Early-life gut dysbiosis linked to juvenile mortality in ostriches.

BACKGROUND: Imbalances in the gut microbial community (dysbiosis) of vertebrates have been associated with several gastrointestinal and autoimmune diseases. However, it is unclear which taxa are associated with gut dysbiosis, and if particular gut regions or specific time periods during ontogeny are more susceptible. We also know very little of this process in non-model organisms, despite an increasing realization of the general importance of gut microbiota for health. METHODS: Here, we examine the changes that occur in the microbiome during dysbiosis in different parts of the gastrointestinal tract in a long-lived bird with high juvenile mortality, the ostrich (Struthio camelus). We evaluated the 16S rRNA gene composition of the ileum, cecum, and colon of 68 individuals that died of suspected enterocolitis during the first 3 months of life (diseased individuals), and of 50 healthy individuals that were euthanized as age-matched controls. We combined these data with longitudinal environmental and fecal sampling to identify potential sources of pathogenic bacteria and to unravel at which stage of development dysbiosis-associated bacteria emerge. RESULTS: Diseased individuals had drastically lower microbial alpha diversity and differed substantially in their microbial beta diversity from control individuals in all three regions of the gastrointestinal tract. The clear relationship between low diversity and disease was consistent across all ages in the ileum, but decreased with age in the cecum and colon. Several taxa were associated with mortality (Enterobacteriaceae, Peptostreptococcaceae, Porphyromonadaceae, Clostridium), while others were associated with health (Lachnospiraceae, Ruminococcaceae, Erysipelotrichaceae, Turicibacter, Roseburia). Environmental samples showed no evidence of dysbiosis-associated bacteria being present in either the food, water, or soil substrate. Instead, the repeated fecal sampling showed that pathobionts were already present shortly after hatching and proliferated in individuals with low microbial diversity, resulting in high mortality several weeks later. CONCLUSIONS: Identifying the origins of pathobionts in neonates and the factors that subsequently influence the establishment of diverse gut microbiota may be key to understanding dysbiosis and host development. Video Abstract.

Prevalence of Campylobacter and Arcobacter Species in Ostriches from Oudtshoorn, South Africa.

ABSTRACT: Cloacal swabs were obtained from live ostriches reared on 30 different farms situated in South Africa (Oudtshoorn) during the period of June 2018 to July 2019 to determine the prevalence of Campylobacter and Arcobacter species. PCR (n = 168 pooled cloacal swabs), the Cape Town protocol (n = 836 cloacal swabs), International Organization for Standardization ISO 10272-1:2006 (n = 836 cloacal swabs), and a selective Arcobacter spp. method (n = 415 cloacal swabs) were used for detection. PCR determined an average prevalence of 24.63% for species belonging to the Campylobacteraceae family. The ISO 10272-1:2006 method determined a Campylobacter spp. prevalence level of 16.83%, while the Cape Town protocol could not detect Campylobacter spp. For Arcobacter spp., a prevalence of 18.80 and 39.14% was determined with the Cape Town protocol and the selective Arcobacter spp. method, respectively. Results showed that prevalence levels could be influenced by season, the source of water, and the presence of wild water birds. Higher prevalence levels for Campylobacter spp. (23.38%) and Arcobacter spp. (68%) were detected in ostriches sampled during spring and autumn, respectively. Higher prevalence levels for Campylobacter spp. (25.23%) and Arcobacter spp. (44.50%) were detected in ostriches reared on farms that made use of borehole water. Higher prevalence levels for Arcobacter spp. (44.38%) were seen in ostriches reared on farms with wild water birds. This research shows that ostriches from South Africa can be considered as potential carriers of species belonging to the Campylobacteraceae family.

Mycoplasma nasistruthionis sp. nov. and Mycoplasma struthionis sp. nov. isolated from ostriches with respiratory disease.

Twelve Mycoplasma (M.) strains isolated from the nose, the trachea, and the lung of ostriches (Struthio camelus) displaying respiratory disease were investigated. Analysis of 16S rRNA gene sequences placed five of these strains within the M. synoviae cluster, and seven strains within the M. hominis cluster of genus Mycoplasma, which was further confirmed by analyses of the 16S-23S rRNA intergenic spacer region, and partial rpoB gene and amino acid sequences. Genomic information as well as phenotypic features obtained by matrix-assisted laser desorption ionization time of flight (MALDI-ToF) mass spectrometry analysis and serological reactions indicated that the strains examined are representatives of two hitherto unclassified species of genus Mycoplasma, for which the names Mycoplasma nasistruthionis sp. nov., with type strain 2F1AT (= ATCC BAA-1893T = DSM 22456T), and Mycoplasma struthionis sp. nov., with type strain 237IAT (= ATCC BAA-1890T = DSM 22453T), are proposed.

Major shifts in gut microbiota during development and its relationship to growth in ostriches.

The development of gut microbiota during ontogeny is emerging as an important process influencing physiology, immunity and fitness in vertebrates. However, knowledge of how bacteria colonize the juvenile gut, how this is influenced by changes in the diversity of gut bacteria and to what extent this influences host fitness, particularly in nonmodel organisms, is lacking. Here we used 16S rRNA gene sequencing to describe the successional development of the faecal microbiome in ostriches (Struthio camelus, n = 66, repeatedly sampled) over the first 3 months of life and its relationship to growth. We found a gradual increase in microbial diversity with age that involved multiple colonization and extinction events and a major taxonomic shift in bacteria that coincided with the cessation of yolk absorption. Comparisons with the microbiota of adults (n = 5) revealed that the chicks became more similar in their microbial diversity and composition to adults as they aged. There was a five-fold difference in juvenile growth during development, and growth during the first week of age was strongly positively correlated with the abundance of the genus Bacteroides and negatively correlated with Akkermansia. After the first week, the abundances of six phylogenetically diverse families (Peptococcaceae, S24-7, Verrucomicrobiae, Anaeroplasmataceae, Streptococcaceae, Methanobacteriaceae) were associated with subsequent reductions in chick growth in an age-specific and transient manner. These results have broad implications for our understanding of the development of gut microbiota and its associations with animal growth.

Measuring the gut microbiome in birds: Comparison of faecal and cloacal sampling.

The gut microbiomes of birds and other animals are increasingly being studied in ecological and evolutionary contexts. Numerous studies on birds and reptiles have made inferences about gut microbiota using cloacal sampling; however, it is not known whether the bacterial community of the cloaca provides an accurate representation of the gut microbiome. We examined the accuracy with which cloacal swabs and faecal samples measure the microbiota in three different parts of the gastrointestinal tract (ileum, caecum, and colon) using a case study on juvenile ostriches, Struthio camelus, and high-throughput 16S rRNA sequencing. We found that faeces were significantly better than cloacal swabs in representing the bacterial community of the colon. Cloacal samples had a higher abundance of Gammaproteobacteria and fewer Clostridia relative to the gut and faecal samples. However, both faecal and cloacal samples were poor representatives of the microbial communities in the caecum and ileum. Furthermore, the accuracy of each sampling method in measuring the abundance of different bacterial taxa was highly variable: Bacteroidetes was the most highly correlated phylum between all three gut sections and both methods, whereas Actinobacteria, for example, was only strongly correlated between faecal and colon samples. Based on our results, we recommend sampling faeces, whenever possible, as this sample type provides the most accurate assessment of the colon microbiome. The fact that neither sampling technique accurately portrayed the bacterial community of the ileum nor the caecum illustrates the difficulty in noninvasively monitoring gut bacteria located further up in the gastrointestinal tract. These results have important implications for the interpretation of avian gut microbiome studies.

The effect of dietary energy and protein levels on body weight, size, and microflora of ostrich chicks.

The aim of this study was to evaluate the effect of different dietary energy and protein supplements on performance, weekly body sizes or body frame size, and microbiota of ostrich chicks during 2-9 weeks of age. Two metabolic energy levels of 2400 and 2600 kcal/kg live weight and three protein levels of 20, 22, and 24% were used. A total of 36 ostrich chickens (Struthio camelus) of the blue and black African breed were used. Body weight, 12 body measurements (i.e., circumference of the head, neck, breast, abdomen, thigh, body height, length of tail, list the other 5 here) and excretion of microbial population (Escherichia coli, Coliforms bacteria, and Lactobacillus bacteria) were measured. Mean body weight in each week of the experiment was generally the lowest when chicks were offered 2600 kcal/kg dietary energy and 24% protein. Of the 12 body measurements, the breast, abdomen, and thigh circumference and also body length were greater at the lower energy (2400 kcal/kg) and higher protein (24%) levels. Total Aerobic bacteria excretion was generally lower in response to the diet containing the higher level of energy. We conclude that ostrich chickens during 2-9 weeks of age can grow on diets that contain lower energy levels.

Sensitivity to Enterocins of Biogenic Amine-Producing Faecal Enterococci from Ostriches and Pheasants.

Enterococci are widespread bacteria forming the third largest genus among lactic acid bacteria. Some possess probiotic properties or they can produce beneficial proteinaceous antimicrobial substances called enterocins. On the other hand, some enterococci produce biogenic amines (BAs), so this study is focused on the sensitivity to enterocins of biogenic amine-producing faecal enterococci from ostriches and pheasants. Altogether, 60 enterococci isolated from faeces of ostriches and pheasants were tested for production of BAs. This target of the identified enterococci involved 46 strains selected from 140 ostriches and 17 from 60 pheasants involving the species Enterococcus hirae, E. faecium, E. faecalis, and E. mundtii. Although BAs histamine, cadaverine, putrescine, and tryptamine were not detected in the enterococci tested, in general high BA production by the tested enterococci was noted. The species E. hirae formed the majority of the enterococcal strains from ostrichs faeces (34 strains). High production of tyramine (TYM) was measured with an average amount of 958.16 ± 28.18 mg/ml. Among the enterococci from pheasants, the highest was production of TYM compared to phenylethylamine, spermidine, and spermine. Enterococci featured high BA production; however, they were sensitive to seven enterocins with inhibition activity ranging from 100 up to 25,600 AU/ml.

Effect of lantibiotic gallidermin against biogenic amine-producing faecal staphylococci from ostriches and pheasants.

In ostriches and pheasants, there is still limited information relating to staphylococci and their properties. Biogenic amines (BAs) are nitrogenous low-molecular-weight substances with biological functions in animals, plants and microorganisms. In this study, we focused on BA production by targeted faecal staphylococci from ostriches and pheasants and their sensitivity to lantibiotic bacteriocin gallidermin. Gallidermin belongs in a group of polycyclic proteinaceous antimicrobial substances. Thirty-six faecal staphylococci (24 strains from 140 ostriches, 12 from 60 pheasants) comprising different species were tested. Staphylococci from ostriches and pheasants did not produce tryptamine-TRYP, putrescine-PUT, cadaverine-CAD or histamine-HIS. Production of tyramine-TYM, phenylethylamine-PEA was high or very high (100-1000 mg/L). Production of spermine-SPM and spermidine-SPD by staphylococci was very low or low although in the case of staphylococci from pheasants medium production of SPM was found. Because of the risk posed by BAs for consumers, the control of BA-producing bacteria is important from the points of view not only of safety assessment of food-producing animals but also of human health safety. The sensitivity to gallidermin in biogenic amine-producing staphylococci from ostriches and pheasants detected here is the most promising indication for further application of gallidermin for veterinary purposes. The novelty of our study lies in testing the ability of faecal staphylococci from ostriches and pheasants to produce BAs and in their treatment with gallidermin which has so far not been tested in this way.

Staphylococci Related to Farm Ostriches and Their Sensitivity to Enterocins.

In Slovakia, ostriches are reared mainly for their meat. There is still limited information related to microflora of ostriches, including staphylococci. Knowing the composition of microflora is very important for the recognition of potential pathogenic agents. Recently, a frequent problem in animals is the occurrence of bacteria resistant to antibiotics. The aim of this study was to detect staphylococcal species in feces of farm ostriches and to test their sensitivity to antibiotics and enterocins. Altogether 140 ostriches from three age groups were sampled (n = 18, faecal mixture samples from each group) on a farm in Slovakia or on Slovak farm. From 54 fecal samples, the staphylococcal count reached an average 4. 3 ± 0. 63 (log10) CFU/g. Twenty-four lactic acid producing strains were taxonomically classified to eight species of the genus Staphylococcus: Staphylococcus equorum, S. xylosus, S. epidermidis, S. haemolyticus, S. cohnii, S. succinus, S. warneri, and S. hominis. Strains were evaluated by secure probable species identification/probable species identification (score value up to 2.299) confirmed also by phenotypization. Most strains were sensitive to antibiotics. Four strains (S. haemolyticus SHae 111, S. haemolyticus SHAe 371, S. xylosus SX 2133, and S. warneri SW 292) were resistant to methicillin but sensitive to six or five of the seven enterocins tested (inhibitory activity 200-12,800 AU/mL). S. warneri SW 292 was sensitive to all enterocins (activity up to 12,800 AU/mL).

Enterococci isolated from farm ostriches and their relation to enterocins.

The present study focuses on the detection of enterococci in ostrich faeces. Forty-six bacterial colonies from 140 ostriches were identified at the species level using the MALDI-TOF MS identification system. According to the score value evaluation, they were allotted to the species Enterococcus hirae, Enterococcus faecium and Enterococcus mundtii confirmed also by phenotypic testing. Dominated species E. hirae (34 strains) were submitted to more detailed testing. Those strains E. hirae produced either no or only slight amount of the enzymes related to disorders (N-acetyl-ß-glucosaminidase, ß-glucuronidase, α-chymotrypsin, trypsin). Most of the strains were not hemolytic. They did not harbour the hiracin-producing gene. Five E. hirae strains harboured virulence factor gene gelE; however, they were phenotypically gelatinase negative. They also harboured other virulence factor genes such as esp, efaAfm and ccf. E. hirae strains were mostly sensitive to antibiotics and those resistant at least to one antibiotic were sensitive to enterocins (200-25,600 AU/mL). This study represents original and novel results concerning the enterococcal microflora in ostriches; enterococci in ostriches have not been described in detail up to now; sensitivity to enterocins of E. hirae strains harbouring virulence factor genes to enterocins is also new.

Use of bacteriocin-producing, probiotic strain Enterococcus faecium AL41 to control intestinal microbiota in farm ostriches.

Probiotic enterococci can produce bacteriocins. Enterococcus faecium AL41 is an Enterocin M-producing, probiotic strain which has previously shown beneficial effect in broiler chickens. In this study, it was used to control intestinal microbiota in farm ostriches in a 42-day experiment with an experimental group (EG, 40 ostriches) and a control group (CG, 46). In addition to feed mixture, the ostriches in EG received Ent. faecium AL41 (10(9) CFU ml(-1); by rifampicin-marked variant) 400 µl per animal per day in their drinking water for 21 days. Sampling was carried out at the start of the experiment (at day 0/1), at day 21 (after 21 days of AL41 application) and at day 42 (21 days after AL41 cessation). Faeces (mixture, n = 6) were treated using the standard microbiological dilution method and cultivated on selective media (ISO). The highest count of AL41 was found at day 42. Its identity was confirmed with PCR and Maldi-Tof. The ostriches were free of Salmonella and Campylobacter cells. At day 21, antimicrobial effect was demonstrated by significant reduction in coagulase-positive and negative staphylococci in EG compared to CG (P < 0·001) and coliforms, Enterobacteria and Pseudomonas-like bacteria (P < 0·001). We conclude that AL41 can be used to control intestinal microbiota in farm ostriches. Significance and impact of the study: Ostriches are excellent for high intensity farming in a wide range of climates, requiring only limited space and giving high yields per hectare. They are reared mainly for their meat. Although adult birds possess quite good immunity, young birds can be threatened by spoilage bacteria, especially when they are transferred from the nests to the farm area. Based on our previous results related to the beneficial effect of bacteriocin-producing, probiotic strain Enterococcus faecium AL41 in poultry or rabbits, we decided to test its ability to control intestinal microbiota in farming ostriches which has never been tested previously.

Genome sequence of Lactobacillus ingluviei, a bacterium associated with weight gain in animals.

We report the draft genome sequence of Lactobacillus ingluviei strain Autruche 4 (CSURP209) isolated from an ostrich. L. ingluviei is associated with weight gain in mice. This genome sequence may help us understand the obesity-induced mechanisms of intestinal bacteria.

Diversity of the formyltetrahydrofolate synthetase (FTHFS) gene in the proximal and mid ostrich colon.

We analysed fragments of the formyltetrahydrofolate synthetase (FTHFS) gene, which encodes a key enzyme in reductive acetogenesis, from the bacterial flora in the proximal (PC) and mid (MC) colon of three ostriches to assess and compare bacterial diversity in this organ. Two clone libraries of FTHFS fragments were constructed from DNA extracted from digesta of the PC and MC, and a total of 46 cloned sequences were analysed from each library. A wide variety of FTHFS sequences were recovered. The coverage of the PC and MC libraries was 90.0% and 83.3%, respectively. Shannon-Wiener index (H') and Chao1 of the MC library were higher than those of PC library. The sequences from each library were classified into 15 operational taxonomic units (OTUs) and clusters. Only four OTUs in cluster I were distantly related to known acetogens from human feces and rumen, suggesting the presence of the novel acetogens. Phylogenetic analysis suggests that composition of FTHFS sequences differs for the PC and MC.

LT-IIc, a new member of the type II heat-labile enterotoxin family encoded by an Escherichia coli strain obtained from a nonmammalian host.

Two families of bacterial heat-labile enterotoxins (HLTs) have been described: the type I HLTs are comprised of cholera toxin (CT) of Vibrio cholerae, LT-I of Escherichia coli, and several related HLTs; the type II HLTs are comprised of LT-IIa and LT-IIb. Herein, we report LT-IIc, a new type II HLT encoded from an enterotoxigenic E. coli (ETEC) strain isolated from an avian host. Using a mouse Y1 adrenal cell bioassay, LT-IIc was shown to be less cytotoxic than CT, LT-IIa, or LT-IIb. Cytotoxicity of LT-IIc was partially neutralized by antisera recognizing LT-IIa or LT-IIb but not by anti-CT antiserum. Genes encoding putative A polypeptide and B polypeptides of LT-IIc were arranged in an operon which was flanked by potential prophage sequences. Analysis of the nucleotide and predicted amino acid sequences demonstrated that the A polypeptide of LT-IIc has moderate homology to the A polypeptides of CT and LT-I and high homology to the A polypeptides of LT-IIa and LT-IIb. The B polypeptide of LT-IIc exhibited no significant homology to the B polypeptides of CT and LT-I and only moderate homology to the B polypeptides of LT-IIa and LT-IIb. The binding pattern of LT-IIc for gangliosides was distinctive from that of either LT-IIa or LT-IIb. The data suggest that other types of the type II HLT subfamily are circulating in the environment and that host specificity of type II HLT is likely governed by changes in the B polypeptide which mediate binding to receptors.

Characterization of vancomycin-resistant enterococci isolated from fecal samples of ostriches by molecular methods.

The aim of this study was to estimate the occurrence of vancomycin-resistant enterococci (VRE) in fecal samples of ostriches from a farm of Southern Portugal, the mechanisms implicated, and the associated virulence factors, 13 years after the banning of the glycopeptide avoparcin as animal growth promoter in the European Union. Fifty-four fecal samples of ostriches were inoculated in Slanetz-Bartley supplemented with vancomycin (4 microg/mL) for VRE recovery. Susceptibility to 11 antibiotics was performed by disk-diffusion agar method in recovered VRE isolates. The mechanism of resistance to vancomycin and to other antibiotics and the presence of the esp and hyl virulence genes were determined by polymerase chain reaction and sequencing. VRE were detected in 7 of the 54 ostrich fecal samples (13%); Enterococcus durans isolates with the vanA genotype were found in 4 of the 54 fecal samples (7.4%), and Enterococcus gallinarum with the intrinsic vanC1 genotype in the remaining three VRE-positive samples. All vanA-containing E. durans isolates showed resistance to tetracycline and erythromycin, and one of them also to ciprofloxacin; they harbored the erm(B) and tet(M) genes, as well as the specific sequences of Tn916 and Tn5397 transposons, but not the esp or hyl virulence genes. Two of the three vanC1 isolates showed resistance to tetracycline [with the tet(M) gene] and one to erythromycin [with the erm(B) gene], and all three contained the hyl gene. Fecal samples of ostriches represent a reservoir of vanA-containing enterococci that could be transmitted to humans through the food chain.

Use of lysozyme, nisin, and EDTA combined treatments for maintaining quality of packed ostrich patties.

UNLABELLED: The antimicrobial effectiveness of lysozyme, nisin, and ethylene diamine tetraacetic acid (EDTA) combination treatments (Mix(1): 250 ppm lysozyme, 250 ppm nisin, 5 mM EDTA; Mix(2): 500 ppm lysozyme, 500 ppm nisin, 5 mM EDTA) on bacterial growth of ostrich patties packaged in air, vacuum, and 2 different modified atmospheres (MAP(1): 80% O(2), 20% CO(2); MAP(2): 5% O(2), 30% CO(2), 65% N(2)) was evaluated. Moreover, the lipid oxidation was evaluated as well as color and sensory characteristics. The growth of total viable counts and lactic acid bacteria were strongly inhibited by the antimicrobial treatments in all the running time (Inhibition Index >97%) whereas for Enterobacteriaceae and Pseudomonas spp. lower inhibition indices from 12% to about 28% were observed. The lipid oxidation was more pronounced in the control respect to the treated meat patties. Moreover, the mixture at low concentration of lysozyme and nisin showed the best antioxidative effect. High concentrations of lysozyme and nisin showed the greatest color loss. Also, off-odors for the untreated patties developed faster than the treated samples. PRACTICAL APPLICATION: Great interest is developing in food bio-preservation, because of the ever-increasing needs to protect consumers' health and to valorize the naturalness and safety of food products.

Detection of CTX-M-14 and TEM-52 extended-spectrum beta-lactamases in fecal Escherichia coli isolates of captive ostrich in Portugal.

The main aim of this study was to determine the frequency of antibiotic resistance among Escherichia coli isolates recovered in Levine agar plates from 54 fecal samples of captive ostriches from a farm in the South of Portugal. Fifty-four nonselected E. coli isolates were obtained (one/sample) and the phenotypes and genotypes of antibiotic resistance were characterized. The following numbers of isolates showed antibiotic resistance: ampicillin (nine), tetracycline (seven), streptomycin (three), amoxicillin-clavulanic acid, cefoxitin, or gentamicin (one), and cefotaxime, ceftazidime, azthreonam, imipenem, nalidixic acid, ciprofloxacin, and trimethoprim/sulfamethoxazole (zero). The bla(TEM) gene was identified in six out of nine ampicillin-resistant isolates, and the tet(A) or tet(B) genes in five out of seven tetracycline-resistant isolates. Mutations at positions -42, -18, -1, and +58 of ampC promoter region were identified in one cefoxitin-resistant isolate. Further, the occurrence of extended-spectrum beta-lactamase (ESBL)-producing E. coli isolates was estimated in the 54 fecal samples of ostriches using cefotaxime-supplemented Levine agar plates for ESBL-positive E. coli recovery. Three samples contained ESBL-positive E. coli isolates of which one isolate/sample was characterized, leading to the detection of the following beta-lactamases: bla(CTX-M-14a) + bla(TEM-1b) (two isolates) and bla(TEM-52c) (one isolate). The three ESBL-positive isolates were classified into the phylogroup B1, and contained class 1 integrons with the gene cassettes dfrA17 + aadA5 (one isolate) and aadA1 (two isolates). This study adds to our knowledge about the wide dissemination of ESBL-producing E. coli isolates in different ecosystems, including captive ostriches, that could be transferred to humans through the food chain.

Prevalent organisms on ostrich carcasses found in a commercial abattoir.

The prevalent microbial growth on carcasses before and after overnight cooling in an ostrich abattoir and de-boning plant was investigated. The effect of warm or cold trimming of the carcasses was examined together with possible causes of contamination along the processing line. An attempt was made to link the prevalent microorganisms that were identified from carcasses to those from specific external contamination sources. Samples of carcasses and possible contaminants were collected in the plant, plated out and selected organisms were typed using a commercial rapid identification system. It was indicated that the cold trim (mainly of bruises) of carcasses was advantageous in terms of microbiological meat quality. Results indicated pooled water in the abattoir as the most hazardous vector for carcass contamination and that contaminants from this source are mostly Gram-negative pathogens. Pseudomonas and Shigella were frequently isolated from surface and air samples and indicated that the control of total plant hygiene is a requirement for producing ostrich meat that is safe to consume and has an acceptable shelf-life.

Microbial diversity in ostrich ceca as revealed by 16S ribosomal RNA gene clone library and detection of novel Fibrobacter species.

The ostrich (Struthio camelus) is a herbivorous bird and although the hindgut is known as the site for fiber digestion, little is known about the microbial diversity in the ostrich hindgut. Our aim was to analyze the microbial diversity in ostrich ceca using a 16S ribosomal RNA gene (rDNA) clone library approach. A total of 310 clones were sequenced and phylogenetically analyzed and were classified into 110 operational taxonomy units (OTUs) based on a 98% similarity criterion. The similarity of the sequences ranged from 86 to 99% and 95 OTUs had less than 98% similarity to the sequences in the public databases. Coverage and the Shannon-Wiener index (H') of the library were 83.9% and 4.29, respectively. The sequences were assigned to the following 6 phyla: Firmicutes (50.9% of the total number of sequences), Bacteroidetes (39.4%), Fibrobacteres (6.5%), Euryarchaeota (1.9%), Spirochaetes (1.0%), and Verrucomicrobia (0.3%); approximately 90% of the sequences were affiliated with Firmicutes and Bacteroidetes. The only OTU of Fibrobacteres (OTU 107), had 93 and 90% similarity to Fibrobacter succinogenes and F. intestinalis, respectively, suggesting a new species of Fibrobacter in ostrich ceca. Clostridium coccoides and C. leptum formed major groups within the Firmicutes. There was no OTU with high similarity (> or =98%) to the 16S rDNA of cultivated fibrolytic bacteria in our library. Although two OTUs were affiliated with Euryarchaeota, no sequence was affiliated with methanogenic Archaea. This study presents the very complex ostrich cecal microbial community, in which the majority of the bacterial species have not yet been cultivated.