Found it! Phantoms (1998)
Dr. Jennifer Pailey brings her sister Lisa to the resort town of Snowfield, Colorado, a small ski resort village nestled in the Rocky Mountains where Jenny works as a doctor. Once in town, the sisters find no one around but a few corpses. At first their suspicions are that of a serial killer on the loose in town. The sisters stumble upon the severed heads of the town baker and his wife in an oven when they are found by Sheriff Bryce Hammond, a former FBI agent, and his deputies Stu Wargle and Steve Shanning. Hammond and his deputies are investigating the killings.
The group arrives at a nearby hotel and find the writing of a victim on the mirror reading "Timothy Flyte". Shanning leaves to investigate a sound outside but doesn't return. The others find only his gun, hat and shoes while the rest of him is gone. They return to the sheriff's office to request aid and create roadblocks around Snowfield. The group gets a strange phone call but are interrupted by an attack by a bizarre moth-like creature that rips Wargle's face off before Hammond is able to kill it. Lisa later encounters Wargle while in the bathroom. They quickly return to the morgue and find his body missing.
Hammond's FBI associates find Flyte, a British academic who theorizes the town has fallen victim to the Ancient Enemy, an entity he generalizes as "chaos in the flesh". It periodically wipes out civilizations including that of the Mayans and the Roanoke Island colonists.
They are soon joined by an Army commando unit and a group of scientists led by General Copperfield who has come to Snowfield. They, along with Flyte, investigate the town. The creature kills soldiers investigating the sewers, while a dog approaches Flyte and the scientists and transforms into a gruesome monster that converts the group, except for Flyte. Flyte regroups with Hammond, Jenny, Lisa, and Copperfield. The creature attacks Copperfield through a manhole, converting him. Copperfield vomits a sample before melting into a puddle of black liquid. Through it, Flyte and the group learn the nature of the Ancient Enemy.
Revealed to actually be an Earth-based amoebic life form that mimics its absorbed victims while gaining their knowledge, the Enemy creates Phantoms as temporary detachments for it to act through before absorbing them back into it. Furthermore, the Enemy absorbs all of the thoughts of its victims, making it extremely intelligent, and because of the previous civilizations' perception of it, it believes itself to be a god. It had arranged all of the prior events so Flyte can assist the creature in revealing its existence to the world. Flyte also learns that the creature's body is physiologically almost identical to crude oil, and could be killed by bacteria bio-engineered to ingest fossil fuels. They deduce that with the limited amount of the bacteria they have, they need to get the bacteria into the nucleus that is within the main body of the Enemy.
This scene is the one with the dog: