Internal transcribed spacer 1 secondary structure analysis reveals a common core throughout the anaerobic fungi (Neocallimastigomycota).

The internal transcribed spacer (ITS) is a popular barcode marker for fungi and in particular the ITS1 has been widely used for the anaerobic fungi (phylum Neocallimastigomycota). A good number of validated reference sequences of isolates as well as a large number of environmental sequences are available in public databases. Its highly variable nature predisposes the ITS1 for low level phylogenetics; however, it complicates the establishment of reproducible alignments and the reconstruction of stable phylogenetic trees at higher taxonomic levels (genus and above).

16S ribosomal DNA-directed PCR primers for ruminal methanogens and identification of methanogens colonising young lambs.

The population densities and identities of methanogens colonising new-born lambs in a grazing flock were determined from rumen samples collected at regular intervals after birth. Methanogen colonisation was found at the first sampling (1-3 days after birth) and population densities reached around 10(4) methanogens per gram at 1 week of age. Population densities increased in an exponential manner to a maximum of 10(8)-10(9) per gram at 3 weeks of age.

Ability of lysozyme and 2-deoxyglucose to differentiate human and bovine Streptococcus bovis strains.

Human and bovine Streptococcus bovis strains had the same 16S ribosomal DNA restriction fragment length polymorphism and often had the same patterns of starch, mannitol, lactose, and raffinose utilization. PCRs of BOX sequences differed, but numerical analyses indicated that some human strains clustered with bovine strains. However, human and bovine strains had distinctly different sensitivities to lysozyme and 2-deoxyglucose.