containing just the citT and dctA mutations fully use citrate, indicating that earlier mutations thought to have potentiated the initial evolution of Cit(+) are not required for expression of the refined version of this trait. Instead, this metabolic innovation may be contingent on a genetic background, and possibly ecological context, that enabled citT mutants to persist among competitors long enough to obtain dctA or equivalent mutations that conferred an overwhelming advantage. More generally, refinement of an emergent trait from a rudimentary form may be crucial to its evolutionary success.

Genomic analysis of a key innovation in an experimental Escherichia coli population

Evolutionary novelties have been important in the history of life, but their origins are usually difficult to examine in detail. We previously described the evolution of a novel trait, aerobic citrate utilization (Cit⁺), in an experimental population of Escherichia coli. Here we analyze genome sequences to investigate the history and genetic basis of this trait. At least three distinct clades coexisted for more than 10,000 generations prior to its emergence. The Cit⁺ trait originated in one clade by a tandem duplication that captured an aerobically-expressed promoter for the expression of a previously silent citrate transporter. The clades varied in their propensity to evolve this novel trait, although genotypes able to do so existed in all three clades, implying that multiple potentiating mutations arose during the population’s history. Our findings illustrate the importance of promoter capture and altered gene regulation in mediating the exaptation events that often underlie evolutionary innovations.

Antibacterial activities of gold and silver nanoparticles against Escherichia coli and bacillus Calmette-Guérin

BACKGROUND

Diseases such as tuberculosis (TB) have always had a large impact on human health. Bacillus Calmette-Guérin (BCG) is used as a surrogate for TB during the development of anti-TB drugs. Nanoparticles (NPs) have attracted great interest in drug development. The purpose of this study was to examine the potential of NPs as anti-TB compounds by studying the interacting mechanisms between NPs and bacteria.

RESULTS

We investigated effects of gold and silver NPs on BCG and Escherichia coli. Experimentally, particle size and shape were characterized using transmission electron microscopy (TEM). Different concentrations of NPs were applied in bacterial culture. The growth of E. coli was monitored through colony forming units (CFU). The mechanism of interaction between NPs and bacteria was analyzed through bacterial thin sections followed by TEM and scanning electron microscopy. Antibacterial effects on BCG were observed by recording fluorescent protein expression levels.

CONCLUSIONS

The results suggest NPs have potential applications as anti-TB compounds. The antibacterial effects and mechanism of action for NPs were dependent upon composition and surface modifications.

The classification of coliform bacteria

A study of the biological characters of 1636 cultures of coliform bacteria, isolated from milk and bovine faeces, shows that the coliform group consists of a large number of different types. These types are so closely interlinked in characters and in relations to environment as to justify their inclusion in one genus. Nevertheless, to facilitate the identification of types, the group may be subdivided into subgroups, the Voges-Proskauer, Koser, inositol and indole reactions being reliable and outstanding criteria for this purpose. These characters show almost perfect correlations with various other characters. Thus Voges-Proskauer-negative types have a low CO2to H2ratio and are methyl-red-positive; Voges-Proskauer-positive types have a high CO2to H2ratio, are methyl-red-negative and Koser-positive. Koser-negative types are not highly resistant to brilliant green, are non-capsulated, do not form thick mucoid colonies and are Voges-Proskauer-negative, inositol-negative and indole-positive. Koser-positive types are highly resistant to brilliant green, and with the exception of group 2 and certain members of group 3, are frequently encapsulated and form thick, mucoid colonies. Non-inositol-fermenters are as a rule motile and adonitol-negative. Inositol-fermenters are Koser-positive, adonitol-positive, sucrose-positive and raffinose-positive; are frequently encapsulated and form thick, mucoid colonies; and as a rule are non-motile. Indole-negative types are Koser-positive, while indole-positive types are generally Koser-positive or negative according to whether the inositol reactions are positive or negative.

The Significance of Bact. aerogenes in Water

1.Bact. aerogenesis practically universally present, although in small numbers in the stools of normal adult humans. The stools of one individual, however, repeatedly gave negative results. The organism has also been isolated from the faeces of horse, cow, sheep, pig, dog, cat, wild rabbit, wild rat and wild mouse.

2. The use of modifications of the citrate medium, containing lithium or barium, is useful in the isolation ofBact. aerogeneswhenB. pyocyaneusis abundant.

3.Bact. aerogenespredominates overB. coliin soil, the contamination of which by faecal material was unlikely. TheB. coliisolated from such soil do not show differences by the tests used from typicalfaecalstrains ofB. coli.

4. In the municipal water supply of Liverpool the proportion ofBact. aerogenestoB. coliis relatively high and increases on storage.

5. In water contaminated with faeces, the proportion ofBact. aerogenestoB. coliis relatively low but is rapidly reversed on storage. This is largely due to the death of theB. coli, but may in part be also due to multiplication of theBact. aerogenespresent.

6. Preponderance ofBact. aerogenesoverB. coliin a water supply is indicative of either (a) contact with soil which is not contaminated with fresh faeces, or (b) long past faecal contamination.

7. Preponderance ofBact. aerogenesoverB. coliin a water supply may, for practical purposes, be regarded as an indication of freedom on the part of the water from pathogenic organisms, includingB. typhosusandB. paratyphosusB.

8. The repeated examination of faeces during storage showed a marked increase followed by a gradual decrease in the total number of organisms present. The decrease coincided with an increase in the numbers ofBact.aerogenesrelative to the organisms present. Whether an absolute increase in the numbers ofBact. aerogenesoccurred, was not determined.

9. A plea is made for uniformity among the tests adopted by future workers for the identification of coliform organisms, and an exact statement of the methods employed.

The writer desires to thank Prof. J. M. Beattie for helpful advice throughout the course of the investigation.

SEROLOGICAL RELATIONSHIP BETWEEN PNEUMOCOCCUS TYPE I AND AN ENCAPSULATED STRAIN OF ESCHERICHIA COLI

An encapsulated strain of Escherichia coli has been isolated which is hemolytic, pathogenic for mice, and which has served to illustrate further evidence of heterogenetic specificity. The relationship appears to be limited to the serological reactions between the colon organism and Type I antipneumococcic horse serum. Type I antipneumococcic rabbit serum failed to agglutinate the organism and no reactions occurred with Types II and III antipneumococcic horse serums, normal horse serum, and a variety of other immune horse serums. Serum from rabbits immunized with the colon bacillus agglutinated the homologous organism and precipitated its soluble substance, but failed to cause agglutination of Type I pneumococci or to precipitate Type I pneumococcic polysaccharide. The evidence indicates a connection somewhat analogous to that between Type II pneumococcus and Type B Friedländer's bacillus.

The Distribution and Sanitary Significance of B. coli, B. lactis aerogenes and Intermediate Types of Coliform Bacilli in Water, Soil, Faeces, and Ice-Cream

This section of the work deals with the routine bacteriological examination of 2144 samples of water, of which 1102 contained lactose-fermenting bacilli, 4333 strains being isolated. Twelve strains which liquefied gelatine and 24 which gave anomalous MR and VP reactions were excluded from the coliform group; the remaining 4297 cultures were classified on the basis of the MR, VP, indol, citrate and uric acid tests.

A Study of the Bacillus mucosus capsulatus Group

The group of organisms included in the termB. mucosus capsulatushas continued to intrigue bacteriologists for more than thirty years, mainly on account of the problems of academic interest which arise when any attempt is made to define the characters of the group as a whole or to classify its members into types. Proof that such problems still exist is to be found in current text-books in which certain discrepancies occur regarding the biochemical reactions ascribed to the various members. There is also uncertainty as to the inclusion ofB. lactis aerogenesin the group (Topley and Wilson, 1929; Wilson, 1929). Much of the difficulty arose from the fact that Friedländer's bacillus, one of the first members of the group to be isolated (1883), was studied from a morphological standpoint, while Escherich who describedB. lactis aerogenesin 1886 stressed its biological similarity toB. coli. A chasm was thus created betweenB. lactis aerogenesand Friedländer's bacillus which has not been bridged to the present day, although these organisms must always have resembled, more than they differed from, each other;e.g. Bergey (1929) classifiesB. lactis aerogeneswith coliform types under Bacterieae and places Friedländer's bacillus in the tribeKlebsielleae Trevisan, i.e. encapsulated Gram negative organisms encountered principally in the respiratory tract, whose fermentation reactions are not given in full. Organisms morphologically similar to Friedländer's bacillus were found to be widely distributed, and in 1896 Fricke named the groupB. mucosus capsulatus. There is still little criticism to be made of his general description to the effect that the members were Gram-negative, possessed capsules, showed marked pleomorphism and did not form spores; they grew on a variety of media in a profuse slimy layer, and in gelatin stabs they did not liquefy, but showed the so-called “nail” growth; in addition to this, most of the bacteria classed under this head formed a moderate amount of indole and fermented carbohydrates in solution with production of acid and gas. In an attempt to type members of this group Perkins (1904) admitted that the current knowledge of technique had been almost exhausted in the effort to separate one member from another, but on the basis of certain biochemical differences he was able to distinguish three classes, of which the first was the largest:

The ecology and significance of the different types of coliform bacteria found in water: A review of the literature

1. A review has been made of literature on the ecology of different types of coliform bacteria. The main object of the review has been to consider whether there is evidence to support the view thatBact. aerogenesand the intermediate types live normally on plants or in the soil and not in the intestines of man and other animals.

2. There is ample evidence thatBact. coliis by far the most common type of coliform in normal human faeces. On the other hand, there is evidence thatBact. aerogenesor intermediate types are usually present in faeces, may sometimes be present in greater numbers thanBact. coli, and on rare occasions may be the only type present. Both quantitatively and qualitatively the coliform flora of the faeces of an individual person may vary from day to day. There is insufficient evidence on the numbers ofBact. aerogenesand intermediate types in faeces to justify any more definite statement, but limited data suggest that such types may be absent or may be present in numbers of the order of a million per gram.

3. When fresh faeces are stored there is first a multiplication of such bacteria as will grow on ordinary laboratory media, including the coliform types. The rate of multiplication, as with the flora of soil, water, and milk, increases with an increase in the incubation temperature to 37° C, but the period of multiplication becomes shorter. In the literature consulted no evidence can be found to show which groups are prominent in the multiplication. Results are in agreement that on further storage the ratio of the numbers ofBact. colito those ofBact. aerogenesand intermediates decreases, the typicalBact. coliflora dying off more rapidly than other conform types. The rapidity of decrease appears to depend partially at least upon the temperature of the environment, and the decrease may be accelerated by intense sunlight.

4. In urine from patients suffering from genito-urinary infections the dominant types of coliform are usually eitherBact. aerogenesor intermediates. No data on the number of such organisms in urine have been obtained from the works consulted.

5. There is no-evidence that coliform bacteria multiply on fresh grasses or grains. Few quantitative data on this question have been found. In some of the older work it is doubtful whether a large proportion of the cultures isolated were actually coliform bacteria or whether they were species of other genera capable of fermenting lactose at 30° C. but not at 37° C. In the decomposition of grasses and legumes during ensilage, a process involving a considerable increase in temperature, it would appear that multiplication of conform bacteria may take place and counts may for a time equal those found in fresh faeces. No indication has been found that this multiplication is confined toBact. aerogenesor intermediates.

6. Most workers who have studied the coliform bacteria in soil have ignored the quantitative aspects and no counts at intervals over long periods of coliform bacteria in any undisturbed soil appear to have been made. No evidence of any multiplication of coliform bacteria in soil has been found. Results, however, are in agreement that where pollution of the soil by animal excreta has taken place, the heavier the pollution the greater is the number of coliform bacteria; soils relatively free from human or other animal pollution either contain no coliform bacteria or only small numbers. It is generally agreed that the ratio of the numbers ofBact. colito those ofBact. aerogenesand intermediates decreases with the increase of time which has elapsed since pollution of the soil. This change is similar to that which occurs in faeces during storage.

7. There is insufficient evidence to justify the definite statement often made thatBact. aerogenesand intermediates are normal inhabitants of soils, grasses, and grains.

The Fermentation of Salts of Organic Acids as an aid to the differentiation of Bacterial Types

(1) Reaction changes and production of gas in organic salt media are not sufficiently constant to form a reliable diagnostic criterion for the differentiation of bacterial types.

(2) The enhancement or inhibition of bacterial growth in such media in the majority of cases bears a direct relationship to the utilisation of the salt by the organism. This furnishes a useful differential test for certain organisms when citrates are used, but cannot be applied in the cases of all salts.

(3) The bacterial decomposition of the salts of those organic acids which form insoluble lead salts can be clearly demonstrated by the addition of suitable quantities of a solution of lead acetate to the culture.

(4) By the use of six organic salts, seven different groupings of the common Salmonella types can be obtained, whereas the sugar reactions have, up to the present, yielded only four different groupings.

(5) Regarding other groups of bacteria, the organic salts form an easy means of distinguishing between pathogenic and certain non-pathogenic vibrios, and between certain of the members of thecoli-aërogenesgroup, and also betweenB. diphtheriaeand Hofmann's bacillus, as well as betweenB. malleiandB. whitmori.

(6) The six organic salts employed in this test are relatively inexpensive, will stand sterilising by autoclave, and can be obtained with certainty in a state of purity much more readily than the rarer “sugars.”

(7) The nature of the decomposition products of citric acid has been fully examined in the case ofBacillus suipestifer; it has been shown that the products are acetic acid, carbon dioxide and succinic acid, and a simple explanation of the mechanism of this reaction is put forward. In the case of fumaric acid a preliminary examination shows that the acid is converted into succinic acid probably by direct reduction. Maleic acid appears to behave in an analogous manner to fumaric acid. Further work on these acids is in progress.

(8) A large number of organic acid salts have been tried, but only the six suggested have given useful results. It appears that simple aliphatic monobasic and dibasic acids, with the exception of formic acid, are not decomposed readily by the bacteria investigated, and this is also true of monohydroxycarboxylic acids. Readiness of decomposition is first shown by the dihydroxydicarboxylic acids (tartaric acids), and appears to be at its best in the hydroxytricarboxylic acid (citric acid).

(9) While organic salt fermentation tests have been found particularly useful in the cases of the bacterial groups dealt with in this paper, they cannot be substituted for the “sugar reactions” in general use.

The Classification of the Colon-Aerogenes Group of Bacteria in Relation to their Habitat and its Application to the Sanitary Examination of Water Supplies in the Tropics and in Temperate Climates: A Comparative Study of 2500 Cultures

(1) The ”lactose+ indol+” index as employed in temperate climate is usually an adequate criterion of water purity.

(2) Where a positive test does not appear to be substantiated by the sanitary findings, a further differentiation of the organisms isolated becomes necessary. The methyl-red and citrate tests have been found to supply that differentiation in a satisfactory manner.

(3) In the Tropics, false positive “lactose-indol” tests are commonly encountered, owing to the presence in large numbers in soil and water of organisms derived from sources other than recently excreted faeces.

(4) In the Tropics, the lactose-indol test should always be confirmed by the methyl-red, citrate and saccharose tests or such other reactions or groups of reactions as may be found by a local survey to be applicable.

My very grateful thanks are due to Dr P. A. Clearkin, Deputy Director of Laboratory Service, Tanganyika Territory, for his ready advice and constant encouragement; and also to Mr W. Whitley, Analytical Chemist, who performed a chemical analysis of the water samples, and very kindly gave me the benefit of his opinion on them. In addition I have to thank Dr R. R. Scott, Medical Officer of Health, and the Staff of the Health Office, Dar-es-Salaam, who have rendered every facility in the choice and collection of samples. It is a pleasure to be able to record once more my indebtedness to Prof. Bigger, of Trinity College, Dublin, whose fund of valuable suggestions and kindly criticism has been ever at my disposal.

58. Coliform Organisms in Milk and Bovine Faeces

The lactose-fermenting coliform organisms in milk and dung have been investigated.

A large proportion of those recovered from raw milk by direct plating proved to be of theBact. aerogenestype and a number of “intermediates” was also present.

In dung faecalBact. colilargely predominated, the proportion ofBact. aerogenesbeing very small.

If the implication of these experiments be accepted it is possible that many of the coliform types found in milk are derived, not from faeces, in which the proportion ofaerogenesis small, but from external sources, such as contaminated utensils, and from food-stuffs.

120. The Types Of Coliform Bacteria in Bovine Faeces

1. In an examination of the coliform flora of 114 specimens of bovine faeces, 342 cultures of coliform bacteria were isolated by the ordinary methods.Of the cultures obtained, 330 (or 96·4 per cent.) were typicalBact. coliandonly twelve (or 3·5 per cent.) were ofBact. aerogenes, Bact. cloacaeand other Koser-positive types. The most prevalent types ofBact. coliwere MacConkey's B, No. 71 orBact. coli communior(185 cultures or 56 per cent.), MacConkey's B, No. 34, orBact. coli communisEscherich (sixty-nine cultures or 20·9 per cent.), and MacConkey's B, No. 1 (twenty-three cultures or 6·9 per cent.).

Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli

The role of historical contingency in evolution has been much debated, but rarely tested. Twelve initially identical populations of Escherichia coli were founded in 1988 to investigate this issue. They have since evolved in a glucose-limited medium that also contains citrate, which E. coli cannot use as a carbon source under oxic conditions. No population evolved the capacity to exploit citrate for >30,000 generations, although each population tested billions of mutations. A citrate-using (Cit+) variant finally evolved in one population by 31,500 generations, causing an increase in population size and diversity. The long-delayed and unique evolution of this function might indicate the involvement of some extremely rare mutation. Alternately, it may involve an ordinary mutation, but one whose physical occurrence or phenotypic expression is contingent on prior mutations in that population. We tested these hypotheses in experiments that "replayed" evolution from different points in that population's history. We observed no Cit+ mutants among 8.4 x 10(12) ancestral cells, nor among 9 x 10(12) cells from 60 clones sampled in the first 15,000 generations. However, we observed a significantly greater tendency for later clones to evolve Cit+, indicating that some potentiating mutation arose by 20,000 generations. This potentiating change increased the mutation rate to Cit+ but did not cause generalized hypermutability. Thus, the evolution of this phenotype was contingent on the particular history of that population. More generally, we suggest that historical contingency is especially important when it facilitates the evolution of key innovations that are not easily evolved by gradual, cumulative selection.

The differentiation of Enterobacteriaceae infecting the urinary tract: A study in male paraplegics

Methods adopted in a routine bacteriology laboratory for the rapid identification of Enterobacteriaceae isolated from urine are described. The incidence of various bacteria causing infection in paraplegics after catheterization of the bladder is recorded, Klebsiella accounting for the majority of infections caused by lactose fermenters and Providence for the majority of ;paracolon' infections. The importance of these bacteria in cross-infection is discussed.