Alex Arzamasov
@arzamasovalex.bsky.social
Postdoc in Osterman lab at SBP Medical Discovery Institute.
Interested in the functional annotation of genomic and metagenomic data, carbohydrate metabolism, #bifidobacteria
Interested in the functional annotation of genomic and metagenomic data, carbohydrate metabolism, #bifidobacteria
We demonstrated that phylogenetically closely related strains can exhibit substantial differences in HMO utilization, which is driven by subtle variations in HMO transporter genes. Species/subspecies names alone don’t tell the full story; one needs to look at gene content in individual strains(6/7)
September 30, 2025 at 9:01 AM
We demonstrated that phylogenetically closely related strains can exhibit substantial differences in HMO utilization, which is driven by subtle variations in HMO transporter genes. Species/subspecies names alone don’t tell the full story; one needs to look at gene content in individual strains(6/7)
Among the new pathways we uncovered was a xyloglucan degradation pathway that was present in rare B. catenulatum subsp. kashiwanohense strains and conserved in B. dentium and B. tsurumiense (5/7)
September 30, 2025 at 9:01 AM
Among the new pathways we uncovered was a xyloglucan degradation pathway that was present in rare B. catenulatum subsp. kashiwanohense strains and conserved in B. dentium and B. tsurumiense (5/7)
We validated phenotypic predictions for 30 bifidobacterial strains, achieving 94% accuracy. For example, we confirmed the unique ability of the new B. longum clade to grow on starch and pullulan, and described an unconventional B. adolescentis strain that can use 2’-fucosyllactose (4/7)
September 30, 2025 at 9:01 AM
We validated phenotypic predictions for 30 bifidobacterial strains, achieving 94% accuracy. For example, we confirmed the unique ability of the new B. longum clade to grow on starch and pullulan, and described an unconventional B. adolescentis strain that can use 2’-fucosyllactose (4/7)
Our analysis revealed notable inter- and intra-species variability. Among notable findings was a new Bifidobacterium longum clade harboring pathways for starch, pullulan, and difructose dianhydride metabolism but lacking pathways for LNB/GNB, N-glycan, and human milk oligosaccharide utilization(3/7)
September 30, 2025 at 9:01 AM
Our analysis revealed notable inter- and intra-species variability. Among notable findings was a new Bifidobacterium longum clade harboring pathways for starch, pullulan, and difructose dianhydride metabolism but lacking pathways for LNB/GNB, N-glycan, and human milk oligosaccharide utilization(3/7)
We reconstructed 68 glycan utilization pathways encoded in 3,083 bif genomes by looking at the distribution of 589 curated metabolic functions (transporters, CAZymes, etc). Several years of manual curation greatly improved the quality of functional gene annotations (>90% for transporters!) (2/7)
September 30, 2025 at 9:01 AM
We reconstructed 68 glycan utilization pathways encoded in 3,083 bif genomes by looking at the distribution of 589 curated metabolic functions (transporters, CAZymes, etc). Several years of manual curation greatly improved the quality of functional gene annotations (>90% for transporters!) (2/7)
Among the new pathways we uncovered was a xyloglucan degradation pathway that was present in rare B. catenulatum subsp. kashiwanohense strains and conserved in B. dentium and B. tsurumiense (5/7)
September 30, 2025 at 8:49 AM
Among the new pathways we uncovered was a xyloglucan degradation pathway that was present in rare B. catenulatum subsp. kashiwanohense strains and conserved in B. dentium and B. tsurumiense (5/7)
We validated phenotypic predictions for 30 bifidobacterial strains, achieving 94% accuracy. For example, we confirmed the unique ability of the new B. longum clade to grow on starch and pullulan, and described a B. adolescentis strain that can use 2’-fucosyllactose (4/7)
September 30, 2025 at 8:49 AM
We validated phenotypic predictions for 30 bifidobacterial strains, achieving 94% accuracy. For example, we confirmed the unique ability of the new B. longum clade to grow on starch and pullulan, and described a B. adolescentis strain that can use 2’-fucosyllactose (4/7)
Our analysis revealed notable inter- and intra-species variability. Among notable findings was a new Bifidobacterium longum clade harboring pathways for starch, pullulan, and difructose dianhydride metabolism but lacking pathways for LNB/GNB, N-glycan, and human milk oligosaccharide utilization(3/7)
September 30, 2025 at 8:49 AM
Our analysis revealed notable inter- and intra-species variability. Among notable findings was a new Bifidobacterium longum clade harboring pathways for starch, pullulan, and difructose dianhydride metabolism but lacking pathways for LNB/GNB, N-glycan, and human milk oligosaccharide utilization(3/7)
We reconstructed 68 glycan utilization pathways encoded in 3,083 bif genomes by looking at the distribution of 589 curated metabolic functions (transporters, CAZymes, etc). Several years of manual curation greatly improved the quality of functional gene annotations (>90% for transporters!) (2/7)
September 30, 2025 at 8:49 AM
We reconstructed 68 glycan utilization pathways encoded in 3,083 bif genomes by looking at the distribution of 589 curated metabolic functions (transporters, CAZymes, etc). Several years of manual curation greatly improved the quality of functional gene annotations (>90% for transporters!) (2/7)
I often flag genomic predictions of SCFA production that clash with “textbook” data. But sometimes it’s the experimental claims that raise eyebrows. This recent paper reports propionate (!) and butyrate (!!) production by Bif. longum ssp. infantis (it shouldn't make either
doi.org/10.3168/jds....
doi.org/10.3168/jds....
May 19, 2025 at 4:13 AM
I often flag genomic predictions of SCFA production that clash with “textbook” data. But sometimes it’s the experimental claims that raise eyebrows. This recent paper reports propionate (!) and butyrate (!!) production by Bif. longum ssp. infantis (it shouldn't make either
doi.org/10.3168/jds....
doi.org/10.3168/jds....
Nice to see such a large proteomic dataset from the human gut. However, certain functional annotation results seem odd to me. E.g., Bacteroides thetaiotaomicron does not produce butyrate; Bifidobacterium longum does not produce propionate and vitamin B5 (1/2)
November 28, 2024 at 3:21 AM
Nice to see such a large proteomic dataset from the human gut. However, certain functional annotation results seem odd to me. E.g., Bacteroides thetaiotaomicron does not produce butyrate; Bifidobacterium longum does not produce propionate and vitamin B5 (1/2)
We also saw interesting pathway enrichment patterns. When looking within each taxon we found that sugar alcohol utilization pathways were enriched in Westernized Bl. infantis and Bifidobacterium adolescentis genomes. Could it be connected to the diet? (35/)
July 19, 2024 at 7:27 PM
We also saw interesting pathway enrichment patterns. When looking within each taxon we found that sugar alcohol utilization pathways were enriched in Westernized Bl. infantis and Bifidobacterium adolescentis genomes. Could it be connected to the diet? (35/)
The substantial variability of predicted carbohydrate utilization capabilities at the strain level contrasted with the conservation of most pathways responsible for the biosynthesis of essential metabolites such as B vitamins and amino acids (32/)
July 19, 2024 at 7:24 PM
The substantial variability of predicted carbohydrate utilization capabilities at the strain level contrasted with the conservation of most pathways responsible for the biosynthesis of essential metabolites such as B vitamins and amino acids (32/)
The results additionally emphasized the pronounced variability of predicted glycan utilization capabilities at species/subspecies at strain levels (31/)
July 19, 2024 at 7:24 PM
The results additionally emphasized the pronounced variability of predicted glycan utilization capabilities at species/subspecies at strain levels (31/)
Finally, we extended the pathway representation analysis to > 2700 Bifidobacterium genomes using a machine-learning approach. The extended dataset included not only genomes of cultured isolates but also metagenome-assembled genomes (MAGs) of very high quality (30/)
July 19, 2024 at 7:23 PM
Finally, we extended the pathway representation analysis to > 2700 Bifidobacterium genomes using a machine-learning approach. The extended dataset included not only genomes of cultured isolates but also metagenome-assembled genomes (MAGs) of very high quality (30/)
Xgl cluster genes were significantly upregulated in the presence of xyloglucan. The transcriptional response was, however, more complex, likely due to the release of xylose, which induced the expression of (arabino)xylooligosaccharide and arabino(xylan) utilization genes (28/)
July 19, 2024 at 7:22 PM
Xgl cluster genes were significantly upregulated in the presence of xyloglucan. The transcriptional response was, however, more complex, likely due to the release of xylose, which induced the expression of (arabino)xylooligosaccharide and arabino(xylan) utilization genes (28/)
We demonstrated that only the strains harboring the xgl cluster (Bg42221_1E1 and a B. dentium strain) grew in the medium supplemented with tamarind xyloglucan (27/)
July 19, 2024 at 7:21 PM
We demonstrated that only the strains harboring the xgl cluster (Bg42221_1E1 and a B. dentium strain) grew in the medium supplemented with tamarind xyloglucan (27/)
In addition to H1, Bc. kashiwanohense Bg42221_1E1 harbored another unique gene cluster, xgl, potentially implicated in xyloglucan degradation (26/)
July 19, 2024 at 7:20 PM
In addition to H1, Bc. kashiwanohense Bg42221_1E1 harbored another unique gene cluster, xgl, potentially implicated in xyloglucan degradation (26/)
A single GlcNAc-containing HMO species (LNT) was sufficient for the induction of most H1 cluster genes, consistent with the proposed regulation by NagR, a transcriptional repressor that senses GlcNAc and its phosphorylated derivatives (25/)
July 19, 2024 at 7:20 PM
A single GlcNAc-containing HMO species (LNT) was sufficient for the induction of most H1 cluster genes, consistent with the proposed regulation by NagR, a transcriptional repressor that senses GlcNAc and its phosphorylated derivatives (25/)
Bc. kashiwanohense Bg42221_1E1 and other H1 cluster-positive Bifidobacterium strains indeed consumed multiple fucosylated and sialylated HMO species compared to H1-negative strains (24/)
July 19, 2024 at 7:19 PM
Bc. kashiwanohense Bg42221_1E1 and other H1 cluster-positive Bifidobacterium strains indeed consumed multiple fucosylated and sialylated HMO species compared to H1-negative strains (24/)
A Bifidobacterium catenulatum subsp. kashiwanohense strain Bg42221_1E1 served as another example of the genomic uniqueness of Bangladeshi strains. This strain also harbored orthologs of H1 cluster genes previously considered as a unique feature of Bl. infantis (23/)
July 19, 2024 at 7:18 PM
A Bifidobacterium catenulatum subsp. kashiwanohense strain Bg42221_1E1 served as another example of the genomic uniqueness of Bangladeshi strains. This strain also harbored orthologs of H1 cluster genes previously considered as a unique feature of Bl. infantis (23/)
The pathway distribution in Bangladeshi Bl. suis-like strain Bg131.S11_17.F6 surprisingly resembled that of Bifidobacterium longum subsp. infantis (Bl. infantis). For example, this strain harbored the H1 gene cluster with human milk oligosaccharide (HMO) utilization genes (20/)
July 19, 2024 at 7:18 PM
The pathway distribution in Bangladeshi Bl. suis-like strain Bg131.S11_17.F6 surprisingly resembled that of Bifidobacterium longum subsp. infantis (Bl. infantis). For example, this strain harbored the H1 gene cluster with human milk oligosaccharide (HMO) utilization genes (20/)
Speaking of subspecies-level clades within B. longum, we observed substantial heterogeneity of predicted carbohydrate utilization phenotypes within Bifidobacterium longum subsp. suis (Bl. suis)-like strains (19/)
July 19, 2024 at 7:17 PM
Speaking of subspecies-level clades within B. longum, we observed substantial heterogeneity of predicted carbohydrate utilization phenotypes within Bifidobacterium longum subsp. suis (Bl. suis)-like strains (19/)
These differences in potential carbohydrate utilization capabilities, coupled with the phylogenomic and ANI analysis, provide a foundation for the future tentative separation of Bl. nov. as a novel subspecies within B. longum (18/)
July 19, 2024 at 7:17 PM
These differences in potential carbohydrate utilization capabilities, coupled with the phylogenomic and ANI analysis, provide a foundation for the future tentative separation of Bl. nov. as a novel subspecies within B. longum (18/)
Analysis of the representation of predicted carbohydrate utilization phenotypes in 263 reference strains revealed "global" differences between species/subspecies (14/)
July 19, 2024 at 7:15 PM
Analysis of the representation of predicted carbohydrate utilization phenotypes in 263 reference strains revealed "global" differences between species/subspecies (14/)