The human gut typically contains bacteria from three major groups: the Firmicutes, Bacteroidetes, and Proteobacteria. The Firmicutes are Gram-positive, and the Bacteroidetes and Proteobacteria are Gram-negative. In line with this, species of Gram-positive Streptococcus, Staphylococcus, and Bacillus were found in the mummy’s gut, and well as species of Gram-negative Pseudomonas. In addition, the group found DNA sequences from Clostridium botulinum type B, which causes food-borne illness.
The mummy also showed evidence of viral and parasitic disease. They found sequences consistent with human papillomavirus types 21 and 49, as well as evidence that the mummy had Chagas’ disease. Chagas’ disease is caused by the eukaryotic parasite Trypanosoma cruzi. The parasites are transmitted by insects known as “kissing bugs”. Chronic Chagas’ disease results in enlargement of the esophagus and colon, both of which were found in the mummy.
The researchers were most surprised to find sequences from antibiotic resistance genes. They found evidence of beta-lactamase genes (beta-lactamases provide resistance to antibiotics such as penicillin) and vancomycin resistance genes. It's not surprising that bacteria had such resistance genes, since penicillin and vancomycin are naturally-occurring antibiotics. What is surprising is that these genes appear to have been prevalent even before the modern use of antibiotics.
Sources: Discovery News, PLOS One, Wikipedia