Folate-producing bifidobacteria: metabolism, genetics, and relevance

Folate (the general term for all bioactive forms of vitamin B9) plays a crucial role in the evolutionary highly conserved one-carbon (1C) metabolism, a network including central reactions such as DNA and protein synthesis and methylation of macromolecules. Folate delivers 1C units, such as methyl and formyl, between reactants. Plants, algae, fungi, and many bacteria can naturally produce folate, whereas animals, including humans, must obtain folate from external sources. For humans, folate deficiency is, however, a widespread problem. Bifidobacteria constitute an important component of human and many animal microbiomes, providing various health advantages to the host, such as producing folate. This review focuses on bifidobacteria and folate metabolism and the current knowledge of the distribution of genes needed for complete folate biosynthesis across different bifidobacterial species. Biotechnologies based on folate-trophic probiotics aim to create fermented products enriched with folate or design probiotic supplements that can synthesize folate in the colon, improving overall health. Therefore, bifidobacteria (alone or in association with other microorganisms) may, in the future, contribute to reducing widespread folate deficiencies prevalent among vulnerable human population groups, such as older people, women at child-birth age, and people in low-income countries.

Bifidobacteria in two-toed sloths (Choloepus didactylus): phylogenetic characterization of the novel taxon Bifidobacterium choloepi sp. nov

Seven bifidobacterial strains were isolated from the faeces of two adult males of the two-toed sloth (Choloepus didactylus) housed in Parco Natura Viva, in Italy. Comparative sequence analysis of 16S rRNA and of five housekeeping (hsp60, rpoB, clpC, dnaJ, dnaG) genes revealed that these strains were classified into two clusters. On the basis of 16S rRNA gene sequence similarity, the type strain of Bifidobacterium catenulatum subsp. kashiwanohense DSM 21854^T (95.4 %) was the closest neighbour to strain in Cluster I (BRDM 6^T), whereas the type strain of Bifidobacterium dentium DSM 20436^T (values were in the range of 98‒99.8 %) was the closest neighbour to the other six strains in Cluster II. The average nucleotide identity (ANI) values of BRDM 6^T and of strains in Cluster II with the closely related type strains were 76.0 and 98.9 % (mean value) respectively. Therefore, genotyping based on the genome sequence of the strain BRDM 6^T combined with phenotypic analyses clearly revealed that the strain BRDM 6^T represents a novel species for which the names Bifidobacterium choloepi sp. nov. (BRDM 6^T=NBRC 114053^T=BCRC 81222^T) is proposed.

The impact of COVID-19 pandemic on blood supplies and transfusion services in Eastern Mediterranean Region

Background

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has spurred a global health crisis. The safety and supply of blood during this pandemic has been a concern of blood banks and transfusion services as it is expected to adversely affect blood system activities. We aim to assess the situation in the Eastern Mediterranean Region (EMR) during the first months of the pandemic.

Materials and methods

A survey was designed to address blood supply, transfusion demand, and donor management during the coronavirus disease-19 (COVID-19) pandemic. Medical directors of different blood banks were invited to participate.

Results

A total of 16 centers participated with representation from 15/19 countries in the region. In total, 75% were from national blood banks. Most centres had a decrease in the blood supply, ranging from 26–50%. Representatives from 14 countries (93.3%) believed that public fear has contributed to a decrease in donations. Most centres (n = 12, 75%) had a reduction in transfusion demand, while those who did not, reported heavy involvement in treating patients with underlying haemoglobinopathies and haematological malignancies. Half of the centres activated their contingency plans. Four centres had to alter the blood donor eligibility criteria to meet demands. All centres implemented donor deferral criteria in relation to SARS-CoV-2, but were variable in measures to mitigate the risk of donor and staff exposure.

Conclusion

Blood services in the region faced variable degrees of blood shortages. We summarize lessons learnt during this pandemic for the blood banks to consider to plan, assess, and respond proportionately to future similar pandemics.

Phylogenetic characterization of two novel species of the genus Bifidobacterium: Bifidobacterium saimiriisciurei sp. nov. and Bifidobacterium platyrrhinorum sp. nov

Three bifidobacterial Gram-stain-positive, non-spore forming and fructose-6-phosphate phosphoketolase-positive strains, SMA1^T, SMB2 and SMA15^T were isolated from the faeces of two adult males of the squirrel monkey (Saimiri sciureus). On the basis of 16S rRNA gene sequence similarities, the type strain of Bifidobacterium primatium DSM 100687^T (99.3%; similarity) was the closest neighbour to strains SMA1^T and SMB2, whereas the type strain of Bifidobacterium stellenboschense DSM 23968^T (96.5%) was the closest neighbour to strain SMA15^T. The average nucleotide identity (ANI) values of SMA1^T and SAM15^T with the closely related type strains were 93.7% and 88.1%, respectively. The in silico DNA‒DNA hybridization values with the closest neighbours were 53.1% and 36.9%, respectively. GC contents of strains SMA1^T and SMA15^T were 63.6 and 66.4 mol%, respectively. Based on the phylogenetic, genotypic and phenotypic data obtained, the strains SMA1^T and SMA15^T clearly represent two novel taxa within the genus Bifidobacterium for which the names Bifidobacterium saimiriisciurei sp. nov. (type strain SMA1^T = BCRC 81223^T = NBRC 114049^T = DSM 106020^T) and Bifidobacterium platyrrhinorum sp. nov. (type strain SMA15^T = BCRC 81224^T = NBRC 114051^T = DSM 106029^T) are proposed.

Characterization of Bifidobacterium species in feaces of the Egyptian fruit bat: Description of B. vespertilionis sp. nov. and B. rousetti sp. nov

Fifteen bifidobacterial strains were obtained from faeces of Rousettus aegyptiacus; after grouping them by RAPD PCR only eight were selected and characterized. Analysis of 16S rRNA and of five housekeeping (hsp60, rpoB, clpC, dnaJ, dna G) genes revealed that these eight strains were classified into five clusters: Cluster I (RST 8 and RST 16^T), Cluster II (RST 9^T and RST 27), Cluster III (RST 7 and RST 11), Cluster IV (RST 19), Cluster V (RST 17) were closest to Bifidobacterium avesanii DSM 100685^T (96.3%), Bifidobacterium callitrichos DSM 23973^T (99.2% and 99.7%), Bifidobacterium tissieri DSM 100201^T (99.7 and 99.2%), Bifidobacterium reuteri DSM 23975 ^T (98.9%) and Bifidobacterium myosotis DSM 100196^T (99.3%), respectively. Strains in Cluster I and strain RST 9 in Cluster II could not be placed within any recognized species while the other ones were identified as known species. The average nucleotide identity values between two novel strains, RST 16^T and RST 9^T and their closest relatives were lower than 79% and 89%, respectively. In silico DNA-DNA hybridization values for those closest relatives were 32.5 and 42.1%, respectively. Phenotypic and genotypic tests demonstrated that strains in Cluster I and RST 9^T in Cluster II represent two novel species for which the names Bifidobacterium vespertilionis sp. nov. (RST 16^T=BCRC 81138^T=NBRC 113380^T=DSM 106025^T ; RST 8=BCRC 81135=NBRC 113377) and Bifidobacterium rousetti sp. nov. (RST 9^T=BCRC 81136^T=NBRC 113378^T=DSM 106027^T) are proposed.

Bifidobacterium jacchi sp. nov., isolated from the faeces of a baby common marmoset (Callithrix jacchus)

A novel Bifidobacterium strain, MRM 9.3^T, was isolated from a faecal sample of a baby common marmoset (Callithrixjacchus). Cells were Gram-stain-positive, non-motile, non-sporulating, non-haemolytic, facultatively anaerobic and fructose 6-phosphate phosphoketolase-positive. Phylogenetic analyses based on 16S rRNA genes as well as multilocus sequences (representing hsp60, rpoB, clpC, dnaJ and dnaG genes) and the core genomes revealed that strain MRM 9.3^T exhibited phylogenetic relatedness to Bifidobacterium myosotis DSM 100196^T. Comparative analysis of 16S rRNA gene sequences confirmed the phylogenetic results showing the highest gene sequence identity with strain B.ifidobacterium myosotis DSM 100196^T (95.6 %). The average nucleotide identity, amino acid average identity and in silico DNA-DNA hybridization values between MRM 9.3^T and DSM 100196^T were 79.9, 72.1 and 28.5 %, respectively. Phenotypic and genotypic features clearly showed that the strain MRM 9.3^T represents a novel species, for which the name Bifidobacterium jacchi sp. nov. is proposed. The type strain is MRM 9.3^T (=DSM 103362^T =JCM 31788^T).

Comparative analysis of probiotic bacteria based on a new definition of core genome

The commensal genus Bifidobacterium has probiotic properties. We prepared a public library of the gene functions of the genus Bifidobacterium for its online annotation. Orthologous gene cluster analysis showed that the pan genomes of Bifidobacterium and Lactobacillus exhibit striking similarities when mapped to the Clusters of Orthologous Group (COG) database of proteins. When the core genes in each genus were selected based on our statistical definition of "core genome", core genes were present in at least 92% of 52 Bifidobacterium and in 97% of 178 Lactobacillus genomes. Functional comparison of the core genes of the two genera revealed a significant difference in the categories "amino acid transport and metabolism" representing their difference in niche specificity. Over-represented Bifidobacterium protein families were primarily involved in host interactions, the complex compound metabolism, and in stress responses. These findings coincide with the published information and validate our bias-resilient definition of the core genome.

The treatment of kala-azar in the Sudan with sodium stibogluconate: a randomized trial of three dosage regimens

In a randomized study in the Sudan, 3 different regimens of sodium stibogluconate were compared in patients with parasitologically confirmed kala-azar (visceral leishmaniasis): 10 mg/kg for 30 d (38 patients), 20 mg/kg for 30 d (29 patients), and 20 mg/kg for 15 d (37 patients). Treatment failures were defined as death, partial response, relapse, or the development of post-kala-azar dermal leishmaniasis. The hazard ratio for failure of 20 mg/kg for 30 d vs. 10 mg/kg for 30 d 2.1 (95% confidence interval [CI] = 0.6, 7.6) and for 20 mg/kg for 15 d vs. 10 mg/kg for 30 d it was 1.7 (95% CI = 0.5, 6.1). No significant difference was detected between the 3 regimens in the rate of return to normal of haematological criteria, regression of spleen size, or weight gain. After 15 d treatment parasite clearance with 20 mg/kg for 30 d and 20 mg/kg for 15 d was more profound than with 10 mg/kg for 30 d (P < 0.05), but the difference was no longer present at the end of treatment. Further investigation of the effectiveness of short, intensive treatment regimens in the treatment of kala-azar is warranted.

Kala-azar: a comparative study of parasitological methods and the direct agglutination test in diagnosis

In a comparative study 88 patients were diagnosed as suffering from kala-azar (visceral leishmaniasis) using 3 parasitological methods simultaneously. Splenomegaly was absent in 4 cases. In 84 patients with splenomegaly, splenic aspiration appeared to be the most sensitive method (96.4%), followed by bone marrow aspiration (70.2%) and lymph node aspiration (58.3%). There was no relation between titres in the direct agglutination test and parasite load as determined by the number of parasitological methods which were positive or parasite density in splenic aspirates. Splenic aspiration and bone marrow aspiration were compared as an assessment of cure in kala-azar. In 6 (13%) of 46 patients tested, parasites were found, all by splenic aspiration. Bone marrow showed parasites in one of these. The literature with regard to parasitological investigations before and after treatment is reviewed.

Post kala-azar dermal leishmaniasis in the Sudan: clinical features, pathology and treatment

The clinical features, pathology, immune responses, diagnosis and treatment of post kala-azar dermal leishmaniasis (PKDL) in the Sudan are described and discussed. The disease is characterized by maculopapular or nodular lesions on the face, limbs or trunk. Lesions appear during or within months after the treatment of visceral leishmaniasis, but in 2 of 19 patients there was no previous history of kala-azar. PKDL may be confused with leprosy both clinically and pathologically. Similarities and differences between the 2 diseases are discussed. Unlike visceral leishmaniasis, the peripheral lymphoid cells of patients with PKDL respond to Leishmania antigen and some are leishmanin positive. The response to intravenous sodium stibogluconate (20 mg/kg for 30 d) was reasonably good but some patients required repeated or more prolonged treatment. Ketoconazole in a dose of 10 mg/kg daily for 4 weeks had no effect on PKDL.

Clinical aspects of kala-azar in children from the Sudan: a comparison with the disease in adults

The clinical presentation of kala-azar in 43 children and 45 adults was compared. In both groups fever, left upper quadrant abdominal pain and swelling, and weight loss were equally the most common presenting symptoms. Lymphadenopathy was observed in 86 per cent of children and 76 per cent of adults. Splenomegaly was absent in 2 per cent of children and 7 per cent of adults. No significant difference was found in frequency distribution of symptoms and signs between children and adults. Haematological indices were compared in both children and adults with kala-azar and their control groups. In both children and adults with kala-azar, haemoglobin concentration, total white cell count, and platelet count were significantly lower before than after treatment. Only haemoglobin concentration was lower in children with kala-azar as compared with adults with the disease. Children in the control group had lower haemoglobin and higher total white cell count than adult controls. Response to therapy was evaluated in 693 patients. Two-hundred-and-fifty children and 373 adults were treated with sodium stibogluconate 10 mg/kg for 30 days; in both groups 12 per cent deaths and 4 per cent relapses occurred. Thirty children and 40 adults were treated with sodium stibogluconate 2 x 10 mg/kg for 15 days. In children, 3 per cent deaths and 7 per cent relapses were noted; in adults there were 8 per cent deaths and 5 per cent relapses. No significant difference in death rate or relapse rate was found between children and adults in both regimens. Both regimens performed equally well in children and adults with regard to death rate and relapse rate.

Direct agglutination test for diagnosis and sero-epidemiological survey of kala-azar in the Sudan

132 patients with suspected kala-azar (visceral leishmaniasis) were included in a prospective study to compare the performance of the direct agglutination test (DAT) with smears of lymph node, bone marrow and splenic aspiration. A titre greater than 1:3200 was considered positive. 67 patients provided positive smears and 65 were smear-negative. Compared with the results obtained from smears, the sensitivity of the DAT was 94% and its specificity 72%. Of 18 patients who were negative by smears but positive by DAT, 3 were treated on strong clinical suspicion of kala-azar and responded well to therapy. One other patient had post-kala-azar dermal leishmaniasis. Of the remaining 14, 8 were tested with the leishmanin skin test; 6 gave a positive result, suggesting past or sub-clinical infection. In 4 smear-positive patients, the DAT was negative; in 2 of these, the test remained negative during 6 months' follow-up. In a sero-epidemiological survey in a camp for displaced people, 30 of 600 sampled individuals gave a positive DAT. Of these, 11 had been treated for kala-azar; 4 others were leishmanin positive. The DAT is a useful screening test (sensitivity 94%; predictive value of a negative test 92%), but it does not differentiate between past kala-azar, sub-clinical infection and active disease.

Kala-azar in displaced people from southern Sudan: epidemiological, clinical and therapeutic findings

Six hundred and ninety-three patients with kala-azar were seen in Khartoum, Sudan, from January 1989 to February 1990. They were almost exclusively from the Nuer tribe, originating from the western Upper Nile province in southern Sudan, an area not known previously to be endemic for kala-azar. Because of the civil war in southern Sudan no treatment was available locally and massive migration to northern Sudan occurred; many died on the way. All age groups were affected; there was a slight male preponderance (56%). In the clinical presentation, marked generalized lymphadenopathy was prominent (84%). Splenomegaly was absent in 4% of cases. Patients usually showed anaemia, leucopenia and/or thrombocytopenia. 623 patients were treated with sodium stibogluconate, 10 mg/kg for 30 d; relapse occurred in 4% and death in 12%. Latterly, 70 patients were treated with sodium stibogluconate at 2 x 10 mg/kg for 15 d, with relapse in 6% and death in 6%. The difference between the 2 regimens in the number of relapses and deaths was not significant. The outbreak may have been caused by a combination of factors: the introduction of the parasite from an endemic area to a non-immune population, the presence of malnutrition caused by loss of cattle and unavailability of other food sources, and possibly an ecological change in favour of the sandfly vector.