Establishment and development of intestinal microbiota in preterm neonates

Microbial colonization of the infant gut is essential for the development of the intestine and the immune system. The profile of intestinal microbiota in the full-term, vaginally delivered, breast-fed infant is considered as ideally healthy. However, in preterm infants this process is challenging, mainly because of organ immaturity, antibiotics use, and hospital stay. To assist in a proper microbiota development in these infants, a detailed knowledge of the colonization process, and the differences from that of full-term breast-fed infants, is needed. We assessed the establishment of the gut microbiota and its metabolic activity in preterm neonates (n?=?21) during the first 3?months of life and compared it with that of vaginally delivered, exclusively breast-fed full-term infants (n?=?20) using qualitative and quantitative culture-independent methods. Differences in the gut microbiota composition between both groups were observed. Preterm infants showed higher levels of facultative anaerobic microorganisms and reduced levels of strict anaerobes such as Bifidobacterium, Bacteroides, and Atopobium. Short-chain fatty acids concentrations were lower in preterm infants during the first days of life. Alterations occur in the process of microbiota establishment in preterm infants, indicating the need for intervention strategies to counteract them.     

Comparative study of bacterial groups within the human cecal and fecal microbiota

The composition of the human cecal microbiota is poorly known because of sampling difficulties. Samples of cecal fluid from eight subjects were collected via an intestinal tube. Feces were also collected. Total anaerobes, facultative anaerobes, bifidobacteria, and Bacteroides were enumerated by culture methods, and the predominant phylogenetic groups were quantified by molecular hybridization using a set of six rRNA-targeted probes. The numbers of strict anaerobes, bifidobacteria, Bacteroides, and members of the Clostridium coccoides group and Clostridium leptum subgroup were lower in the cecum. Facultative anaerobes represented 25% of total bacteria in the cecum versus 1% in the feces.     

Fecal Microflora in Healthy Persons in a Preindustrial Region

Procedures for quantitating the fecal microflora of man were described. Special attention was given to criteria for characterizing the culturable aerobic, Micro-aerophilic, and anaerobic bacteria. Three groups of healthy persons were studied: wholly breast-fed infants (2 to 4 month-olds), weanlings (1 to 2 year-olds), and adults. In breast-fed children, bifidobacteria predominate and outnumber by one or several logs all other culturable bacteria. The fecal flora of wholly breast-fed infants is "simpler" and more numerous [10(11) to 10(12) per g (wet weight) of feces than that of the adult 10(2) to 10(11) per g]. In the adult, gram-negative anaerobic bacilli (bacteroides) outnumber all other groups by a factor of 1 log or more. Weanlings receiving an adult-type diet, but still breast-fed, showed a flora intermediate between that of the wholly breast-fed infant and that of the adult, but more similar to the latter. Anaerobes always constitute the predominant component of the culturable flora of children and adults and are always found in large numbers under conditions of health. The aerobes are significantly less numerous, and vary widely in their number and in the frequency with which they appear in feces.     

The intestinal microflora during the first weeks of life

Bacterial colonization of the neonatal gastrointestinal tract begins during birth when the neonate comes into contact with the maternal cervical and vaginal flora. In infants delivered by Caesarean section, bacteria colonizing the neonate gastrointestinal tract are provided by the environment. The first bacteria encountered in the majority of healthy infants, are facultative anaerobes, which remain predominant during the first 2 weeks of life. Among them, Staphylococcus, Enterobacteriaceae and Streptococcus were the genera most commonly isolated from the newborn faecal flora at birth. Facultative anaerobic bacteria are followed closely by Bifidobacterium sp. Clostridium perfringens is present within 2 days with an increase incidence in newborns delivered by a Caesarean section. Clostridium perfringens seems to be the precursor for installation of other anaerobic putrefactive bacteria, as Bacteroides and other Clostridium sp. The impact of Caesarean section and the period and quality of hospitalization are mainly implicated in changes of the normal newborn flora. Feeding seems to modulate the colonization pattern. In humans, breast milk plays a role in passive immunization of the neonatal intestine, and contains factors that promote the growth of Bifidobacterium bifidum in the intestinal flora. Formula feeding seems to promote implantation and persistence of Clostridium perfringens, and clearly enhances intestinal colonization of C. difficile in newborns.     

Comparative Study of Bacterial Groups within the Human Cecal and Fecal Microbiota

The composition of the human cecal microbiota is poorly known because of sampling difficulties. Samples of cecal fluid from eight subjects were collected via an intestinal tube. Feces were also collected. Total anaerobes, facultative anaerobes, bifidobacteria, and Bacteroides were enumerated by culture methods, and the predominant phylogenetic groups were quantified by molecular hybridization using a set of six rRNA-targeted probes. The numbers of strict anaerobes, bifidobacteria, Bacteroides, and members of the Clostridium coccoides group and Clostridium leptum subgroup were lower in the cecum. Facultative anaerobes represented 25% of total bacteria in the cecum versus 1% in the feces.     

Determination of mercury and organomercurial resistance in obligate anaerobic bacteria

A methodology for determining the minimum inhibitory concentration of inorganic and organomercurial compounds for obligate anaerobic bacteria is described. A wide variation in the susceptibility of anaerobic clinical and sewage isolates was observed. Isolates of Bacteroides ruminicola and Clostridium perfringens resistant to mercury were examined for their plasmid content and ability to demonstrate inducible resistance. None of the resistant anaerobes contained any plasmids, while resistant facultative isolates from the same source contained several plasmids. In 24 h, resistant strains of clostridia and Bacteroides volatilized 20 and 43% of the 203Hg2+ added to cultures, while Escherichia coli R100 and a sewage isolate of Enterobacter cloacae volatilized 63 and 27%, respectively, of the added 203Hg2+. Attempts to induce mercury resistance in the aerobic isolates were successful, but no induction was seen in the anaerobes. Thus, mercury resistance in these anaerobic isolates was neither inducible nor plasmid mediated.     

草鱼肠道黏膜厌氧细菌的分离与鉴定

研究以草鱼(Ctenopharyngodon idellus)为实验对象, 运用厌氧培养的方法, 研究了饥饿状态下草鱼肠道黏膜固有微生物的类群及其在不同肠段的分布。实验结果显示草鱼前肠、中肠与后肠中细菌的数量分别是3.17×103、1.63×104和1.79×107 cfu/g。研究共分离到274株单菌落, 经16S rRNA鉴定, 分别属于拟杆菌属(Bacteroides spp.)、鲸杆菌属(Cetobacterium spp.)、梭形杆菌属(Fusobacterium spp.)、气单胞菌属(Aeromonas spp.)、希瓦氏菌属(Shewanella spp.)、芽孢杆菌属(Bacillus spp.)、泛菌属(Pantoea spp.)和柠檬酸杆菌属(Citrobacter spp.)8个种类, 其中专性厌氧细菌的数量占9.1%, 兼性厌氧细菌的数量占90.9%。进一步分析发现, 前肠中只分离到兼性厌氧细菌, 中肠与后肠专性厌氧细菌和兼性厌氧细菌都有分布。专性厌氧细菌Bacteroides paurosaccharolyticus和Bacteroides luti在中肠与后肠都有分布, 而Cetobacterium somerae和Fusobacterium ulcerans只在后肠有发现。兼性厌氧细菌是草鱼肠道黏膜的优势菌群, 其中嗜水气单胞菌Aeromonas hydrophila占73.7%。草鱼肠道不同部位固有厌氧微生物组成存在差异, 细菌数量也明显不同, 后肠中具有更高的细菌丰度和多样性。     

Characteristics of bacteria isolated by the anaerobic roll-tube method from cheeses and ground beef.

In this study the methods of Hungate were used to quantitate the anaerobic bacteria present in commercially available ground beef, cheddar cheese, and German hand cheese. Of 235 anaerobic roll-tube isolates from ground beef and German hand cheese, all were facultative anaerobes. Of 213 anaerobic roll-tube isolates from cheddar cheese, 91% were facultative anaerobes and 9% were obligate anaerobes. Using results of biochemical tests, 14 or the 17 obligately anaerobic isolates from cheddar cheese were Propionibacterium acnes, two were strains of Propionibacterium that could not be speciated, and one was tentatively identified as a strain of Streptococcus evolutus. Obligate anaerobes were estimated to be present in the cheddar cheese at a level of about 10(6)/g. The possible significance of these levels of P. acnes in nonsterile foods is discussed.     

Comparison between cultured small-intestinal and fecal microbiotas in beagle dogs

The microbiota of the small intestine is poorly known because of difficulties in sampling. In this study, we examined whether the organisms cultured from the jejunum and feces resemble each other. Small-intestinal fluid samples were collected from 22 beagle dogs with a permanent jejunal fistula in parallel with fecal samples. In addition, corresponding samples from seven of the dogs were collected during a 4-week period (days 4, 10, 14, and 28) to examine the stability of the microbiota. In the jejunal samples, aerobic/facultative and anaerobic bacteria were equally represented, whereas anaerobes dominated in the fecal samples. Despite lower numbers of bacteria in the jejunum (range, 10(2) to 10(6) CFU/g) than in feces (range, 10(8) to 10(11) CFU/g), some microbial groups were more prevalent in the small intestine: staphylococci, 64% versus 36%; nonfermentative gram-negative rods, 27% versus 9%; and yeasts, 27% versus 5%, respectively. In contrast, part of the fecal dominant microbiota (bile-resistant Bacteroides spp., Clostridium hiranonis-like organisms, and lactobacilli) was practically absent in the jejunum. Many species were seldom isolated simultaneously from both sample types, regardless of their overall prevalence. In conclusion, the small intestine contains a few bacterial species at a time with vastly fluctuating counts, opposite to the results obtained for the colon, where the major bacterial groups remain relatively constant over time. Qualitative and quantitative differences between the corresponding jejunal and fecal samples indicate the inability of fecal samples to represent the microbiotas present in the upper gut.     

小鼠盲肠内容物中正常菌群的分离和定量

本文报道了采用厌氧培养技术,从小鼠盲肠内容物中分离到6株严格厌氧和兼性厌氧菌。鉴定为拟杆菌、乳酸杆菌、双歧杆菌、难辨梭菌、粪链球菌和大肠扦菌。它们在小鼠盲肠内容物的正常菌群中占优势,含菌量与国外文献中报告的相似。     

Oral anaerobes cannot survive oxygen stress without interacting with facuItative/aerobic species as a microbial commmunity

D.J. Bradshaw, P.D. Marsh, G.K. Watson and C. Allison. 1997. Anaerobic bacteria are found commonly as components of mixed culture biofilms in many aerated habitats, including the mouth. Previous studies showed that anaerobes could survive in planktonic and biofilm communities in aerated conditions when part of a community including facultative and/or aerobic species, and the numbers and proportions of anaerobic species increased as biofilms aged. When the obligate anaerobes were grown in the absence of aerobic/facultative species, however, they were unable to grow in either the planktonic or biofilm culture. The mean survival times of organisms in the aerated culture containing four anaerobic species varied from around 5 min for Fusobacterium nucleatum and Veillonella dispar , to less than 4 min for Porphyromonas gingivalis and Prevotella nigrescens . In addition, in this culture, the biofilm mode of growth did not provide a haven for these bacteria in the absence of oxygen-consuming species.     

Catalase and Superoxide Dismutase: Distribution, Properties, and Physiological Role in Cells of Strict Anaerobes

This review considers the distribution of the main enzymes of antioxidative defense, superoxide dismutase (SOD) and catalase, in various groups of strictly anaerobic microorganisms: bacteria of the genus Clostridium, Bacteroides, sulfate-reducing and acetogenic bacteria, methanogenic archaea, etc. Molecular and biochemical properties of purified Fe-containing SODs, cambialistic SODs, and heme catalases are presented. The physiological role and origin of the enzymes of antioxidative defense in strict anaerobes are discussed. Physiological responses (induction of SOD and catalase) to factors provoking oxidative stress in the cells of strict anaerobes able to maintain viability under aerobic conditions are also considered.     

The role of encapsulated anaerobic bacteria in synergistic infections

Abstract: The effect of encapsulation on the virulence, survival, and protection of anaerobic bacteria from phagocytosis is reviewed. Support for the importance of encapsulated Gram-negative anaerobic rods ( Bacteroides sp., Prevotella sp. and Porphyromonas sp.), anaerobic and facultative Gram-positive cocci (AFGPC) was provided by their higher recovery rate in oropharyngeal infections, abscesses and blood, compared to their number in the normal flora. The pathogenicity of Bacteroides, Fusobacterium, Clostridium , and AFGPC was studied by inoculating them into mice and observing their ability to induce subcutaneous abscesses. Encapsulated Bacteroides, Fusobacteria , and AFGPC generally induced abscesses, whereas non-encapsulated organisms did not. However, many of the strains that had only a minimal number of encapsulated organisms (< 1%) survived in the abscesses, and they became heavily encapsulated when inoculated with other viable or non-viable encapsulated bacteria. Thereafter, these strains were able to induce abscesses when injected alone. Encapsulated Gram-negative anaerobic rods and AFGPC-induced bacteraemia and translocation, and increased the mortality of the infected animals more often than did the non-encapsulated form of the same strains. As determined by using selective antimicrobial therapy and quantitative cultures of abscesses induced in mice, possession of a capsule generally made Gram-negative anaerobic rods more important than their aerobic counterparts. Synergistic potentials were seen between encapsulated Gram-negative anaerobic rods and all tested aerobic bacteria and most AFGPC, and also between most AFGPC and Pseudomonas aeruginosa or Staphylococcus aureus . These studies demonstrated the importance of encapsulated anaerobes in mixed infections.     

感染根管的厌氧菌培养结果分析

从64只感染根管中的58只根管分离到144株无芽胞厌氧菌,其中类杆菌54株,厌氧性链球菌23株,韦荣氏球菌17株,真杆菌11株,梭杆菌10株,放线菌8株,双岐杆菌2株,消化链球菌和消化球菌19株。40只根管为厌氧菌和兼性厌氧菌或需氧菌混合感染,18只根管和6只根管分别为单独厌氧菌和兼性厌氧菌感染。33只根尖周炎根管分别采集牙髓和根尖渗出物样本进行培养,实验结果表明牙髓样本中革兰氏阳性厌氧杆菌检出率较高,根尖渗出物中以产黑素类杆菌属的细菌检出率较高。根尖周炎和牙槽脓肿患者的感染根管中产黑素类杆菌属的细菌检出率明显高于蜂窝组织炎患者。     

An Evaluation of the Gaspak System in the Culture of Anaerobic Bacteria

S ummary : Comparable results were obtained with a commercially available disposable system for the production of H₂ and CO₂ in an anaerobic jar (the Gaspak system) and with a standard anaerobic jar procedure. Both systems were used with the Baird & Tatlock anaerobic jar and a room temperature catalyst. The test organisms included strict anaerobes such as Clostridium oedematiens type D and Cl. tetani. Comparative tests were also made with Bacteroides species from laboratory stock cultures and with freshly isolated strains of Bacteroides. On occasion, higher recoveries were obtained with the standard system when relatively demanding models were set up but it has limitations, having been developed initially for research purposes. The Gaspak system probably gives more reliable and more reproducible results in a laboratory in which experience with strict anaerobes is limited or sporadic.     

The Influence of Antimicrobial Agents on the Percentage of Tetracycline resistant Bacteria in Faeces of Humans and Animals

The effect of antimicrobial administration on the percentage of tetracycline-resistant facultative and anaerobic bacteria in the intestines of humans and animals was studied. Tetracycline was chosen because it is an antibiotic commonly used both as a feed supplement for animals, and therapeutically for humans and animals. More than 200 faecal specimens of bovine, porcine, equine, canine, feline and human origin were collected into pre-reduced anaerobic media. Ninety-one subjects from groups receiving antimicrobials as feed supplements, therapeutically or with no recent antibiotic exposure were included in the study. Counts of both facultative and anaerobic bacteria were determined from media with and without tetracycline. The percentage of normal faecal specimens harbouring tetracycline-resistant coliforms was 56 for humans. 100 for calves. 100 for pigs. 36 for horses, 90 for dogs and 67 for cats. All samples contained Gram negative anaerobes resistant to tetracycline. Subjects from all species receiving antimicrobials showed higher percentages of tetracycline-resistant coliforms and anaerobes than subjects not receiving antibiotics. Greater increases in the percentage of tetracycline-resistant facultative organisms were noted in subjects which received antibiotics as feed supplements compared with subjects which were given therapeutic doses of antibiotics. Percentages of tetracycline-resistant anaerobes showed the opposite trend with more increase among those subjects receiving therapeutic levels of antimicrobial agents.     

The role of pH in determining the species composition of the human colonic microbiota

The pH of the colonic lumen varies with anatomical site and microbial fermentation of dietary residue. We have investigated the impact of mildly acidic pH, which occurs in the proximal colon, on the growth of different species of human colonic bacteria in pure culture and in the complete microbial community. Growth was determined for 33 representative human colonic bacteria at three initial pH values (approximately 5.5, 6.2 and 6.7) in anaerobic YCFA medium, which includes a mixture of short-chain fatty acids (SCFA) with 0.2% glucose as energy source. Representatives of all eight Bacteroides species tested grew poorly at pH 5.5, as did Escherichia coli , whereas 19 of the 23 Gram-positive anaerobes tested gave growth rates at pH 5.5 that were at least 50% of those at pH 6.7. Growth inhibition of B. thetaiotaomicron at pH 5.5 was increased by the presence of the SCFA mix (33 mM acetate, 9 mM propionate and 1 mM each of iso-valerate, valerate and iso-butyrate). Analysis of amplified 16S rRNA sequences demonstrated a major pH-driven shift within a human faecal bacterial community in a continuous flow fermentor. Bacteroides spp. accounted for 27% of 16S rRNA sequences detected at pH 5.5, but 86% of sequences at pH 6.7. Conversely, butyrate-producing Gram-positive bacteria related to Eubacterium rectale represented 50% of all 16S rRNA sequences at pH 5.5, but were not detected at pH 6.7. Inhibition of the growth of a major group of Gram-negative bacteria at mildly acidic pH apparently creates niches that can be exploited by more low pH-tolerant microorganisms.     

Presence of anaerobic bacteroides in aerobically grown microbial granules

Microbial granules were grown in a column-type sequential aerobic sludge blanket reactor inoculated with activated sludge flocs taken from a wastewater treatment plant and containing a medium with glucose as the main carbon source. The reactor selected for granules that could settle rapidly by employing a short settling time of 2 min. Matured granules with diameters between 2 and 3 mm were examined for anaerobic bacteria as their presence can signal the onset of diffusion limitation problems that can potentially diminish granule stability due to the bacterial production of fermentation gases and organic acids under anaerobic conditions. To detect the anaerobes in the granules, clones were constructed from 16S rRNA PCR amplicons. Two sequence types associated with a strict anaerobe Bacteroides spp. were identified from these clones. Fluorescence in situ hybridization (FISH) followed by confocal laser scanning microscopy (CLSM) demonstrated that cells of Bacteroides spp. were concentrated at a depth of approximately 800 mm below the surface of the granule. Cell enumeration using flow cytometry showed that the percentage of labeled cells of Bacteroides spp. compared to total bacterial cells in the granules was 0.56%. This is the first study to use a suite of culture-independent techniques to report the presence of a defined species of anaerobic bacteria in aerobically grown microbial granules.     

The place of molecular genetic methods in the diagnostics of human pathogenic anaerobic bacteria. A minireview

Anaerobic infections are common and can cause diseases associated with severe morbidity, but are easily overlooked in clinical settings. Both the relatively small number of infections due to exogenous anaerobes and the much larger number of infections involving anaerobic species that are originally members of the normal flora, may lead to a life-threatening situation unless appropriate treatment is instituted. Special laboratory procedures are needed for the isolation, identification and susceptibility testing of this diverse group of bacteria. Since many anaerobes grow more slowly than the facultative or aerobic bacteria, and particularly since clinical specimens yielding anaerobic bacteria commonly contain several organisms and often very complex mixtures of aerobic and anaerobic bacteria, considerable time may elapse before the laboratory is able to provide a final report. Species definition based on phenotypic features is often time-consuming and is not always easy to carry out. Molecular genetic methods may help in the everyday clinical microbiological practice in laboratories dealing with the diagnostics of anaerobic infections. Methods have been introduced for species diagnostics, such as 16S rRNA PCR-RFLP profile determination, which can help to distinguish species of Bacteroides, Prevotella, Actinomyces, etc. that are otherwise difficult to differentiate. The use of DNA-DNA hybridization and the sequencing of special regions of the 16S rRNA have revealed fundamental taxonomic changes among anaerobic bacteria. Some anaerobic bacteria are extremely slow growing or not cultivatable at all. To detect them in special infections involving flora changes due to oral malignancy or periodontitis, for instance, a PCR-based hybridization technique is used. Molecular methods have demonstrated the spread of specific resistance genes among the most important anaerobic bacteria, the members of the Bacteroides genus. Their detection and investigation of the IS elements involved in their expression may facilitate following of the spread of antibiotic resistance among anaerobic bacteria involved in infections and in the normal flora members. Molecular methods (a search for toxin genes and ribotyping) may promote a better understanding of the pathogenic features of some anaerobic infections, such as the nosocomial diarrhoea caused by C. difficile and its spread in the hospital environment and the community. The investigation of toxin production at a molecular level helps in the detection of new toxin types. This mini-review surveys some of the results obtained by our group and others using molecular genetic methods in anaerobic diagnostics.