Uploaded December 2025 | Updated September 2026, 4 hours ago
At PRISM 2025 Athens, Assistant Professor Ibrahim Bitar of Gene Omics discusses the critical limitations of short-read sequencing for microbial genomics. He details his lab's shift to PacBio HiFi sequencing to overcome assembly challenges with mobile genetic elements and plasmids, enabling the generation of complete and accurate microbial genomes.
Dr. Bitar illustrates how highly repetitive insertion sequences and transposons, common in bacteria, frequently break short-read assemblies into hundreds of contigs. This fragmentation requires complex, time-consuming, and often unsuccessful workarounds like PCR gap closing, which can take months per plasmid. He demonstrates how PacBio long reads resolve these issues, turning a plasmid that was 18 separate contigs into a single, circularized sequence. This capability has been instrumental in his work, from depositing over 30 complete Candida auris genomes to investigating a deadly Acinetobacter baumannii outbreak.
00:00 Introduction: the era of long reads
00:51 Why short reads fail in microbial genomics
04:47 The limits of short-read assembly workarounds
12:17 Achieving complete assemblies with PacBio HiFi reads
13:46 Case study: sequencing the Candida auris outbreak
15:48 Investigating an Acinetobacter baumannii outbreak
18:06 Comparing HiFi reads to other sequencing methods
20:50 The future of long-read microbial genomics
Subscribe for more insights from PacBio: youtube.com/@PacificBiosciences?sub_confirmation=1
Learn more about PacBio at pacb.com
Legal & Trademarks: Visit pacb.com/legal-and-trademarks
At PRISM 2025 Athens, Assistant Professor Ibrahim Bitar of Gene Omics discusses the critical limitations of short-read sequencing for microbial genomics. He details his lab's shift to PacBio HiFi sequencing to overcome assembly challenges with mobile genetic elements and plasmids, enabling the generation of complete and accurate microbial genomes.
Dr. Bitar illustrates how highly repetitive insertion sequences and transposons, common in bacteria, frequently break short-read assemblies into hundreds of contigs. This fragmentation requires complex, time-consuming, and often unsuccessful workarounds like PCR gap closing, which can take months per plasmid. He demonstrates how PacBio long reads resolve these issues, turning a plasmid that was 18 separate contigs into a single, circularized sequence. This capability has been instrumental in his work, from depositing over 30 complete Candida auris genomes to investigating a deadly Acinetobacter baumannii outbreak.
00:00 Introduction: the era of long reads
00:51 Why short reads fail in microbial genomics
04:47 The limits of short-read assembly workarounds
12:17 Achieving complete assemblies with PacBio HiFi reads
13:46 Case study: sequencing the Candida auris outbreak
15:48 Investigating an Acinetobacter baumannii outbreak
18:06 Comparing HiFi reads to other sequencing methods
20:50 The future of long-read microbial genomics
Subscribe for more insights from PacBio: youtube.com/@PacificBiosciences?sub_confirmation=1
Learn more about PacBio at pacb.com
Legal & Trademarks: Visit pacb.com/legal-and-trademarks
